From 145b70ba0b4cba1e5f81c4b3a5cbd4269bf44c0d Mon Sep 17 00:00:00 2001 From: Mattias Date: Fri, 2 Jun 2017 18:09:28 +0200 Subject: [PATCH 001/116] Add R package micropan --- recipes/r-micropan/build.sh | 13 ++++++++ recipes/r-micropan/meta.yaml | 72 ++++++++++++++++++++++++++++++++++++++++++++ 2 files changed, 85 insertions(+) create mode 100644 recipes/r-micropan/build.sh create mode 100644 recipes/r-micropan/meta.yaml diff --git a/recipes/r-micropan/build.sh b/recipes/r-micropan/build.sh new file mode 100644 index 0000000000..0c37df6e8e --- /dev/null +++ b/recipes/r-micropan/build.sh @@ -0,0 +1,13 @@ +#!/bin/bash + +# R refuses to build packages that mark themselves as Priority: Recommended +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION + +$R CMD INSTALL --build . + +# Add more build steps here, if they are necessary. + +# See +# http://docs.continuum.io/conda/build.html +# for a list of environment variables that are set during the build process. diff --git a/recipes/r-micropan/meta.yaml b/recipes/r-micropan/meta.yaml new file mode 100644 index 0000000000..fe332a4e0c --- /dev/null +++ b/recipes/r-micropan/meta.yaml @@ -0,0 +1,72 @@ +{% set version = '1.1.2' %} + +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} + +package: + name: r-micropan + version: {{ version|replace("-", "_") }} + +source: + fn: micropan_{{ version }}.tar.gz + url: + - https://cran.r-project.org/src/contrib/micropan_{{ version }}.tar.gz + - https://cran.r-project.org/src/contrib/Archive/micropan/micropan_{{ version }}.tar.gz + + + sha256: efb4491b04f781a99fb9180689b7788618800618c3433a8af897ee926f556a67 + +build: + number: 0 + + # This is required to make R link correctly on Linux. + rpaths: + - lib/R/lib/ + - lib/ + + +requirements: + build: + - r-base + - r-igraph + - r-microseq + + run: + - r-base + - r-igraph + - r-microseq + +test: + commands: + - $R -e "library('micropan')" # [not win] + - "\"%R%\" -e \"library('micropan')\"" # [win] + +about: + home: https://CRAN.R-project.org/package=micropan + license: GPL-2 + summary: A collection of functions for computations and visualizations of microbial pan-genomes. + license_family: GPL2 + +# The original CRAN metadata for this package was: + +# Package: micropan +# Type: Package +# Title: Microbial Pan-Genome Analysis +# Version: 1.1.2 +# Date: 2017-01-17 +# Author: Lars Snipen and Kristian Hovde Liland +# Maintainer: Lars Snipen +# Description: A collection of functions for computations and visualizations of microbial pan-genomes. +# Depends: R (>= 3.3.1), igraph, microseq +# License: GPL-2 +# LazyData: FALSE +# ZipData: TRUE +# RoxygenNote: 5.0.1 +# NeedsCompilation: no +# Packaged: 2017-01-17 13:08:57 UTC; larssn +# Repository: CRAN +# Date/Publication: 2017-01-17 19:41:22 + +# See +# http://docs.continuum.io/conda/build.html for +# more information about meta.yaml From fcead0af74458fcb1893600954076f0d1b319119 Mon Sep 17 00:00:00 2001 From: Mattias Date: Fri, 2 Jun 2017 18:24:03 +0200 Subject: [PATCH 002/116] Add R package microseq --- recipes/r-microseq/build.sh | 13 ++++++++ recipes/r-microseq/meta.yaml | 70 ++++++++++++++++++++++++++++++++++++++++++++ 2 files changed, 83 insertions(+) create mode 100644 recipes/r-microseq/build.sh create mode 100644 recipes/r-microseq/meta.yaml diff --git a/recipes/r-microseq/build.sh b/recipes/r-microseq/build.sh new file mode 100644 index 0000000000..0c37df6e8e --- /dev/null +++ b/recipes/r-microseq/build.sh @@ -0,0 +1,13 @@ +#!/bin/bash + +# R refuses to build packages that mark themselves as Priority: Recommended +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION + +$R CMD INSTALL --build . + +# Add more build steps here, if they are necessary. + +# See +# http://docs.continuum.io/conda/build.html +# for a list of environment variables that are set during the build process. diff --git a/recipes/r-microseq/meta.yaml b/recipes/r-microseq/meta.yaml new file mode 100644 index 0000000000..fe7e79401c --- /dev/null +++ b/recipes/r-microseq/meta.yaml @@ -0,0 +1,70 @@ +{% set version = '1.2' %} + +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} + +package: + name: r-microseq + version: {{ version|replace("-", "_") }} + +source: + fn: microseq_{{ version }}.tar.gz + url: + - https://cran.r-project.org/src/contrib/microseq_{{ version }}.tar.gz + - https://cran.r-project.org/src/contrib/Archive/microseq/microseq_{{ version }}.tar.gz + + + sha256: 9ac33165011c856bf149c0e15340a4677888844c7a3e0f5e61f949c099778193 + +build: + number: 0 + + # This is required to make R link correctly on Linux. + rpaths: + - lib/R/lib/ + - lib/ + + +requirements: + build: + - r-base + - r-rcpp >=0.11.1 + - gcc + + run: + - r-base + - r-rcpp >=0.11.1{indent}libgcc + +test: + commands: + - $R -e "library('microseq')" + +about: + home: https://CRAN.R-project.org/package=microseq + license: GPL-2 + summary: Basic functions for microbial sequence data analysis. + license_family: GPL2 + +# The original CRAN metadata for this package was: + +# Package: microseq +# Type: Package +# Title: Basic Biological Sequence Analysis +# Version: 1.2 +# Date: 2017-01-13 +# Author: Lars Snipen, Kristian Hovde Liland +# Maintainer: Lars Snipen +# Description: Basic functions for microbial sequence data analysis. +# License: GPL-2 +# Depends: R (>= 3.3.1) +# Imports: Rcpp (>= 0.11.1) +# LinkingTo: Rcpp (>= 0.11.1) +# RoxygenNote: 5.0.1 +# NeedsCompilation: yes +# Packaged: 2017-01-13 11:28:56 UTC; larssn +# Repository: CRAN +# Date/Publication: 2017-01-13 15:40:55 + +# See +# http://docs.continuum.io/conda/build.html for +# more information about meta.yaml From 2dead830e9731940d44356dc6ed7bcca3e84d0d6 Mon Sep 17 00:00:00 2001 From: Bjoern Gruening Date: Sat, 3 Jun 2017 15:05:36 +0200 Subject: [PATCH 003/116] start rebuilding for R 3.3.2 without the r-channel --- .travis.yml | 2 +- config.yml | 1 - scripts/env_matrix.yml | 2 +- 3 files changed, 2 insertions(+), 3 deletions(-) diff --git a/.travis.yml b/.travis.yml index a9515727ff..a536251f6f 100644 --- a/.travis.yml +++ b/.travis.yml @@ -16,7 +16,7 @@ script: scripts/travis-run.sh env: global: - SUBDAGS=1 - - BIOCONDA_UTILS_TAG=master + - BIOCONDA_UTILS_TAG=kill_r - BIOCONDA_UTILS_BUILD_ARGS="--loglevel=info" - BIOCONDA_UTILS_LINT_ARGS= - MINICONDA_VER="4.2.12" diff --git a/config.yml b/config.yml index cb1943760d..7fd72b66c4 100644 --- a/config.yml +++ b/config.yml @@ -12,7 +12,6 @@ docker_image: "condaforge/linux-anvil" # be added in reverse (from low to high priority). channels: - bioconda - - r - defaults - conda-forge docker_client_version: '1.20' diff --git a/scripts/env_matrix.yml b/scripts/env_matrix.yml index 34db3100b3..5ee9685df5 100644 --- a/scripts/env_matrix.yml +++ b/scripts/env_matrix.yml @@ -4,7 +4,7 @@ CONDA_PY: - 36 CONDA_HTSLIB: "1.4" CONDA_BOOST: "1.61" -CONDA_R: "3.3.1" +CONDA_R: "3.3.2" CONDA_PERL: "5.22.0" CONDA_NPY: "112" CONDA_NCURSES: "5.9" From c5e52414888598df24108b0eff180e6022365117 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= Date: Sat, 3 Jun 2017 15:20:57 +0200 Subject: [PATCH 004/116] change channel order --- config.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/config.yml b/config.yml index 7fd72b66c4..04d1d5aa7b 100644 --- a/config.yml +++ b/config.yml @@ -12,6 +12,6 @@ docker_image: "condaforge/linux-anvil" # be added in reverse (from low to high priority). channels: - bioconda - - defaults - conda-forge + - defaults docker_client_version: '1.20' From e2288cc024660bead6cee27c814994d8f6c20185 Mon Sep 17 00:00:00 2001 From: Bjoern Gruening Date: Sat, 3 Jun 2017 15:56:18 +0200 Subject: [PATCH 005/116] various fixes --- recipes/r-gbm/meta.yaml | 5 ++--- recipes/r-matrixeqtl/meta.yaml | 7 ++++--- recipes/r-ore/meta.yaml | 6 +++--- recipes/r-scatterplot3d/meta.yaml | 6 +++--- recipes/r-vgam/meta.yaml | 5 ++--- 5 files changed, 14 insertions(+), 15 deletions(-) diff --git a/recipes/r-gbm/meta.yaml b/recipes/r-gbm/meta.yaml index 9d6314e1b7..68a7015a9a 100644 --- a/recipes/r-gbm/meta.yaml +++ b/recipes/r-gbm/meta.yaml @@ -5,7 +5,6 @@ package: source: fn: gbm_2.1.1.tar.gz url: - - http://cran.r-project.org/src/contrib/gbm_2.1.1.tar.gz - http://cran.r-project.org/src/contrib/Archive/gbm/gbm_2.1.1.tar.gz md5: 8126037a1a9a216735db074d04d362ed @@ -18,14 +17,14 @@ build: # Suggests: RUnit requirements: build: - - r + - r-base - r-lattice - r-survival - gcc # [not osx] - llvm # [osx] run: - - r + - r-base - r-lattice - r-survival - libgcc # [not osx] diff --git a/recipes/r-matrixeqtl/meta.yaml b/recipes/r-matrixeqtl/meta.yaml index ebaf380f5f..039d9eb536 100644 --- a/recipes/r-matrixeqtl/meta.yaml +++ b/recipes/r-matrixeqtl/meta.yaml @@ -21,10 +21,11 @@ build: requirements: build: - - r - + - r-base + - icu 58.* run: - - r + - r-base + - icu 58.* test: commands: diff --git a/recipes/r-ore/meta.yaml b/recipes/r-ore/meta.yaml index fe348abf4b..9f8a8e19c6 100644 --- a/recipes/r-ore/meta.yaml +++ b/recipes/r-ore/meta.yaml @@ -5,8 +5,8 @@ package: source: fn: ore_1.3.0.tar.gz url: - - http://cran.r-project.org/src/contrib/ore_1.3.0.tar.gz - http://cran.r-project.org/src/contrib/Archive/ore/ore_1.3.0.tar.gz + sha256: 4f3279a7550ff32c9f0fbef8b551c565873bc4485be47fcc80a55ae1eec5cd21 build: number: 0 @@ -17,11 +17,11 @@ build: requirements: build: - - r + - r-base - gcc # [not win] run: - - r + - r-base - libgcc # [not win] test: diff --git a/recipes/r-scatterplot3d/meta.yaml b/recipes/r-scatterplot3d/meta.yaml index 8d893462ed..e1c422067f 100644 --- a/recipes/r-scatterplot3d/meta.yaml +++ b/recipes/r-scatterplot3d/meta.yaml @@ -5,8 +5,8 @@ package: source: fn: scatterplot3d_0.3-36.tar.gz url: - - http://cran.r-project.org/src/contrib/scatterplot3d_0.3-36.tar.gz - http://cran.r-project.org/src/contrib/Archive/scatterplot3d/scatterplot3d_0.3-36.tar.gz + sha256: 906b681751a70338c548a23e5ed29cf7d3dba3221ee0bbf28041a4217873bd2d build: rpaths: @@ -15,10 +15,10 @@ build: requirements: build: - - r + - r-base run: - - r + - r-base test: commands: diff --git a/recipes/r-vgam/meta.yaml b/recipes/r-vgam/meta.yaml index 61aa0277d0..fbdd3b2e75 100644 --- a/recipes/r-vgam/meta.yaml +++ b/recipes/r-vgam/meta.yaml @@ -10,7 +10,6 @@ package: source: fn: VGAM_1.0-2.tar.gz url: - - http://cran.r-project.org/src/contrib/VGAM_1.0-2.tar.gz - http://cran.r-project.org/src/contrib/Archive/VGAM/VGAM_1.0-2.tar.gz @@ -34,13 +33,13 @@ build: # Suggests: VGAMdata, MASS, mgcv requirements: build: - - r + - r-base - posix # [win] - {{native}}toolchain # [win] - gcc # [not win] run: - - r + - r-base test: commands: From a6204274b628a1cd12e832cf279665e0d6533386 Mon Sep 17 00:00:00 2001 From: Bjoern Gruening Date: Sat, 3 Jun 2017 16:35:20 +0200 Subject: [PATCH 006/116] various fixes --- recipes/r-algdesign/meta.yaml | 4 ++-- recipes/r-findpython/meta.yaml | 5 ++--- recipes/r-logging/meta.yaml | 33 ++++----------------------------- recipes/r-maldiquant/meta.yaml | 5 ++--- recipes/r-maldiquantforeign/meta.yaml | 5 ++--- recipes/r-matrixstats/meta.yaml | 1 - recipes/r-plasmidprofiler/meta.yaml | 4 ++-- recipes/r-rcppgsl/meta.yaml | 4 ++-- 8 files changed, 16 insertions(+), 45 deletions(-) diff --git a/recipes/r-algdesign/meta.yaml b/recipes/r-algdesign/meta.yaml index da8d203352..354ccba704 100644 --- a/recipes/r-algdesign/meta.yaml +++ b/recipes/r-algdesign/meta.yaml @@ -18,12 +18,12 @@ build: requirements: build: - - r + - r-base - gcc # [not osx] - llvm # [osx] run: - - r + - r-base - libgcc # [not osx] test: diff --git a/recipes/r-findpython/meta.yaml b/recipes/r-findpython/meta.yaml index 5371d7eb58..0de8c90934 100644 --- a/recipes/r-findpython/meta.yaml +++ b/recipes/r-findpython/meta.yaml @@ -7,7 +7,6 @@ package: source: fn: findpython_1.0.1.tar.gz url: - - http://cran.r-project.org/src/contrib/findpython_1.0.1.tar.gz - http://cran.r-project.org/src/contrib/Archive/findpython/findpython_1.0.1.tar.gz md5: 04cf40ab0339703453a0022b1e861c68 @@ -22,10 +21,10 @@ build: # Suggests: testthat requirements: build: - - r + - r-base run: - - r + - r-base test: commands: diff --git a/recipes/r-logging/meta.yaml b/recipes/r-logging/meta.yaml index d36181c9fc..94907352f7 100644 --- a/recipes/r-logging/meta.yaml +++ b/recipes/r-logging/meta.yaml @@ -15,17 +15,16 @@ build: - lib/R/lib/ - lib/ -# Suggests: svUnit, XML requirements: build: - - r - + - r-base + - icu 58.* run: - - r + - r-base + - icu 58.* test: commands: - # You can put additional test commands to be run here. - $R -e "library('logging')" about: @@ -33,27 +32,3 @@ about: license: GPL (>= 2) summary: logging is a pure R package that implements the ubiquitous log4j package. license_family: GPL3 - -# The original CRAN metadata for this package was: - -# Package: logging -# Version: 0.7-103 -# Date: 2013-04-08 -# Title: R logging package -# Author: Mario Frasca -# Maintainer: Mario Frasca -# Description: logging is a pure R package that implements the ubiquitous log4j package. -# License: GPL (>= 2) -# Depends: R (>= 2.12.0), methods -# Suggests: svUnit, XML -# Repository: CRAN -# Repository/R-Forge/Project: logging -# Repository/R-Forge/Revision: 103 -# Repository/R-Forge/DateTimeStamp: 2013-04-08 09:57:38 -# Date/Publication: 2013-04-12 08:30:00 -# Packaged: 2013-04-10 01:16:35 UTC; rforge -# NeedsCompilation: no - -# See -# http://docs.continuum.io/conda/build.html for -# more information about meta.yaml diff --git a/recipes/r-maldiquant/meta.yaml b/recipes/r-maldiquant/meta.yaml index 629276c0ee..a46e5ef5f2 100644 --- a/recipes/r-maldiquant/meta.yaml +++ b/recipes/r-maldiquant/meta.yaml @@ -5,7 +5,6 @@ package: source: fn: MALDIquant_1.14.tar.gz url: - - http://cran.r-project.org/src/contrib/MALDIquant_1.14.tar.gz - http://cran.r-project.org/src/contrib/Archive/MALDIquant/MALDIquant_1.14.tar.gz sha256: ea4ea0c2b4d2099813fe4df4cd32a9a5b7f695017035ff706f306e28540ecfb8 @@ -21,11 +20,11 @@ build: # Suggests: knitr, testthat (>= 0.8) requirements: build: - - r + - r-base - gcc # [not win] run: - - r + - r-base - libgcc # [not win] test: diff --git a/recipes/r-maldiquantforeign/meta.yaml b/recipes/r-maldiquantforeign/meta.yaml index 22a22cb880..9cdffd77d7 100644 --- a/recipes/r-maldiquantforeign/meta.yaml +++ b/recipes/r-maldiquantforeign/meta.yaml @@ -5,7 +5,6 @@ package: source: fn: MALDIquantForeign_0.10.tar.gz url: - - http://cran.r-project.org/src/contrib/MALDIquantForeign_0.10.tar.gz - http://cran.r-project.org/src/contrib/Archive/MALDIquantForeign/MALDIquantForeign_0.10.tar.gz sha256: 2356bdc2437c147614c1398c391e3ce21b5970b146ddcd837f7c0c3178dd34c0 @@ -22,7 +21,7 @@ build: # Suggests: knitr, testthat (>= 0.8), RNetCDF (>= 1.6.1) requirements: build: - - r + - r-base - r-maldiquant >=1.11.7 - r-xml - r-base64enc @@ -31,7 +30,7 @@ requirements: - r-readmzxmldata >=2.7 run: - - r + - r-base - r-maldiquant >=1.11.7 - r-xml - r-base64enc diff --git a/recipes/r-matrixstats/meta.yaml b/recipes/r-matrixstats/meta.yaml index 2280851015..90b80da965 100644 --- a/recipes/r-matrixstats/meta.yaml +++ b/recipes/r-matrixstats/meta.yaml @@ -5,7 +5,6 @@ package: source: fn: matrixStats_0.51.0.tar.gz url: - - http://cran.r-project.org/src/contrib/matrixStats_0.51.0.tar.gz - http://cran.r-project.org/src/contrib/Archive/matrixStats/matrixStats_0.51.0.tar.gz sha256: f2b22c2dab2f28e9bcae9e5e744fd2a9f969230ed8ba7aa84debcd024ca74a2f diff --git a/recipes/r-plasmidprofiler/meta.yaml b/recipes/r-plasmidprofiler/meta.yaml index cad508f5f9..faa61a10b2 100644 --- a/recipes/r-plasmidprofiler/meta.yaml +++ b/recipes/r-plasmidprofiler/meta.yaml @@ -17,7 +17,7 @@ build: requirements: build: - - r 3.3.1 + - r-base - r-ape 3.5 - r-dplyr 0.5.0 - r-gdata 2.17.0 @@ -35,7 +35,7 @@ requirements: - pandoc 1.19.2 run: - - r 3.3.1 + - r-base - r-ape 3.5 - r-dplyr 0.5.0 - r-gdata 2.17.0 diff --git a/recipes/r-rcppgsl/meta.yaml b/recipes/r-rcppgsl/meta.yaml index 1888c41b1d..39d6e5fa71 100644 --- a/recipes/r-rcppgsl/meta.yaml +++ b/recipes/r-rcppgsl/meta.yaml @@ -11,12 +11,12 @@ build: package: {name: r-rcppgsl, version: 0.3.1} requirements: build: - - r >=2.14 + - r-base - r-rcpp >=0.11 - gsl {{CONDA_GSL}}* conflicts: [] run: - - r >=2.14 + - r-base - r-rcpp >=0.11 - gsl {{CONDA_GSL}}* source: From e9bf5a8ae8ded719a0215fa7e1007da457ca9a8c Mon Sep 17 00:00:00 2001 From: Bjoern Gruening Date: Sat, 3 Jun 2017 16:36:27 +0200 Subject: [PATCH 007/116] fixes to bioc packages --- recipes/bioconductor-bsgenome/meta.yaml | 48 +++++----- recipes/bioconductor-genomation/meta.yaml | 100 ++++++++++----------- recipes/bioconductor-genomicalignments/meta.yaml | 49 +++++----- recipes/bioconductor-motifrg/meta.yaml | 29 +++--- recipes/bioconductor-org.dm.eg.db/meta.yaml | 12 ++- recipes/bioconductor-seqpattern/meta.yaml | 27 +++--- .../bioconductor-summarizedexperiment/meta.yaml | 35 +++----- 7 files changed, 136 insertions(+), 164 deletions(-) diff --git a/recipes/bioconductor-bsgenome/meta.yaml b/recipes/bioconductor-bsgenome/meta.yaml index 54bd5d4b8b..3dd71fe177 100644 --- a/recipes/bioconductor-bsgenome/meta.yaml +++ b/recipes/bioconductor-bsgenome/meta.yaml @@ -13,37 +13,29 @@ build: - lib/R/lib/ - lib/ -#Suggests: BiocInstaller, Biobase, BSgenome.Celegans.UCSC.ce2, -# BSgenome.Hsapiens.UCSC.hg38, BSgenome.Hsapiens.UCSC.hg38.masked, -# BSgenome.Mmusculus.UCSC.mm10, BSgenome.Rnorvegicus.UCSC.rn5, -# TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, -# SNPlocs.Hsapiens.dbSNP141.GRCh38, XtraSNPlocs.Hsapiens.dbSNP141.GRCh38, -# hgu95av2probe, RUnit - -#for each dependency, the used version for building the package is in comment requirements: build: - - bioconductor-biocgenerics >=0.13.8 # 0.20.0 - - bioconductor-biostrings >=2.35.3 # 2.40.0 - - bioconductor-genomeinfodb >=1.3.19 # 1.8.7 - - bioconductor-genomicranges >=1.23.15 # 1.26.1 - - bioconductor-iranges >=2.1.33 # 2.8.0 - - bioconductor-rsamtools # 1.26.1 - - bioconductor-rtracklayer >=1.25.8 # 1.34.0 - - bioconductor-s4vectors >=0.9.36 # 0.12.0 - - bioconductor-xvector # 0.12.1 - - r #>=2.8.0 + - bioconductor-biocgenerics >=0.13.8 + - bioconductor-biostrings >=2.35.3 + - bioconductor-genomeinfodb >=1.3.19 + - bioconductor-genomicranges >=1.23.15 + - bioconductor-iranges >=2.1.33 + - bioconductor-rsamtools + - bioconductor-rtracklayer >=1.25.8 + - bioconductor-s4vectors >=0.9.36 + - bioconductor-xvector + - r-base run: - - bioconductor-biocgenerics >=0.13.8 # 0.20.0 - - bioconductor-biostrings >=2.35.3 # 2.40.0 - - bioconductor-genomeinfodb >=1.3.19 # 1.8.7 - - bioconductor-genomicranges >=1.23.15 # 1.26.1 - - bioconductor-iranges >=2.1.33 # 2.8.0 - - bioconductor-rsamtools # 1.26.1 - - bioconductor-rtracklayer >=1.25.8 # 1.34.0 - - bioconductor-s4vectors >=0.9.36 # 0.12.0 - - bioconductor-xvector # 0.12.1 - - r #>=2.8.0 + - bioconductor-biocgenerics >=0.13.8 + - bioconductor-biostrings >=2.35.3 + - bioconductor-genomeinfodb >=1.3.19 + - bioconductor-genomicranges >=1.23.15 + - bioconductor-iranges >=2.1.33 + - bioconductor-rsamtools + - bioconductor-rtracklayer >=1.25.8 + - bioconductor-s4vectors >=0.9.36 + - bioconductor-xvector + - r-base test: commands: diff --git a/recipes/bioconductor-genomation/meta.yaml b/recipes/bioconductor-genomation/meta.yaml index 2ba8f8e5ff..622d8dd8f7 100644 --- a/recipes/bioconductor-genomation/meta.yaml +++ b/recipes/bioconductor-genomation/meta.yaml @@ -13,61 +13,57 @@ build: - lib/R/lib/ - lib/ -#Suggests: BiocGenerics, genomationData, knitr, knitrBootstrap, -#RColorBrewer, rmarkdown - -#for each dependency, the used version for building the package is in comment requirements: build: - - bioconductor-biostrings #2.40.0 - - bioconductor-bsgenome #1.42.0 - - bioconductor-genomeinfodb #1.8.7 - - bioconductor-genomicalignments #1.10.0 - - bioconductor-genomicranges >=1.23.26 #1.26.1 - - bioconductor-impute #1.46.0 - - bioconductor-iranges #2.8.0 - - bioconductor-rsamtools #1.26.1 - - bioconductor-seqpattern #1.6.0 - - bioconductor-rtracklayer #1.34.0 - - bioconductor-s4vectors >=0.9.25 #0.12.0 - - bioconductor-rhtslib #1.6.0 - - r #>=3.0.0 - - r-data.table #1.9.6 - - r-ggplot2 #2.1.0 - - r-gridbase #0.4_7 - - r-matrixstats #0.50.1 - - r-plotrix #3.6_1 - - r-plyr #1.8.4 - - r-readr #0.2.2 - - r-reshape2 #1.4.1 - - r-rcpp #0.12.5 - - r-runit #0.4.31 - - gcc # [linux] - - llvm # [osx] + - bioconductor-biostrings + - bioconductor-bsgenome + - bioconductor-genomeinfodb + - bioconductor-genomicalignments + - bioconductor-genomicranges >=1.23.26 + - bioconductor-impute + - bioconductor-iranges + - bioconductor-rsamtools + - bioconductor-seqpattern + - bioconductor-rtracklayer + - bioconductor-s4vectors >=0.9.25 + - bioconductor-rhtslib + - r-base + - r-data.table + - r-ggplot2 + - r-gridbase + - r-matrixstats + - r-plotrix + - r-plyr + - r-readr + - r-reshape2 + - r-rcpp + - r-runit + - gcc # [linux] + - llvm # [osx] run: - - bioconductor-biostrings #2.40.0 - - bioconductor-bsgenome #1.42.0 - - bioconductor-genomeinfodb #1.8.7 - - bioconductor-genomicalignments #1.10.0 - - bioconductor-genomicranges >=1.23.26 #1.26.1 - - bioconductor-impute #1.46.0 - - bioconductor-iranges #2.8.0 - - bioconductor-rsamtools #1.26.1 - - bioconductor-seqpattern #1.6.0 - - bioconductor-rtracklayer #1.34.0 - - bioconductor-s4vectors >=0.9.25 #0.12.0 - - bioconductor-rhtslib #1.6.0 - - r #>=3.0.0 - - r-data.table #1.9.6 - - r-ggplot2 #2.1.0 - - r-gridbase #0.4_7 - - r-matrixstats #0.50.1 - - r-plotrix #3.6_1 - - r-plyr #1.8.4 - - r-readr #0.2.2 - - r-reshape2 #1.4.1 - - r-rcpp #0.12.5 - - r-runit #0.4.31 + - bioconductor-biostrings + - bioconductor-bsgenome + - bioconductor-genomeinfodb + - bioconductor-genomicalignments + - bioconductor-genomicranges >=1.23.26 + - bioconductor-impute + - bioconductor-iranges + - bioconductor-rsamtools + - bioconductor-seqpattern + - bioconductor-rtracklayer + - bioconductor-s4vectors >=0.9.25 + - bioconductor-rhtslib + - r-base + - r-data.table + - r-ggplot2 + - r-gridbase + - r-matrixstats + - r-plotrix + - r-plyr + - r-readr + - r-reshape2 + - r-rcpp + - r-runit - libgcc # [linux] test: diff --git a/recipes/bioconductor-genomicalignments/meta.yaml b/recipes/bioconductor-genomicalignments/meta.yaml index 3d972b0543..8ab1488454 100644 --- a/recipes/bioconductor-genomicalignments/meta.yaml +++ b/recipes/bioconductor-genomicalignments/meta.yaml @@ -13,38 +13,29 @@ build: - lib/R/lib/ - lib/ -#Suggests: ShortRead, rtracklayer, BSgenome, GenomicFeatures, -# RNAseqData.HNRNPC.bam.chr14, pasillaBamSubset, -# TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Dmelanogaster.UCSC.dm3.ensGene, -# BSgenome.Dmelanogaster.UCSC.dm3, BSgenome.Hsapiens.UCSC.hg19, DESeq2, edgeR, -# RUnit, BiocStyle - -#I specify the versions of respective dependencies while buiding the package, -#whereas in the comments, I document -#the version ranges specified in the origianl R description file. requirements: build: - - bioconductor-biocgenerics 0.20.0 #>=0.15.3 - - bioconductor-biocparallel 1.6.6 - - bioconductor-biostrings 2.40.0 #>=2.37.1 - - bioconductor-genomeinfodb 1.8.7 #>=1.1.20 - - bioconductor-genomicranges 1.26.1 #>= 1.25.6 - - bioconductor-iranges 2.8.0 #>= 2.5.36 - - bioconductor-rsamtools 1.26.1 #>=1.21.4 - - bioconductor-s4vectors 0.12.0 #>= 0.9.40 - - bioconductor-summarizedexperiment 1.4.0 #>=0.3.1 - - r #>= 2.10 + - bioconductor-biocgenerics + - bioconductor-biocparallel + - bioconductor-biostrings + - bioconductor-genomeinfodb + - bioconductor-genomicranges + - bioconductor-iranges + - bioconductor-rsamtools + - bioconductor-s4vectors + - bioconductor-summarizedexperiment + - r-base run: - - bioconductor-biocgenerics 0.20.0 #>=0.15.3 - - bioconductor-biocparallel 1.6.6 - - bioconductor-biostrings 2.40.0 #>=2.37.1 - - bioconductor-genomeinfodb 1.8.7 #>=1.1.20 - - bioconductor-genomicranges 1.26.1 #>= 1.25.6 - - bioconductor-iranges 2.8.0 #>= 2.5.36 - - bioconductor-rsamtools 1.26.1 #>=1.21.4 - - bioconductor-s4vectors 0.12.0 #>= 0.9.40 - - bioconductor-summarizedexperiment 1.4.0 #>=0.3.1 - - r #>= 2.10 + - bioconductor-biocgenerics + - bioconductor-biocparallel + - bioconductor-biostrings + - bioconductor-genomeinfodb + - bioconductor-genomicranges + - bioconductor-iranges + - bioconductor-rsamtools + - bioconductor-s4vectors + - bioconductor-summarizedexperiment + - r-base test: commands: diff --git a/recipes/bioconductor-motifrg/meta.yaml b/recipes/bioconductor-motifrg/meta.yaml index 9451a4b884..c3f74baa15 100644 --- a/recipes/bioconductor-motifrg/meta.yaml +++ b/recipes/bioconductor-motifrg/meta.yaml @@ -13,24 +13,23 @@ build: - lib/R/lib/ - lib/ -#for each dependency, the used version for building the package is in comment requirements: build: - - r #>= 2.15 - - bioconductor-biostrings >=2.26 #2.40.0 - - bioconductor-iranges #2.8.0 - - bioconductor-seqlogo #1.38.0 - - bioconductor-bsgenome #1.42.0 - - bioconductor-xvector #0.12.1 - - bioconductor-bsgenome.hsapiens.ucsc.hg19 #1.4.0 + - r-base + - bioconductor-biostrings + - bioconductor-iranges + - bioconductor-seqlogo + - bioconductor-bsgenome + - bioconductor-xvector + - bioconductor-bsgenome.hsapiens.ucsc.hg19 run: - - r #>= 2.15 - - bioconductor-biostrings >=2.26 #2.40.0 - - bioconductor-iranges #2.8.0 - - bioconductor-seqlogo #1.38.0 - - bioconductor-bsgenome #1.42.0 - - bioconductor-xvector #0.12.1 - - bioconductor-bsgenome.hsapiens.ucsc.hg19 #1.4.0 + - r-base + - bioconductor-biostrings + - bioconductor-iranges + - bioconductor-seqlogo + - bioconductor-bsgenome + - bioconductor-xvector + - bioconductor-bsgenome.hsapiens.ucsc.hg19 test: diff --git a/recipes/bioconductor-org.dm.eg.db/meta.yaml b/recipes/bioconductor-org.dm.eg.db/meta.yaml index 026208cc6d..a386b440f2 100644 --- a/recipes/bioconductor-org.dm.eg.db/meta.yaml +++ b/recipes/bioconductor-org.dm.eg.db/meta.yaml @@ -6,10 +6,12 @@ package: name: bioconductor-org.dm.eg.db version: 3.4.0 + source: fn: org.Dm.eg.db_3.4.0.tar.gz url: http://bioconductor.org/packages/release/data/annotation/src/contrib/org.Dm.eg.db_3.4.0.tar.gz md5: c5ad88582d5c12355d3fb4b98cf559a0 + build: number: 0 rpaths: @@ -17,14 +19,16 @@ build: - lib/ requirements: build: - - bioconductor-annotationdbi >=1.35.4 - - r >=2.7.0 + - bioconductor-annotationdbi + - r-base run: - - bioconductor-annotationdbi >=1.35.4 - - r >=2.7.0 + - bioconductor-annotationdbi + - r-base + test: commands: - $R -e "library('org.Dm.eg.db')" + about: home: http://bioconductor.org/packages/release/data/annotation/html/org.Dm.eg.db.html license: Artistic-2.0 diff --git a/recipes/bioconductor-seqpattern/meta.yaml b/recipes/bioconductor-seqpattern/meta.yaml index 454aa2622d..0b7cd93d4b 100644 --- a/recipes/bioconductor-seqpattern/meta.yaml +++ b/recipes/bioconductor-seqpattern/meta.yaml @@ -12,24 +12,21 @@ build: - lib/R/lib/ - lib/ -#Suggests: BSgenome.Drerio.UCSC.danRer7, CAGEr, RUnit, BiocGenerics, BiocStyle - -#for each dependency, the used version for building the package is in comment requirements: build: - - bioconductor-biostrings #2.40.0 - - bioconductor-genomicranges #1.26.1 - - bioconductor-iranges #2.8.0 - - r #>=2.15.0 - - r-plotrix #3.6_1 - - r-kernsmooth #2.23_15 + - bioconductor-biostrings + - bioconductor-genomicranges + - bioconductor-iranges + - r-base + - r-plotrix + - r-kernsmooth run: - - bioconductor-biostrings #2.40.0 - - bioconductor-genomicranges #1.26.1 - - bioconductor-iranges #2.8.0 - - r #>=2.15.0 - - r-plotrix #3.6_1 - - r-kernsmooth #2.23_15 + - bioconductor-biostrings + - bioconductor-genomicranges + - bioconductor-iranges + - r-base + - r-plotrix + - r-kernsmooth test: commands: diff --git a/recipes/bioconductor-summarizedexperiment/meta.yaml b/recipes/bioconductor-summarizedexperiment/meta.yaml index 025897f812..ac7c09d886 100644 --- a/recipes/bioconductor-summarizedexperiment/meta.yaml +++ b/recipes/bioconductor-summarizedexperiment/meta.yaml @@ -13,31 +13,24 @@ build: - lib/R/lib/ - lib/ -#Suggests: annotate, AnnotationDbi, hgu95av2.db, GenomicFeatures, -# TxDb.Hsapiens.UCSC.hg19.knownGene, BiocStyle, knitr, rmarkdown, digest, -# jsonlite, rhdf5, airway, RUnit - -#I specify the versions of respective dependencies while buiding the package, -#whereas in the comments, I document -#the version ranges specified in the origianl R description file. requirements: build: - - bioconductor-biobase 2.32.0 - - bioconductor-biocgenerics 0.20.0 #>=0.15.3 - - bioconductor-genomeinfodb 1.8.7 - - bioconductor-genomicranges 1.26.1 #>= 1.23.15 - - bioconductor-iranges 2.8.0 #>= 2.7.2 - - bioconductor-s4vectors 0.12.0 #>= 0.11.7 - - r #>=3.2 + - bioconductor-biobase + - bioconductor-biocgenerics + - bioconductor-genomeinfodb + - bioconductor-genomicranges + - bioconductor-iranges + - bioconductor-s4vectors + - r-base - r-matrix 1.2_6 run: - - bioconductor-biobase 2.32.0 - - bioconductor-biocgenerics 0.20.0 #>=0.15.3 - - bioconductor-genomeinfodb 1.8.7 - - bioconductor-genomicranges 1.26.1 #>= 1.23.15 - - bioconductor-iranges 2.8.0 #>= 2.7.2 - - bioconductor-s4vectors 0.12.0 #>= 0.11.7 - - r #>=3.2 + - bioconductor-biobase + - bioconductor-biocgenerics + - bioconductor-genomeinfodb + - bioconductor-genomicranges + - bioconductor-iranges + - bioconductor-s4vectors + - r-base - r-matrix 1.2_6 test: From 593cf9b9eb75d707858e0977e21d998d5693b234 Mon Sep 17 00:00:00 2001 From: Bjoern Gruening Date: Sat, 3 Jun 2017 18:38:12 +0200 Subject: [PATCH 008/116] fixes --- recipes/bioconductor-hilbertvis/meta.yaml | 4 +-- recipes/r-base64/meta.yaml | 53 +++------------------------- recipes/r-compquadform/meta.yaml | 1 - recipes/r-corpcor/meta.yaml | 30 +++------------- recipes/r-data.table/meta.yaml | 33 +----------------- recipes/r-futile.options/meta.yaml | 58 ++++--------------------------- recipes/r-multicool/meta.yaml | 41 ++-------------------- recipes/r-nor1mix/meta.yaml | 55 +++-------------------------- recipes/r-params/meta.yaml | 58 +++---------------------------- recipes/r-pcapp/meta.yaml | 52 +++------------------------ recipes/r-polynom/meta.yaml | 44 +++-------------------- recipes/r-r.methodss3/meta.yaml | 31 ++--------------- recipes/r-splancs/meta.yaml | 38 ++++---------------- 13 files changed, 49 insertions(+), 449 deletions(-) diff --git a/recipes/bioconductor-hilbertvis/meta.yaml b/recipes/bioconductor-hilbertvis/meta.yaml index 71a658fd1e..9ddc47aae2 100644 --- a/recipes/bioconductor-hilbertvis/meta.yaml +++ b/recipes/bioconductor-hilbertvis/meta.yaml @@ -12,9 +12,9 @@ build: - lib/ requirements: build: - - r + - r-base run: - - r + - r-base test: commands: - '$R -e "library(''HilbertVis'')"' diff --git a/recipes/r-base64/meta.yaml b/recipes/r-base64/meta.yaml index d903ae6b4c..b05562c943 100644 --- a/recipes/r-base64/meta.yaml +++ b/recipes/r-base64/meta.yaml @@ -1,29 +1,15 @@ package: name: r-base64 - # Note that conda versions cannot contain -, so any -'s in the version have - # been replaced with _'s. version: "1.1" source: fn: base64_1.1.tar.gz url: - - http://cran.r-project.org/src/contrib/base64_1.1.tar.gz - http://cran.r-project.org/src/contrib/Archive/base64/base64_1.1.tar.gz - - - # You can add a hash for the file here, like md5 or sha1 - # md5: 49448ba4863157652311cc5ea4fea3ea - # sha1: 3bcfbee008276084cbb37a2b453963c61176a322 - # patches: - # List any patch files here - # - fix.patch + sha256: bd501bd412de09bf5cee1b21e878133787873dddd0644b5afccb3f8a83fcc3f2 build: - # If this is a new build for the same version, increment the build - # number. If you do not include this key, it defaults to 0. - # number: 1 - - # This is required to make R link correctly on Linux. + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -31,11 +17,11 @@ build: requirements: build: - - r + - r-base - gcc # [not win] run: - - r + - r-base - libgcc # [not win] test: @@ -44,38 +30,7 @@ test: - $R -e "library('base64')" # [not win] - "\"%R%\" -e \"library('base64')\"" # [win] - # You can also put a file called run_test.py, run_test.sh, or run_test.bat - # in the recipe that will be run at test time. - - # requires: - # Put any additional test requirements here. - about: home: http://romainfrancois.blog.free.fr/index.php?category/R-package/base64 license: GPL (>= 2) summary: Base 64 encoder/decoder - -# The original CRAN metadata for this package was: - -# Package: base64 -# Type: Package -# Title: Base 64 encoder/decoder -# Version: 1.1 -# Date: 2010-04-04 -# Author: Romain Francois, based on code by Bob Trower available at http://base64.sourceforge.net/ -# Maintainer: ORPHANED -# Description: Base 64 encoder/decoder -# License: GPL (>= 2) -# LazyLoad: yes -# URL: http://romainfrancois.blog.free.fr/index.php?category/R-package/base64 -# Packaged: 2011-12-03 12:22:31 UTC; romain -# Repository: CRAN -# Date/Publication: 2011-12-03 11:23:14 -# X-CRAN-Original-Package: base64 -# X-CRAN-Original-Maintainer: Romain Francois -# X-CRAN-Comment: Orphaned on 2012-07-18 as the original maintainer, Romain Francois , is unresponsive. -# NeedsCompilation: yes - -# See -# http://docs.continuum.io/conda/build.html for -# more information about meta.yaml diff --git a/recipes/r-compquadform/meta.yaml b/recipes/r-compquadform/meta.yaml index 0a09f0b037..bdf6673f3a 100644 --- a/recipes/r-compquadform/meta.yaml +++ b/recipes/r-compquadform/meta.yaml @@ -10,7 +10,6 @@ package: source: fn: CompQuadForm_1.4.1.tar.gz url: - - http://cran.r-project.org/src/contrib/CompQuadForm_1.4.1.tar.gz - http://cran.r-project.org/src/contrib/Archive/CompQuadForm/CompQuadForm_1.4.1.tar.gz build: diff --git a/recipes/r-corpcor/meta.yaml b/recipes/r-corpcor/meta.yaml index fc8e166599..340f1a5200 100644 --- a/recipes/r-corpcor/meta.yaml +++ b/recipes/r-corpcor/meta.yaml @@ -1,29 +1,17 @@ package: name: r-corpcor - # Note that conda versions cannot contain -, so any -'s in the version have - # been replaced with _'s. version: "1.6.8" source: fn: corpcor_1.6.8.tar.gz url: - - https://cran.r-project.org/src/contrib/corpcor_1.6.8.tar.gz - http://cran.r-project.org/src/contrib/Archive/corpcor/corpcor_1.6.8.tar.gz + sha256: 69feda67c0919da75ada95e2ada444a8d86b054deabd2ffb3fbec30eddc7dc3e - # You can add a hash for the file here, like md5 or sha1 - # md5: 49448ba4863157652311cc5ea4fea3ea - # sha1: 3bcfbee008276084cbb37a2b453963c61176a322 - # patches: - # List any patch files here - # - fix.patch build: - # If this is a new build for the same version, increment the build - # number. If you do not include this key, it defaults to 0. - # number: 1 - - # This is required to make R link correctly on Linux. + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -31,24 +19,16 @@ build: requirements: build: - - r + - r-base - gcc # [not win] run: - - r + - r-base - libgcc # [not win] test: commands: - # You can put additional test commands to be run here. - - $R -e "library('corpcor')" # [not win] - - "\"%R%\" -e \"library('corpcor')\"" # [win] - - # You can also put a file called run_test.py, run_test.sh, or run_test.bat - # in the recipe that will be run at test time. - - # requires: - # Put any additional test requirements here. + - $R -e "library('corpcor')" about: home: http://strimmerlab.org/software/corpcor/ diff --git a/recipes/r-data.table/meta.yaml b/recipes/r-data.table/meta.yaml index 4d434b3164..463948e4ac 100644 --- a/recipes/r-data.table/meta.yaml +++ b/recipes/r-data.table/meta.yaml @@ -8,7 +8,6 @@ package: source: fn: data.table_1.10.0.tar.gz url: - - http://cran.r-project.org/src/contrib/data.table_1.10.0.tar.gz - http://cran.r-project.org/src/contrib/Archive/data.table/data.table_1.10.0.tar.gz md5: f0e08dd5ba1b3f46c59dd1574fe497c1 @@ -18,12 +17,9 @@ build: - lib/R/lib/ - lib/ -# Suggests: bit64, knitr, chron, ggplot2 (>= 0.9.0), plyr, reshape, reshape2, testthat (>= 0.4), hexbin, fastmatch, nlme, xts, gdata, GenomicRanges, caret, curl, zoo, plm, rmarkdown, parallel requirements: build: - - r - - posix # [win] - - {{native}}toolchain # [win] + - r-base - gcc # [not win] run: @@ -41,30 +37,3 @@ about: of columns by group using no copies at all, list columns, a fast friendly file reader and parallel file writer. Offers a natural and flexible syntax, for faster development. license_family: GPL3 - -# The original CRAN metadata for this package was: - -# Package: data.table -# Version: 1.10.0 -# Title: Extension of `data.frame` -# Authors@R: c( person("Matt","Dowle", role=c("aut","cre"), email="mattjdowle@gmail.com"), person("Arun","Srinivasan", role="aut", email="arunkumar.sriniv@gmail.com"), person("Jan","Gorecki", role="ctb"), person("Tom","Short", role="ctb"), person("Steve","Lianoglou", role="ctb"), person("Eduard","Antonyan", role="ctb") ) -# Depends: R (>= 3.0.0) -# Imports: methods -# Suggests: bit64, knitr, chron, ggplot2 (>= 0.9.0), plyr, reshape, reshape2, testthat (>= 0.4), hexbin, fastmatch, nlme, xts, gdata, GenomicRanges, caret, curl, zoo, plm, rmarkdown, parallel -# Description: Fast aggregation of large data (e.g. 100GB in RAM), fast ordered joins, fast add/modify/delete of columns by group using no copies at all, list columns, a fast friendly file reader and parallel file writer. Offers a natural and flexible syntax, for faster development. -# License: GPL-3 | file LICENSE -# URL: http://r-datatable.com -# BugReports: https://github.com/Rdatatable/data.table/issues -# MailingList: datatable-help@lists.r-forge.r-project.org -# VignetteBuilder: knitr -# ByteCompile: TRUE -# NeedsCompilation: yes -# Packaged: 2016-12-02 19:25:45.346 UTC; mdowle -# Author: Matt Dowle [aut, cre], Arun Srinivasan [aut], Jan Gorecki [ctb], Tom Short [ctb], Steve Lianoglou [ctb], Eduard Antonyan [ctb] -# Maintainer: Matt Dowle -# Repository: CRAN -# Date/Publication: 2016-12-03 11:05:23 - -# See -# http://docs.continuum.io/conda/build.html for -# more information about meta.yaml diff --git a/recipes/r-futile.options/meta.yaml b/recipes/r-futile.options/meta.yaml index 2ea39be121..0115169cdc 100644 --- a/recipes/r-futile.options/meta.yaml +++ b/recipes/r-futile.options/meta.yaml @@ -1,29 +1,16 @@ package: name: r-futile.options - # Note that conda versions cannot contain -, so any -'s in the version have - # been replaced with _'s. version: "1.0.0" source: fn: futile.options_1.0.0.tar.gz url: - - http://cran.r-project.org/src/contrib/futile.options_1.0.0.tar.gz + - https://cran.r-project.org/src/contrib/futile.options_1.0.0.tar.gz - http://cran.r-project.org/src/contrib/Archive/futile.options/futile.options_1.0.0.tar.gz - - - # You can add a hash for the file here, like md5 or sha1 - # md5: 49448ba4863157652311cc5ea4fea3ea - # sha1: 3bcfbee008276084cbb37a2b453963c61176a322 - # patches: - # List any patch files here - # - fix.patch + sha256: ee84ece359397fbb63f145d11af678f5c8618570971e78cc64ac60dc0d14e8c2 build: - # If this is a new build for the same version, increment the build - # number. If you do not include this key, it defaults to 0. - # number: 1 - - # This is required to make R link correctly on Linux. + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -31,47 +18,16 @@ build: requirements: build: - - r - + - r-base run: - - r + - r-base test: commands: - # You can put additional test commands to be run here. - - $R -e "library('futile.options')" # [not win] - - "\"%R%\" -e \"library('futile.options')\"" # [win] - - # You can also put a file called run_test.py, run_test.sh, or run_test.bat - # in the recipe that will be run at test time. + - $R -e "library('futile.options')" - # requires: - # Put any additional test requirements here. about: #home: license: LGPL-3 - summary: !!python/unicode 'A scoped options management framework' - - -# The original CRAN metadata for this package was: - -# Package: futile.options -# Type: Package -# Title: Futile options management -# Version: 1.0.0 -# Date: 2010-04-05 -# Author: Brian Lee Yung Rowe -# Maintainer: Brian Lee Yung Rowe -# Depends: R (>= 2.8.0) -# Description: A scoped options management framework -# License: LGPL-3 -# LazyLoad: yes -# Packaged: Mon Apr 5 21:09:07 2010; brian -# Repository: CRAN -# Date/Publication: 2010-04-06 08:57:40 -# NeedsCompilation: no - -# See -# http://docs.continuum.io/conda/build.html for -# more information about meta.yaml + summary: 'A scoped options management framework' diff --git a/recipes/r-multicool/meta.yaml b/recipes/r-multicool/meta.yaml index 7b0741fb2c..6c902ffd03 100644 --- a/recipes/r-multicool/meta.yaml +++ b/recipes/r-multicool/meta.yaml @@ -1,20 +1,16 @@ package: name: r-multicool - # Note that conda versions cannot contain -, so any -'s in the version have - # been replaced with _'s. version: "0.1_9" source: fn: multicool_0.1-9.tar.gz url: - - http://cran.r-project.org/src/contrib/multicool_0.1-9.tar.gz - http://cran.r-project.org/src/contrib/Archive/multicool/multicool_0.1-9.tar.gz sha256: bdf92571cef1b649952d155395a92b8683099ee13114f73a9d41fc5d7d49d329 build: number: 2 - # This is required to make R link correctly on Linux. rpaths: - lib/R/lib/ - lib/ @@ -22,26 +18,18 @@ build: requirements: build: - - r + - r-base - r-rcpp >=0.11.2 - gcc run: - - r + - r-base - r-rcpp >=0.11.2 - libgcc # [not osx] test: commands: - # You can put additional test commands to be run here. - - $R -e "library('multicool')" # [not win] - - "\"%R%\" -e \"library('multicool')\"" # [win] - - # You can also put a file called run_test.py, run_test.sh, or run_test.bat - # in the recipe that will be run at test time. - - # requires: - # Put any additional test requirements here. + - $R -e "library('multicool')" about: #home: @@ -59,26 +47,3 @@ about: from Jerome Kelleher which can be found here http://jeromekelleher.net/partitions.php. The C++ code and Python code are distributed without conditions.' - -# The original CRAN metadata for this package was: - -# Package: multicool -# Type: Package -# Title: Permutations of Multisets in Cool-Lex Order -# Version: 0.1-9 -# Date: 2015-10-28 -# Author: James Curran, Aaron Williams, Jerome Kelleher, Dave Barber -# Maintainer: James Curran -# Description: A set of tools to permute multisets without loops or hash tables and to generate integer partitions. The permutation functions are based on C code from Aaron Williams. Cool-lex order is similar to colexicographical order. The algorithm is described in Williams, A. Loopless Generation of Multiset Permutations by Prefix Shifts. SODA 2009, Symposium on Discrete Algorithms, New York, United States. The permutation code is distributed without restrictions. The code for stable and efficient computation of multinomial coefficients comes from Dave Barber. The code can be download from http://home.comcast.net/~tamivox/dave/multinomial/index.html and is distributed without conditions. The package also generates the integer partitions of a positive, non-zero integer n. The C++ code for this is based on Python code from Jerome Kelleher which can be found here http://jeromekelleher.net/partitions.php. The C++ code and Python code are distributed without conditions. -# License: GPL-2 -# Depends: methods, Rcpp (>= 0.11.2) -# LinkingTo: Rcpp -# RcppModules: Multicool -# NeedsCompilation: yes -# Packaged: 2015-10-28 08:46:16 UTC; jcur002 -# Repository: CRAN -# Date/Publication: 2015-10-28 18:39:18 - -# See -# http://docs.continuum.io/conda/build.html for -# more information about meta.yaml diff --git a/recipes/r-nor1mix/meta.yaml b/recipes/r-nor1mix/meta.yaml index 0b29abddc3..283c1f7fe2 100644 --- a/recipes/r-nor1mix/meta.yaml +++ b/recipes/r-nor1mix/meta.yaml @@ -1,78 +1,31 @@ package: name: r-nor1mix - # Note that conda versions cannot contain -, so any -'s in the version have - # been replaced with _'s. version: "1.2_1" source: fn: nor1mix_1.2-1.tar.gz url: - - http://cran.r-project.org/src/contrib/nor1mix_1.2-1.tar.gz - http://cran.r-project.org/src/contrib/Archive/nor1mix/nor1mix_1.2-1.tar.gz - - - # You can add a hash for the file here, like md5 or sha1 - # md5: 49448ba4863157652311cc5ea4fea3ea - # sha1: 3bcfbee008276084cbb37a2b453963c61176a322 - # patches: - # List any patch files here - # - fix.patch + sha256: a38a9e0471f73cab41d7c61bcdf8d0e1dd5396ea9f6f8ee6c4357cc4c71907ea build: - # If this is a new build for the same version, increment the build - # number. If you do not include this key, it defaults to 0. - # number: 1 - - # This is required to make R link correctly on Linux. + number: 0 rpaths: - lib/R/lib/ - lib/ -# Suggests: cluster requirements: build: - - r - + - r-base run: - - r + - r-base test: commands: - # You can put additional test commands to be run here. - $R -e "library('nor1mix')" # [not win] - - "\"%R%\" -e \"library('nor1mix')\"" # [win] - - # You can also put a file called run_test.py, run_test.sh, or run_test.bat - # in the recipe that will be run at test time. - - # requires: - # Put any additional test requirements here. - about: #home: license: GPL (>= 2) summary: Onedimensional Normal Mixture Models Classes, for, e.g., density estimation or clustering algorithms research and teaching; providing the widely used Marron-Wand densities. Now fitting to data by ML (Maximum Likelihood) or EM estimation. - -# The original CRAN metadata for this package was: - -# Package: nor1mix -# Title: Normal (1-d) Mixture Models (S3 Classes and Methods) -# Version: 1.2-1 -# Date: 2015-07-25 -# Author: Martin Machler -# Maintainer: Martin Maechler -# Description: Onedimensional Normal Mixture Models Classes, for, e.g., density estimation or clustering algorithms research and teaching; providing the widely used Marron-Wand densities. Now fitting to data by ML (Maximum Likelihood) or EM estimation. -# Imports: stats, graphics -# Suggests: cluster -# License: GPL (>= 2) -# Encoding: latin1 -# NeedsCompilation: no -# Packaged: 2015-07-25 20:47:00 UTC; maechler -# Repository: CRAN -# Date/Publication: 2015-07-27 10:52:09 - -# See -# http://docs.continuum.io/conda/build.html for -# more information about meta.yaml diff --git a/recipes/r-params/meta.yaml b/recipes/r-params/meta.yaml index 5c28ea7158..f4f9da403f 100644 --- a/recipes/r-params/meta.yaml +++ b/recipes/r-params/meta.yaml @@ -1,83 +1,35 @@ package: name: r-params - # Note that conda versions cannot contain -, so any -'s in the version have - # been replaced with _'s. version: "0.4" source: fn: params_0.4.tar.gz url: - - http://cran.r-project.org/src/contrib/params_0.4.tar.gz - http://cran.r-project.org/src/contrib/Archive/params/params_0.4.tar.gz - - - # You can add a hash for the file here, like md5 or sha1 - # md5: 49448ba4863157652311cc5ea4fea3ea - # sha1: 3bcfbee008276084cbb37a2b453963c61176a322 - # patches: - # List any patch files here - # - fix.patch + sha256: e62860635ba0b16d974b63773fe8ada7fe770f36269797e2b39b34aa7e2abaab build: - # If this is a new build for the same version, increment the build - # number. If you do not include this key, it defaults to 0. - # number: 1 + number: 0 - # This is required to make R link correctly on Linux. rpaths: - lib/R/lib/ - lib/ -# Suggests: openxlsx, testthat requirements: build: - - r + - r-base - r-whisker run: - - r + - r-base - r-whisker test: commands: - # You can put additional test commands to be run here. - - $R -e "library('params')" # [not win] - - "\"%R%\" -e \"library('params')\"" # [win] - - # You can also put a file called run_test.py, run_test.sh, or run_test.bat - # in the recipe that will be run at test time. - - # requires: - # Put any additional test requirements here. + - $R -e "library('params')" about: home: https://github.com/sahilseth/params license: GPL-2 summary: An interface to simplify organizing parameters used in a package, using external configuration files. This attempts to provide a cleaner alternative to options(). - -# The original CRAN metadata for this package was: - -# Package: params -# Type: Package -# Title: Simplify Parameters -# Description: An interface to simplify organizing parameters used in a package, using external configuration files. This attempts to provide a cleaner alternative to options(). -# Version: 0.4 -# Depends: R (>= 3.0.2), whisker -# Imports: utils -# Suggests: openxlsx, testthat -# License: GPL-2 -# Authors@R: c( person("Sahil", "Seth", role = c("aut", "cre"), email = "me@sahilseth.com"), person("Yihui", "Xie", role = c("ctb"), comment = "kable from knitr R/table.R") ) -# URL: https://github.com/sahilseth/params -# BugReports: https://github.com/sahilseth/params/issues -# RoxygenNote: 5.0.1.9000 -# NeedsCompilation: no -# Packaged: 2015-12-01 21:01:18 UTC; sahilseth -# Author: Sahil Seth [aut, cre], Yihui Xie [ctb] (kable from knitr R/table.R) -# Maintainer: Sahil Seth -# Repository: CRAN -# Date/Publication: 2015-12-02 00:01:53 - -# See -# http://docs.continuum.io/conda/build.html for -# more information about meta.yaml diff --git a/recipes/r-pcapp/meta.yaml b/recipes/r-pcapp/meta.yaml index b0c393aadf..a2d8da6fb9 100644 --- a/recipes/r-pcapp/meta.yaml +++ b/recipes/r-pcapp/meta.yaml @@ -1,29 +1,16 @@ package: name: r-pcapp - # Note that conda versions cannot contain -, so any -'s in the version have - # been replaced with _'s. version: "1.9_60" source: fn: pcaPP_1.9-60.tar.gz url: - - http://cran.r-project.org/src/contrib/pcaPP_1.9-60.tar.gz - http://cran.r-project.org/src/contrib/Archive/pcaPP/pcaPP_1.9-60.tar.gz - - - # You can add a hash for the file here, like md5 or sha1 - # md5: 49448ba4863157652311cc5ea4fea3ea - # sha1: 3bcfbee008276084cbb37a2b453963c61176a322 - # patches: - # List any patch files here - # - fix.patch + sha256: 9a4b471957ac39ed7c860e3165bf8e099b5b55cf814654adb58f9d19df2718e7 build: - # If this is a new build for the same version, increment the build - # number. If you do not include this key, it defaults to 0. - # number: 1 + number: 0 - # This is required to make R link correctly on Linux. rpaths: - lib/R/lib/ - lib/ @@ -31,47 +18,18 @@ build: requirements: build: - - r + - r-base - r-mvtnorm run: - - r + - r-base - r-mvtnorm test: commands: - # You can put additional test commands to be run here. - - $R -e "library('pcaPP')" # [not win] - - "\"%R%\" -e \"library('pcaPP')\"" # [win] - - # You can also put a file called run_test.py, run_test.sh, or run_test.bat - # in the recipe that will be run at test time. - - # requires: - # Put any additional test requirements here. + - $R -e "library('pcaPP')" about: #home: license: GPL (>= 3) summary: !!python/unicode 'Robust PCA by Projection Pursuit' - - -# The original CRAN metadata for this package was: - -# Package: pcaPP -# Version: 1.9-60 -# Date: 2014-10-20 -# Title: Robust PCA by Projection Pursuit -# Author: Peter Filzmoser, Heinrich Fritz, Klaudius Kalcher -# Maintainer: Valentin Todorov -# Imports: mvtnorm -# Description: Robust PCA by Projection Pursuit -# License: GPL (>= 3) -# Packaged: 2014-10-21 19:51:01 UTC; Share -# NeedsCompilation: yes -# Repository: CRAN -# Date/Publication: 2014-10-22 00:46:26 - -# See -# http://docs.continuum.io/conda/build.html for -# more information about meta.yaml diff --git a/recipes/r-polynom/meta.yaml b/recipes/r-polynom/meta.yaml index cafdade17b..1b4eca6947 100644 --- a/recipes/r-polynom/meta.yaml +++ b/recipes/r-polynom/meta.yaml @@ -1,27 +1,16 @@ package: name: r-polynom - # Note that conda versions cannot contain -, so any -'s in the version have - # been replaced with _'s. version: "1.3_8" source: fn: polynom_1.3-8.tar.gz url: - - http://cran.r-project.org/src/contrib/polynom_1.3-8.tar.gz - http://cran.r-project.org/src/contrib/Archive/polynom/polynom_1.3-8.tar.gz + sah256: 0d218b8cf9095da0192fbc64b46fdf07bbb5a0a17b53931293824ae4cbc16982 - # You can add a hash for the file here, like md5 or sha1 - # md5: 49448ba4863157652311cc5ea4fea3ea - # sha1: 3bcfbee008276084cbb37a2b453963c61176a322 - # patches: - # List any patch files here - # - fix.patch - build: - # If this is a new build for the same version, increment the build - # number. If you do not include this key, it defaults to 0. - # number: 1 + number: 0 # This is required to make R link correctly on Linux. rpaths: @@ -31,10 +20,10 @@ build: requirements: build: - - r + - r-base run: - - r + - r-base test: commands: @@ -42,33 +31,8 @@ test: - $R -e "library('polynom')" # [not win] - "\"%R%\" -e \"library('polynom')\"" # [win] - # You can also put a file called run_test.py, run_test.sh, or run_test.bat - # in the recipe that will be run at test time. - - # requires: - # Put any additional test requirements here. - about: #home: license: GPL-2 summary: A collection of functions to implement a class for univariate polynomial manipulations. -# The original CRAN metadata for this package was: - -# Package: polynom -# Version: 1.3-8 -# Title: A Collection of Functions to Implement a Class for Univariate Polynomial Manipulations -# Authors@R: c(person("Bill", "Venables", role = "aut", email = "Bill.Venables@adelaide.edu.au", comment = "S original"), person("Kurt", "Hornik", role = c("aut", "cre"), email = "Kurt.Hornik@R-project.org", comment = "R port"), person("Martin", "Maechler", role = "aut", email = "maechler@stat.math.ethz.ch", comment = "R port")) -# Description: A collection of functions to implement a class for univariate polynomial manipulations. -# Imports: stats, graphics -# License: GPL-2 -# NeedsCompilation: no -# Packaged: 2015-06-24 15:41:06 UTC; hornik -# Author: Bill Venables [aut] (S original), Kurt Hornik [aut, cre] (R port), Martin Maechler [aut] (R port) -# Maintainer: Kurt Hornik -# Repository: CRAN -# Date/Publication: 2015-06-24 17:59:08 - -# See -# http://docs.continuum.io/conda/build.html for -# more information about meta.yaml diff --git a/recipes/r-r.methodss3/meta.yaml b/recipes/r-r.methodss3/meta.yaml index 3607090ae9..da85cc8c28 100644 --- a/recipes/r-r.methodss3/meta.yaml +++ b/recipes/r-r.methodss3/meta.yaml @@ -8,7 +8,6 @@ package: source: fn: R.methodsS3_1.7.1.tar.gz url: - - http://cran.r-project.org/src/contrib/R.methodsS3_1.7.1.tar.gz - http://cran.r-project.org/src/contrib/Archive/R.methodsS3/R.methodsS3_1.7.1.tar.gz md5: c88e815837f268affd4f2a39c737d969 @@ -20,15 +19,14 @@ build: requirements: build: - - r + - r-base run: - - r + - r-base test: commands: - - $R -e "library('R.methodsS3')" # [not win] - - "\"%R%\" -e \"library('R.methodsS3')\"" # [win] + - $R -e "library('R.methodsS3')" about: @@ -42,26 +40,3 @@ about: to S4. This is a cross-platform package implemented in pure R that generates standard S3 methods. license_family: LGPL - -# The original CRAN metadata for this package was: - -# Package: R.methodsS3 -# Version: 1.7.1 -# Depends: R (>= 2.13.0) -# Imports: utils -# Date: 2016-02-15 -# Title: S3 Methods Simplified -# Authors@R: c(person("Henrik", "Bengtsson", role=c("aut", "cre", "cph"), email = "henrikb@braju.com")) -# Author: Henrik Bengtsson [aut, cre, cph] -# Maintainer: Henrik Bengtsson -# Description: Methods that simplify the setup of S3 generic functions and S3 methods. Major effort has been made in making definition of methods as simple as possible with a minimum of maintenance for package developers. For example, generic functions are created automatically, if missing, and naming conflict are automatically solved, if possible. The method setMethodS3() is a good start for those who in the future may want to migrate to S4. This is a cross-platform package implemented in pure R that generates standard S3 methods. -# License: LGPL (>= 2.1) -# LazyLoad: TRUE -# NeedsCompilation: no -# Packaged: 2016-02-16 03:21:35 UTC; hb -# Repository: CRAN -# Date/Publication: 2016-02-16 13:48:09 - -# See -# http://docs.continuum.io/conda/build.html for -# more information about meta.yaml diff --git a/recipes/r-splancs/meta.yaml b/recipes/r-splancs/meta.yaml index b87edaccb2..4f87bcdf04 100644 --- a/recipes/r-splancs/meta.yaml +++ b/recipes/r-splancs/meta.yaml @@ -3,34 +3,31 @@ package: name: r-splancs - # Note that conda versions cannot contain -, so any -'s in the version have - # been replaced with _'s. version: "2.01_38" source: fn: splancs_2.01-38.tar.gz url: - - http://cran.r-project.org/src/contrib/splancs_2.01-38.tar.gz - http://cran.r-project.org/src/contrib/Archive/splancs/splancs_2.01-38.tar.gz md5: e2ee3eab61569779c228243288029f67 + build: rpaths: - lib/R/lib/ - lib/ requirements: build: - - r + - r-base - r-sp >=0.9 - - posix # [win] - - {{native}}toolchain # [win] - gcc # [not win] run: - - r + - r-base - r-sp >=0.9 + test: commands: - - $R -e "library('splancs')" # [not win] - - "\"%R%\" -e \"library('splancs')\"" # [win] + - $R -e "library('splancs')" + about: home: http://www.maths.lancs.ac.uk/~rowlings/Splancs/ license: GPL (>= 2) @@ -38,26 +35,3 @@ about: of spatial point pattern data; it has been ported to R and is in "maintenance mode". ' license_family: GPL3 - -# The original CRAN metadata for this package was: - -# Package: splancs -# Version: 2.01-38 -# Date: 2015-09-27 -# Title: Spatial and Space-Time Point Pattern Analysis -# Authors@R: c( person("Roger", "Bivand", role = c("cre"), email = "Roger.Bivand@nhh.no"), person("Barry", "Rowlingson", role = "aut"), person("Peter", "Diggle", role = "aut"), person("Giovanni", "Petris", role = "ctb"), person("Stephen", "Eglen", role = "ctb")) -# Depends: R (>= 2.10.0), sp (>= 0.9) -# Imports: stats, graphics, grDevices, methods -# Description: The Splancs package was written as an enhancement to S-Plus for display and analysis of spatial point pattern data; it has been ported to R and is in "maintenance mode". -# License: GPL (>= 2) -# URL: http://www.maths.lancs.ac.uk/~rowlings/Splancs/ -# NeedsCompilation: yes -# Packaged: 2015-09-28 17:57:23 UTC; rsb -# Author: Roger Bivand [cre], Barry Rowlingson [aut], Peter Diggle [aut], Giovanni Petris [ctb], Stephen Eglen [ctb] -# Maintainer: Roger Bivand -# Repository: CRAN -# Date/Publication: 2015-09-29 01:08:31 - -# See -# http://docs.continuum.io/conda/build.html for -# more information about meta.yaml From 25a406b957e7ca9f7afcc1c9226fe49e16ca5cc3 Mon Sep 17 00:00:00 2001 From: Bjoern Gruening Date: Sat, 3 Jun 2017 19:12:21 +0200 Subject: [PATCH 009/116] remove blacklist --- config.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/config.yml b/config.yml index 04d1d5aa7b..e4c4b6475e 100644 --- a/config.yml +++ b/config.yml @@ -1,6 +1,5 @@ env_matrix: "scripts/env_matrix.yml" blacklists: - - "sorted-r-blacklist" - "build-fail-blacklist" - "boost-1.61-migration-blacklist" - "perl-unable-to-find-blacklist" From 4003cf348446822aedd76a2d0c75bcda80aeef12 Mon Sep 17 00:00:00 2001 From: Bjoern Gruening Date: Sat, 3 Jun 2017 20:40:14 +0200 Subject: [PATCH 010/116] multiple fixes --- recipes/r-biom/meta.yaml | 17 ++++--------- recipes/r-docopt/meta.yaml | 49 +++--------------------------------- recipes/r-funr/meta.yaml | 49 +++--------------------------------- recipes/r-globaloptions/meta.yaml | 53 +++------------------------------------ recipes/r-nleqslv/meta.yaml | 1 - recipes/r-plotrix/meta.yaml | 1 - recipes/r-rann/meta.yaml | 22 ---------------- recipes/r-rappdirs/meta.yaml | 53 +++------------------------------------ recipes/r-rjson/meta.yaml | 10 +++++--- recipes/r-viridislite/meta.yaml | 46 +++------------------------------ recipes/r-yaml/meta.yaml | 43 +++---------------------------- 11 files changed, 35 insertions(+), 309 deletions(-) diff --git a/recipes/r-biom/meta.yaml b/recipes/r-biom/meta.yaml index 138bdaca9b..36245d498e 100644 --- a/recipes/r-biom/meta.yaml +++ b/recipes/r-biom/meta.yaml @@ -7,15 +7,8 @@ package: source: fn: biom_0.3.12.tar.gz url: - - https://cran.r-project.org/src/contrib/biom_0.3.12.tar.gz - - - # You can add a hash for the file here, like md5 or sha1 - # md5: 49448ba4863157652311cc5ea4fea3ea - # sha1: 3bcfbee008276084cbb37a2b453963c61176a322 - # patches: - # List any patch files here - # - fix.patch + - https://cran.r-project.org/src/contrib/Archive/biom/biom_0.3.12.tar.gz + sha256: 4ad17f7811c7346dc4923bd6596a007c177eebb1944a9f46e5674afcc5fdd5a1 build: # If this is a new build for the same version, increment the build @@ -30,13 +23,13 @@ build: # Suggests: XML, RCurl, lattice, ncdf, igraph, bigmemory, knitr, testthat (>= 0.9.1) requirements: build: - - r + - r-base - r-plyr - r-rjsonio - r-matrix run: - - r + - r-base - r-plyr - r-rjsonio - r-matrix @@ -56,4 +49,4 @@ test: about: home: https://github.com/joey711/biom/, http://biom-format.org/ license: GPL-2 - summary: This is an R package for interfacing with the BIOM format. \ No newline at end of file + summary: This is an R package for interfacing with the BIOM format. diff --git a/recipes/r-docopt/meta.yaml b/recipes/r-docopt/meta.yaml index 4e4ff77136..1e9c868915 100644 --- a/recipes/r-docopt/meta.yaml +++ b/recipes/r-docopt/meta.yaml @@ -7,36 +7,23 @@ package: source: fn: docopt_0.4.3.3.tar.gz url: - - http://cran.r-project.org/src/contrib/docopt_0.4.3.3.tar.gz - http://cran.r-project.org/src/contrib/Archive/docopt/docopt_0.4.3.3.tar.gz - - - # You can add a hash for the file here, like md5 or sha1 - # md5: 49448ba4863157652311cc5ea4fea3ea - # sha1: 3bcfbee008276084cbb37a2b453963c61176a322 - # patches: - # List any patch files here - # - fix.patch + sha256: b5c5babef6f13fe7e36dad520b552ea7023e71bfd16dba5e96913f37072ef8ee build: - # If this is a new build for the same version, increment the build - # number. If you do not include this key, it defaults to 0. - # number: 1 - - # This is required to make R link correctly on Linux. + number: 0 skip: True # [osx] rpaths: - lib/R/lib/ - lib/ -# Suggests: testthat requirements: build: - - r + - r-base - r-stringr run: - - r + - r-base - r-stringr test: @@ -45,37 +32,9 @@ test: - $R -e "library('docopt')" # [not win] - "\"%R%\" -e \"library('docopt')\"" # [win] - # You can also put a file called run_test.py, run_test.sh, or run_test.bat - # in the recipe that will be run at test time. - - # requires: - # Put any additional test requirements here. about: home: https://github.com/docopt/docopt.R license: MIT + file LICENSE summary: Define a command-line interface by just giving it a description in the specific format. -# The original CRAN metadata for this package was: - -# Package: docopt -# Type: Package -# Title: Command-Line Interface Specification Language -# Version: 0.4.3.3 -# Date: 2015-05-03 -# Author: Edwin de Jonge (edwindjonge@gmail.com) -# Maintainer: Edwin de Jonge -# Description: Define a command-line interface by just giving it a description in the specific format. -# License: MIT + file LICENSE -# URL: https://github.com/docopt/docopt.R -# Imports: stringr -# Depends: methods -# Suggests: testthat -# Packaged: 2015-05-04 09:26:29 UTC; Edwin -# NeedsCompilation: no -# Repository: CRAN -# Date/Publication: 2015-05-04 12:06:41 - -# See -# http://docs.continuum.io/conda/build.html for -# more information about meta.yaml diff --git a/recipes/r-funr/meta.yaml b/recipes/r-funr/meta.yaml index aaf7ed8173..1b8def433f 100644 --- a/recipes/r-funr/meta.yaml +++ b/recipes/r-funr/meta.yaml @@ -7,23 +7,12 @@ package: source: fn: funr_0.2.0.tar.gz url: - - http://cran.r-project.org/src/contrib/funr_0.2.0.tar.gz - http://cran.r-project.org/src/contrib/Archive/funr/funr_0.2.0.tar.gz + sha256: 5656a2647d53ef8c1373d31623d7eeb7f6348738dc7e57905ef2b0fbb7ccb83a - # You can add a hash for the file here, like md5 or sha1 - # md5: 49448ba4863157652311cc5ea4fea3ea - # sha1: 3bcfbee008276084cbb37a2b453963c61176a322 - # patches: - # List any patch files here - # - fix.patch - build: - # If this is a new build for the same version, increment the build - # number. If you do not include this key, it defaults to 0. - # number: 1 - - # This is required to make R link correctly on Linux. + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -31,10 +20,9 @@ build: requirements: build: - - r - + - r-base run: - - r + - r-base test: commands: @@ -42,38 +30,9 @@ test: - $R -e "library('funr')" # [not win] - "\"%R%\" -e \"library('funr')\"" # [win] - # You can also put a file called run_test.py, run_test.sh, or run_test.bat - # in the recipe that will be run at test time. - - # requires: - # Put any additional test requirements here. - about: home: https://github.com/sahilseth/funr license: MIT + file LICENSE summary: A small utility which wraps Rscript and provides access to all R functions from the shell. -# The original CRAN metadata for this package was: - -# Package: funr -# Title: Simple Utility Providing Terminal Access to all R Functions -# Description: A small utility which wraps Rscript and provides access to all R functions from the shell. -# Version: 0.2.0 -# Authors@R: person("Sahil", "Seth", email = "me@sahilseth.com", role = c("aut", "cre")) -# License: MIT + file LICENSE -# LazyData: true -# Imports: utils -# URL: https://github.com/sahilseth/funr -# BugReports: https://github.com/sahilseth/funr/issues -# RoxygenNote: 5.0.1.9000 -# NeedsCompilation: no -# Packaged: 2015-12-01 22:08:27 UTC; sahilseth -# Author: Sahil Seth [aut, cre] -# Maintainer: Sahil Seth -# Repository: CRAN -# Date/Publication: 2015-12-02 00:03:25 - -# See -# http://docs.continuum.io/conda/build.html for -# more information about meta.yaml diff --git a/recipes/r-globaloptions/meta.yaml b/recipes/r-globaloptions/meta.yaml index 7de6b27858..e1db92b072 100644 --- a/recipes/r-globaloptions/meta.yaml +++ b/recipes/r-globaloptions/meta.yaml @@ -1,79 +1,34 @@ package: name: r-globaloptions - # Note that conda versions cannot contain -, so any -'s in the version have - # been replaced with _'s. version: "0.0.8" source: fn: GlobalOptions_0.0.8.tar.gz url: - - http://cran.r-project.org/src/contrib/GlobalOptions_0.0.8.tar.gz - http://cran.r-project.org/src/contrib/Archive/GlobalOptions/GlobalOptions_0.0.8.tar.gz - - - # You can add a hash for the file here, like md5 or sha1 - # md5: 49448ba4863157652311cc5ea4fea3ea - # sha1: 3bcfbee008276084cbb37a2b453963c61176a322 - # patches: - # List any patch files here - # - fix.patch + sha256: 49d23cb934462bb752813dd1b2905b48c33fa45651255a546a90609c834748ce build: - # If this is a new build for the same version, increment the build - # number. If you do not include this key, it defaults to 0. - # number: 1 + number: 0 - # This is required to make R link correctly on Linux. rpaths: - lib/R/lib/ - lib/ -# Suggests: testthat (>= 0.3), knitr requirements: build: - - r + - r-base run: - - r + - r-base test: commands: - # You can put additional test commands to be run here. - $R -e "library('GlobalOptions')" # [not win] - "\"%R%\" -e \"library('GlobalOptions')\"" # [win] - # You can also put a file called run_test.py, run_test.sh, or run_test.bat - # in the recipe that will be run at test time. - - # requires: - # Put any additional test requirements here. - about: home: https://github.com/jokergoo/GlobalOptions license: GPL (>= 2) summary: It provides more controls on the option values such as validation and filtering on the values, making options invisible or private. - -# The original CRAN metadata for this package was: - -# Package: GlobalOptions -# Type: Package -# Title: Generate Functions to Get or Set Global Options -# Version: 0.0.8 -# Date: 2015-8-14 -# Author: Zuguang Gu -# Maintainer: Zuguang Gu -# Depends: R (>= 2.10.0), methods -# Suggests: testthat (>= 0.3), knitr -# VignetteBuilder: knitr -# Description: It provides more controls on the option values such as validation and filtering on the values, making options invisible or private. -# URL: https://github.com/jokergoo/GlobalOptions -# License: GPL (>= 2) -# Packaged: 2015-08-18 15:49:10 UTC; jokergoo -# Repository: CRAN -# Date/Publication: 2015-08-18 20:20:53 -# NeedsCompilation: no - -# See -# http://docs.continuum.io/conda/build.html for -# more information about meta.yaml diff --git a/recipes/r-nleqslv/meta.yaml b/recipes/r-nleqslv/meta.yaml index 242f3c7237..c37938dccb 100644 --- a/recipes/r-nleqslv/meta.yaml +++ b/recipes/r-nleqslv/meta.yaml @@ -8,7 +8,6 @@ package: source: fn: {{ name }}_{{ version }}.tar.gz url: - - https://cran.r-project.org/src/contrib/{{ name }}_{{ version }}.tar.gz - https://cran.r-project.org/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz md5: a80cb89e109cb2547dd1ed1e397385de diff --git a/recipes/r-plotrix/meta.yaml b/recipes/r-plotrix/meta.yaml index d0788632bc..13568d7ef8 100644 --- a/recipes/r-plotrix/meta.yaml +++ b/recipes/r-plotrix/meta.yaml @@ -8,7 +8,6 @@ package: source: fn: {{ name }}_{{ version }}.tar.gz url: - - https://cran.r-project.org/src/contrib/{{ name }}_{{ version }}.tar.gz - https://cran.r-project.org/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz md5: efe9b9b093d8903228a9b56c46d943fa diff --git a/recipes/r-rann/meta.yaml b/recipes/r-rann/meta.yaml index 410f9a1e41..50fdce03a5 100644 --- a/recipes/r-rann/meta.yaml +++ b/recipes/r-rann/meta.yaml @@ -8,7 +8,6 @@ package: source: fn: RANN_2.5.tar.gz url: - - http://cran.r-project.org/src/contrib/RANN_2.5.tar.gz - http://cran.r-project.org/src/contrib/Archive/RANN/RANN_2.5.tar.gz md5: 3e9db2e60893c5e4c4b72435d38291c4 @@ -39,24 +38,3 @@ about: using Arya and Mount's ANN library (v1.1.3). There is support for approximate as well as exact searches, fixed radius searches and bd as well as kd trees. license_family: GPL3 - -# The original CRAN metadata for this package was: - -# Package: RANN -# Title: Fast Nearest Neighbour Search (Wraps Arya and Mount's ANN Library) -# Version: 2.5 -# Author: Sunil Arya and David Mount (for ANN), Samuel E. Kemp, Gregory Jefferis -# Copyright: ANN library is copyright University of Maryland and Sunil Arya and David Mount. See file COPYRIGHT for details. -# Description: Finds the k nearest neighbours for every point in a given dataset in O(N log N) time using Arya and Mount's ANN library (v1.1.3). There is support for approximate as well as exact searches, fixed radius searches and bd as well as kd trees. -# Maintainer: Gregory Jefferis -# License: GPL (>= 3) -# URL: https://github.com/jefferis/RANN -# Suggests: testthat -# NeedsCompilation: yes -# Packaged: 2015-04-20 13:21:59 UTC; jefferis -# Repository: CRAN -# Date/Publication: 2015-04-20 17:50:07 - -# See -# http://docs.continuum.io/conda/build.html for -# more information about meta.yaml diff --git a/recipes/r-rappdirs/meta.yaml b/recipes/r-rappdirs/meta.yaml index d4161688bb..83a2732f79 100644 --- a/recipes/r-rappdirs/meta.yaml +++ b/recipes/r-rappdirs/meta.yaml @@ -1,29 +1,15 @@ package: name: r-rappdirs - # Note that conda versions cannot contain -, so any -'s in the version have - # been replaced with _'s. version: "0.3" source: fn: rappdirs_0.3.tar.gz url: - - http://cran.r-project.org/src/contrib/rappdirs_0.3.tar.gz - http://cran.r-project.org/src/contrib/Archive/rappdirs/rappdirs_0.3.tar.gz - - - # You can add a hash for the file here, like md5 or sha1 - # md5: 49448ba4863157652311cc5ea4fea3ea - # sha1: 3bcfbee008276084cbb37a2b453963c61176a322 - # patches: - # List any patch files here - # - fix.patch + sha256: ed6b3d3edfecb9000b00e695ff850945a4738ba04a36524bcc4fd91960484dfa build: - # If this is a new build for the same version, increment the build - # number. If you do not include this key, it defaults to 0. - # number: 1 - - # This is required to make R link correctly on Linux. + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -31,11 +17,11 @@ build: # Suggests: testthat, roxygen2 requirements: build: - - r + - r-base - gcc # [not win] run: - - r + - r-base - libgcc # [not win] test: @@ -44,40 +30,9 @@ test: - $R -e "library('rappdirs')" # [not win] - "\"%R%\" -e \"library('rappdirs')\"" # [win] - # You can also put a file called run_test.py, run_test.sh, or run_test.bat - # in the recipe that will be run at test time. - - # requires: - # Put any additional test requirements here. - about: home: https://github.com/hadley/rappdirs https://github.com/ActiveState/appdirs license: MIT + file LICENSE summary: An easy way to determine which directories on the users computer you should use to save data, caches and logs. A port of Python's Appdirs (\url{https://github.com/ActiveState/appdirs}) to R. - -# The original CRAN metadata for this package was: - -# Package: rappdirs -# Type: Package -# Title: Application directories: determine where to save data, caches and logs. -# Version: 0.3 -# Authors@R: c( person("Hadley", "Wickham", email = "h.wickham@gmail.com", role = c("trl", "cre", "cph")), person("RStudio", role = "cph"), person("Sridhar", "Ratnakumar", role = "aut"), person("Trent", "Mick", role = "aut"), person("ActiveState", role = "cph", comment = "R/appdir.r, R/cache.r, R/data.r, R/log.r translated from appdirs"), person("Eddy", "Petrisor", role = "ctb"), person("Trevor", "Davis", role = c("trl", "aut")), person("Gabor", "Csardi", role = "ctb"), person("Gregory", "Jefferis", role = "ctb") ) -# Depends: R (>= 2.14), methods -# Suggests: testthat, roxygen2 -# Description: An easy way to determine which directories on the users computer you should use to save data, caches and logs. A port of Python's Appdirs (\url{https://github.com/ActiveState/appdirs}) to R. -# BugReports: https://github.com/hadley/rappdirs/issues -# URL: https://github.com/hadley/rappdirs https://github.com/ActiveState/appdirs -# License: MIT + file LICENSE -# Copyright: Original python appdirs module copyright (c) 2010 ActiveState Software Inc. R port copyright Hadley Wickham, RStudio. See file LICENSE for details. -# Packaged: 2014-09-02 15:34:08 UTC; hadley -# Author: Hadley Wickham [trl, cre, cph], RStudio [cph], Sridhar Ratnakumar [aut], Trent Mick [aut], ActiveState [cph] (R/appdir.r, R/cache.r, R/data.r, R/log.r translated from appdirs), Eddy Petrisor [ctb], Trevor Davis [trl, aut], Gabor Csardi [ctb], Gregory Jefferis [ctb] -# Maintainer: Hadley Wickham -# NeedsCompilation: yes -# Repository: CRAN -# Date/Publication: 2014-09-02 19:44:02 - -# See -# http://docs.continuum.io/conda/build.html for -# more information about meta.yaml diff --git a/recipes/r-rjson/meta.yaml b/recipes/r-rjson/meta.yaml index c8f351cd12..b44a9caa7c 100644 --- a/recipes/r-rjson/meta.yaml +++ b/recipes/r-rjson/meta.yaml @@ -1,24 +1,28 @@ package: name: r-rjson version: 0.2.15 + source: fn: rjson_0.2.15.tar.gz url: https://cran.r-project.org/src/contrib/rjson_0.2.15.tar.gz md5: 87d0e29bc179c6aeaf312b138089f8e9 + build: number: 0 - skip: True # [osx] rpaths: - lib/R/lib/ - lib/ + requirements: build: - - r + - r-base run: - - r + - r-base + test: commands: - '$R -e "library(''rjson'')"' + about: home: https://cran.r-project.org/web/packages/rjson/index.html license: GPL-2 diff --git a/recipes/r-viridislite/meta.yaml b/recipes/r-viridislite/meta.yaml index 31e5b720e2..5c05c0a53e 100644 --- a/recipes/r-viridislite/meta.yaml +++ b/recipes/r-viridislite/meta.yaml @@ -1,28 +1,14 @@ package: name: r-viridislite - # Note that conda versions cannot contain -, so any -'s in the version have - # been replaced with _'s. version: "0.1.3" source: fn: viridisLite_0.1.3.tar.gz - url: https://cran.rstudio.com/src/contrib/viridisLite_0.1.3.tar.gz + url: https://cran.r-project.org/src/contrib/Archive/viridisLite/viridisLite_0.1.3.tar.gz md5: 93b848f4eeffcc3a1210ab6780e97ad1 - - # You can add a hash for the file here, like md5 or sha1 - # md5: 49448ba4863157652311cc5ea4fea3ea - # sha1: 3bcfbee008276084cbb37a2b453963c61176a322 - # patches: - # List any patch files here - # - fix.patch - build: - # If this is a new build for the same version, increment the build - # number. If you do not include this key, it defaults to 0. number: 0 - - # This is required to make R link correctly on Linux. rpaths: - lib/R/lib/ - lib/ @@ -30,10 +16,10 @@ build: # Suggests: hexbin >= 1.27.0, ggplot2 >= 1.0.1 requirements: build: - - r + - r-base run: - - r + - r-base test: commands: @@ -41,12 +27,6 @@ test: - $R -e "library('viridisLite')" # [not win] - "\"%R%\" -e \"library('viridisLite')\"" # [win] - # You can also put a file called run_test.py, run_test.sh, or run_test.bat - # in the recipe that will be run at test time. - - # requires: - # Put any additional test requirements here. - about: home: https://github.com/sjmgarnier/viridisLite license: MIT + file LICENSE @@ -61,23 +41,3 @@ about: This is the 'lite' version of the more complete 'viridis' package that can be found at ." - -# The original CRAN metadata for this package was: - -# Version: 0.1.3 -# Depends: R (≥ 2.10) -# Imports: stats, grDevices -# Suggests: hexbin (≥ 1.27.0), ggplot2 (≥ 1.0.1) -# Published: 2016-03-12 -# Author: Simon Garnier [aut, cre], Noam Ross [ctb, cph], Bob Rudis [ctb, cph] -# Maintainer: Simon Garnier -# BugReports: https://github.com/sjmgarnier/viridisLite/issues -# License: MIT + file LICENSE -# URL: https://github.com/sjmgarnier/viridisLite -# NeedsCompilation: no -# Materials: README -# CRAN checks: viridisLite results - -# See -# http://docs.continuum.io/conda/build.html for -# more information about meta.yaml diff --git a/recipes/r-yaml/meta.yaml b/recipes/r-yaml/meta.yaml index 6e1eb47312..6bd9b70822 100644 --- a/recipes/r-yaml/meta.yaml +++ b/recipes/r-yaml/meta.yaml @@ -1,42 +1,28 @@ package: name: r-yaml - # Note that conda versions cannot contain -, so any -'s in the version have - # been replaced with _'s. version: "2.1.13" source: fn: yaml_2.1.13.tar.gz url: - http://cran.r-project.org/src/contrib/Archive/yaml/yaml_2.1.13.tar.gz + sha256: 26f69aa2008bcacf3b2f95ef82a4667eaec2f2da8487646f71f1e2635d2d7fa2 - # You can add a hash for the file here, like md5 or sha1 - # md5: 49448ba4863157652311cc5ea4fea3ea - # sha1: 3bcfbee008276084cbb37a2b453963c61176a322 - # patches: - # List any patch files here - # - fix.patch - build: number: 1 - # If this is a new build for the same version, increment the build - # number. If you do not include this key, it defaults to 0. - # number: 1 - - # This is required to make R link correctly on Linux. skip: True # [osx] rpaths: - lib/R/lib/ - lib/ -# Suggests: testthat requirements: build: - - r + - r-base - gcc # [not win] run: - - r + - r-base - libgcc # [not win] test: @@ -54,26 +40,5 @@ test: about: #home: license: BSD_3_clause + file LICENSE - summary: This package implements the libyaml YAML 1.1 parser and emitter (http://pyyaml.org/wiki/LibYAML) - for R. - -# The original CRAN metadata for this package was: - -# Package: yaml -# Type: Package -# Title: Methods to convert R data to YAML and back -# Version: 2.1.13 -# Suggests: testthat -# Date: 2014-06-12 -# Author: Jeremy Stephens -# Maintainer: Jeremy Stephens -# License: BSD_3_clause + file LICENSE -# Description: This package implements the libyaml YAML 1.1 parser and emitter (http://pyyaml.org/wiki/LibYAML) for R. -# Packaged: 2014-06-12 18:04:44 UTC; stephej1 -# NeedsCompilation: yes -# Repository: CRAN -# Date/Publication: 2014-06-12 21:01:16 + summary: This package implements the libyaml YAML 1.1 parser and emitter (http://pyyaml.org/wiki/LibYAML) for R. -# See -# http://docs.continuum.io/conda/build.html for -# more information about meta.yaml From 53d2853532447a096de2adb0aba23992606ae553 Mon Sep 17 00:00:00 2001 From: Bjoern Gruening Date: Sat, 3 Jun 2017 20:40:34 +0200 Subject: [PATCH 011/116] multiple fixes --- recipes/bioconductor-hpar/meta.yaml | 9 +++++++-- recipes/bioconductor-limma/meta.yaml | 12 ++++++++---- 2 files changed, 15 insertions(+), 6 deletions(-) diff --git a/recipes/bioconductor-hpar/meta.yaml b/recipes/bioconductor-hpar/meta.yaml index 03b81c3b3e..0dc2c66f24 100644 --- a/recipes/bioconductor-hpar/meta.yaml +++ b/recipes/bioconductor-hpar/meta.yaml @@ -1,23 +1,28 @@ package: name: bioconductor-hpar version: 1.15.0 + source: fn: hpar_1.15.0.tar.gz url: https://bioarchive.galaxyproject.org/hpar_1.15.0.tar.gz md5: c27602ea84d160c0b71b65c68dea6bf0 + build: number: 0 rpaths: - lib/R/lib/ - lib/ + requirements: build: - - r + - r-base run: - - r + - r-base + test: commands: - '$R -e "library(''hpar'')"' + about: home: http://bioconductor.org/packages/release/bioc/html/hpar.html license: Artistic-2.0 diff --git a/recipes/bioconductor-limma/meta.yaml b/recipes/bioconductor-limma/meta.yaml index 88563a1723..5a92ec503f 100644 --- a/recipes/bioconductor-limma/meta.yaml +++ b/recipes/bioconductor-limma/meta.yaml @@ -1,24 +1,28 @@ package: name: bioconductor-limma version: 3.30.13 + source: - url: https://bioconductor.org/packages/release/bioc/src/contrib/limma_3.30.13.tar.gz - md5: 6505fdccd7ae146652224377cd104e6a + url: https://depot.galaxyproject.org/software/bioconductor-limma/bioconductor-limma_3.30.13_src_all.tar.gz + sha256: a092cf82fe93d5a089dfe8df1a662d67da4cf19f22c65f4011985b95c29a28ca + build: number: 0 rpaths: - lib/R/lib/ - lib/ + requirements: build: - r-base run: - r-base + test: commands: - '$R -e "library(''limma'')"' + about: home: http://bioconductor.org/packages/release/bioc/html/limma.html license: 'GPL (>=2)' - summary: 'Data analysis, linear models and differential expression for microarray - data.' + summary: 'Data analysis, linear models and differential expression for microarray data.' From 7dbaa18a9e3f9fe561c28082c6b86ebf6d911c47 Mon Sep 17 00:00:00 2001 From: Bjoern Gruening Date: Sat, 3 Jun 2017 20:40:54 +0200 Subject: [PATCH 012/116] fixes --- recipes/kmergenie/meta.yaml | 2 -- 1 file changed, 2 deletions(-) diff --git a/recipes/kmergenie/meta.yaml b/recipes/kmergenie/meta.yaml index a6c3fc70b8..f40ced35e2 100644 --- a/recipes/kmergenie/meta.yaml +++ b/recipes/kmergenie/meta.yaml @@ -22,13 +22,11 @@ requirements: - llvm # [osx] - zlib - r-base - - r-essentials run: - python - libgcc # [linux] - zlib - r-base - - r-essentials test: commands: From 1be8468b9c152e09e1aef21242ec40b0e6c2b5f8 Mon Sep 17 00:00:00 2001 From: Bjoern Gruening Date: Sat, 3 Jun 2017 20:52:05 +0200 Subject: [PATCH 013/116] r fixes --- recipes/nanoraw/0.3.1/meta.yaml | 4 ++-- recipes/nanoraw/meta.yaml | 4 ++-- recipes/poretools/0.5.0/meta.yaml | 9 +++++---- recipes/seq2hla/meta.yaml | 2 +- 4 files changed, 10 insertions(+), 9 deletions(-) diff --git a/recipes/nanoraw/0.3.1/meta.yaml b/recipes/nanoraw/0.3.1/meta.yaml index 3f0769b44d..cea5d7fa2d 100644 --- a/recipes/nanoraw/0.3.1/meta.yaml +++ b/recipes/nanoraw/0.3.1/meta.yaml @@ -21,7 +21,7 @@ requirements: - rpy2 - numpy - scipy - - r + - r-base - r-ggplot2 run: @@ -30,7 +30,7 @@ requirements: - rpy2 - numpy - scipy - - r + - r-base - r-ggplot2 test: diff --git a/recipes/nanoraw/meta.yaml b/recipes/nanoraw/meta.yaml index b51b6b2e8b..b45393ac6d 100644 --- a/recipes/nanoraw/meta.yaml +++ b/recipes/nanoraw/meta.yaml @@ -24,7 +24,7 @@ requirements: - rpy2 - numpy - scipy - - r + - r-base - r-ggplot2 run: @@ -33,7 +33,7 @@ requirements: - rpy2 - numpy - scipy - - r + - r-base - r-ggplot2 test: diff --git a/recipes/poretools/0.5.0/meta.yaml b/recipes/poretools/0.5.0/meta.yaml index e4a2d47bbc..362359ca3e 100644 --- a/recipes/poretools/0.5.0/meta.yaml +++ b/recipes/poretools/0.5.0/meta.yaml @@ -1,29 +1,30 @@ package: name: poretools version: "0.5.0" + source: fn: poretools_v0.5.0.tar.gz url: https://github.com/arq5x/poretools/archive/v0.5.0.tar.gz md5: c647561ea603e84bca14fdf56a5c962f +build: + skip: True # [not py27] + requirements: build: - python - rpy2 >=2.4.2 - h5py >=2.0 - watchdog >=0.8.3 - run: - python - hdf5 >=1.8.7 - - r >=3.0.0 + - r-base - rpy2 >=2.4.2 - h5py >=2.0 - watchdog >=0.8.3 - qcli >=0.1.1 - r-ggplot2 -build: - skip: True # [not py27] test: commands: diff --git a/recipes/seq2hla/meta.yaml b/recipes/seq2hla/meta.yaml index d06e565420..b03e965195 100644 --- a/recipes/seq2hla/meta.yaml +++ b/recipes/seq2hla/meta.yaml @@ -16,7 +16,7 @@ requirements: - python - biopython >=1.58 - bowtie ==1.1.2 - - r >=2.12.2 + - r-base test: commands: - seq2HLA -h From 776d5d72c6401d42ef8caf74a040884ed31a177d Mon Sep 17 00:00:00 2001 From: Bjoern Gruening Date: Sat, 3 Jun 2017 21:05:23 +0200 Subject: [PATCH 014/116] change r to r-base --- recipes/r-abind/meta.yaml | 4 ++-- recipes/r-ada/meta.yaml | 4 ++-- recipes/r-ade4/meta.yaml | 4 ++-- recipes/r-agricolae/meta.yaml | 4 ++-- recipes/r-amap/meta.yaml | 4 ++-- recipes/r-ampvis/meta.yaml | 4 ++-- recipes/r-aod/meta.yaml | 4 ++-- recipes/r-argparse/meta.yaml | 4 ++-- recipes/r-aroma.affymetrix/meta.yaml | 4 ++-- recipes/r-aroma.apd/meta.yaml | 4 ++-- recipes/r-aroma.core/meta.yaml | 4 ++-- recipes/r-batch/meta.yaml | 4 ++-- recipes/r-batchjobs/meta.yaml | 4 ++-- recipes/r-bbmisc/meta.yaml | 4 ++-- recipes/r-beanplot/meta.yaml | 4 ++-- recipes/r-bh/meta.yaml | 4 ++-- recipes/r-bigmemory.sri/meta.yaml | 4 ++-- recipes/r-bigmemory/meta.yaml | 4 ++-- recipes/r-bio3d/meta.yaml | 4 ++-- recipes/r-bit/meta.yaml | 4 ++-- recipes/r-bit64/meta.yaml | 4 ++-- recipes/r-bma/meta.yaml | 4 ++-- recipes/r-calibrate/meta.yaml | 4 ++-- recipes/r-car/meta.yaml | 4 ++-- recipes/r-catools/meta.yaml | 4 ++-- recipes/r-cghflasso/meta.yaml | 4 ++-- recipes/r-chbutils/meta.yaml | 4 ++-- recipes/r-checkmate/meta.yaml | 4 ++-- recipes/r-cimpl/meta.yaml | 4 ++-- recipes/r-circlize/meta.yaml | 4 ++-- recipes/r-combinat/meta.yaml | 4 ++-- recipes/r-compute.es/meta.yaml | 4 ++-- recipes/r-corrplot/meta.yaml | 4 ++-- recipes/r-dbchip/meta.yaml | 4 ++-- recipes/r-delaporte/meta.yaml | 4 ++-- recipes/r-dendextend/meta.yaml | 4 ++-- recipes/r-deoptimr/meta.yaml | 4 ++-- recipes/r-diagram/meta.yaml | 4 ++-- recipes/r-discriminer/meta.yaml | 4 ++-- recipes/r-dorng/meta.yaml | 4 ++-- recipes/r-dpeak/meta.yaml | 4 ++-- recipes/r-dt/meta.yaml | 4 ++-- recipes/r-dunn.test/meta.yaml | 4 ++-- recipes/r-ellipse/meta.yaml | 4 ++-- recipes/r-empiricalfdr.deseq2/meta.yaml | 4 ++-- recipes/r-exomedepth/meta.yaml | 4 ++-- recipes/r-fail/meta.yaml | 4 ++-- recipes/r-fastcluster/meta.yaml | 4 ++-- recipes/r-fda/meta.yaml | 4 ++-- recipes/r-fdrtool/meta.yaml | 4 ++-- recipes/r-fftwtools/meta.yaml | 4 ++-- recipes/r-fitdistrplus/meta.yaml | 4 ++-- recipes/r-flowr/meta.yaml | 4 ++-- recipes/r-futile.logger/meta.yaml | 4 ++-- recipes/r-future/0.9.0/meta.yaml | 4 ++-- recipes/r-future/meta.yaml | 4 ++-- recipes/r-gam/meta.yaml | 4 ++-- recipes/r-gamlss.data/meta.yaml | 4 ++-- recipes/r-gamlss.dist/meta.yaml | 4 ++-- recipes/r-gamlss/meta.yaml | 4 ++-- recipes/r-genabel.data/meta.yaml | 4 ++-- recipes/r-genenet/meta.yaml | 4 ++-- recipes/r-geomap/meta.yaml | 4 ++-- recipes/r-getopt/meta.yaml | 4 ++-- recipes/r-getoptlong/meta.yaml | 4 ++-- recipes/r-ggally/0.5.0/meta.yaml | 4 ++-- recipes/r-ggally/meta.yaml | 4 ++-- recipes/r-ggalt/meta.yaml | 4 ++-- recipes/r-ggdendro/meta.yaml | 4 ++-- recipes/r-ggrepel/meta.yaml | 4 ++-- recipes/r-globals/0.6.0/meta.yaml | 4 ++-- recipes/r-globals/meta.yaml | 4 ++-- recipes/r-gmd/meta.yaml | 4 ++-- recipes/r-gmodels/meta.yaml | 4 ++-- recipes/r-googlevis/meta.yaml | 4 ++-- recipes/r-gplots/meta.yaml | 4 ++-- recipes/r-grimport/meta.yaml | 4 ++-- recipes/r-gsalib/meta.yaml | 4 ++-- recipes/r-gsmoothr/meta.yaml | 4 ++-- recipes/r-htmltools/meta.yaml | 4 ++-- recipes/r-htmlwidgets/meta.yaml | 4 ++-- recipes/r-hwriter/meta.yaml | 4 ++-- recipes/r-idr/meta.yaml | 4 ++-- recipes/r-inlinedocs/meta.yaml | 4 ++-- recipes/r-ipo/meta.yaml | 4 ++-- recipes/r-jsonlite/meta.yaml | 4 ++-- recipes/r-klar/meta.yaml | 4 ++-- recipes/r-knitr/meta.yaml | 4 ++-- recipes/r-knitrbootstrap/meta.yaml | 4 ++-- recipes/r-lambda.r/meta.yaml | 4 ++-- recipes/r-learnbayes/meta.yaml | 4 ++-- recipes/r-listenv/0.5.0/meta.yaml | 4 ++-- recipes/r-listenv/meta.yaml | 4 ++-- recipes/r-longitudinal/meta.yaml | 4 ++-- recipes/r-lsd/meta.yaml | 4 ++-- recipes/r-mba/meta.yaml | 4 ++-- recipes/r-misc3d/meta.yaml | 4 ++-- recipes/r-mitools/meta.yaml | 4 ++-- recipes/r-mmgenome/meta.yaml | 4 ++-- recipes/r-multitaper/meta.yaml | 4 ++-- recipes/r-mutationalpatterns/meta.yaml | 4 ++-- recipes/r-mutoss/meta.yaml | 4 ++-- recipes/r-nanostringnorm/meta.yaml | 4 ++-- recipes/r-nastiseq/meta.yaml | 4 ++-- recipes/r-nozzle.r1/meta.yaml | 4 ++-- recipes/r-optparse/meta.yaml | 4 ++-- recipes/r-outliers/meta.yaml | 4 ++-- recipes/r-patpro/meta.yaml | 4 ++-- recipes/r-peer/meta.yaml | 4 ++-- recipes/r-penalized/meta.yaml | 4 ++-- recipes/r-permute/meta.yaml | 4 ++-- recipes/r-pheatmap/meta.yaml | 4 ++-- recipes/r-phonr/meta.yaml | 4 ++-- recipes/r-pmcmr/meta.yaml | 4 ++-- recipes/r-png/meta.yaml | 4 ++-- recipes/r-pore/meta.yaml | 4 ++-- recipes/r-pracma/meta.yaml | 4 ++-- recipes/r-preseqr/meta.yaml | 4 ++-- recipes/r-prettyunits/meta.yaml | 4 ++-- recipes/r-probmetab/1.0/meta.yaml | 4 ++-- recipes/r-probmetab/1.1/meta.yaml | 4 ++-- recipes/r-progress/meta.yaml | 4 ++-- recipes/r-proj4/meta.yaml | 4 ++-- recipes/r-prroc/meta.yaml | 4 ++-- recipes/r-pscbs/meta.yaml | 4 ++-- recipes/r-pscl/meta.yaml | 4 ++-- recipes/r-psych/meta.yaml | 4 ++-- recipes/r-qiimer/meta.yaml | 4 ++-- recipes/r-r.cache/meta.yaml | 4 ++-- recipes/r-r.devices/meta.yaml | 4 ++-- recipes/r-r.filesets/meta.yaml | 4 ++-- recipes/r-r.huge/meta.yaml | 4 ++-- recipes/r-r.methodss3/1.7.0/meta.yaml | 4 ++-- recipes/r-r.oo/1.19.0/meta.yaml | 4 ++-- recipes/r-r.oo/meta.yaml | 4 ++-- recipes/r-r.rsp/meta.yaml | 4 ++-- recipes/r-r.utils/2.2.0/meta.yaml | 4 ++-- recipes/r-r.utils/meta.yaml | 4 ++-- recipes/r-rBLAST/meta.yaml | 4 ++-- recipes/r-rainbow/meta.yaml | 4 ++-- recipes/r-rcircos/1.1.3/meta.yaml | 4 ++-- recipes/r-rcircos/meta.yaml | 4 ++-- recipes/r-rcppparallel/meta.yaml | 4 ++-- recipes/r-readbrukerflexdata/meta.yaml | 4 ++-- recipes/r-readmzxmldata/meta.yaml | 4 ++-- recipes/r-readr/meta.yaml | 4 ++-- recipes/r-relaimpo/meta.yaml | 4 ++-- recipes/r-rfoc/meta.yaml | 4 ++-- recipes/r-rgraphics/meta.yaml | 4 ++-- recipes/r-rmarkdown/meta.yaml | 4 ++-- recipes/r-rniftyreg/meta.yaml | 4 ++-- recipes/r-robustrankaggreg/meta.yaml | 4 ++-- recipes/r-rocr/meta.yaml | 2 +- recipes/r-rpmg/meta.yaml | 4 ++-- recipes/r-rrcov/meta.yaml | 4 ++-- recipes/r-rseis/meta.yaml | 4 ++-- recipes/r-rsm/meta.yaml | 4 ++-- recipes/r-rsolnp/meta.yaml | 4 ++-- recipes/r-runit/meta.yaml | 4 ++-- recipes/r-rwave/meta.yaml | 4 ++-- recipes/r-sartools/1.2.0/meta.yaml | 4 ++-- recipes/r-sartools/1.3.2/meta.yaml | 4 ++-- recipes/r-scales/meta.yaml | 4 ++-- recipes/r-sendmailr/meta.yaml | 4 ++-- recipes/r-seqinr/meta.yaml | 4 ++-- recipes/r-shape/meta.yaml | 4 ++-- recipes/r-signal/meta.yaml | 4 ++-- recipes/r-skellam/meta.yaml | 4 ++-- recipes/r-sleuth/meta.yaml | 4 ++-- recipes/r-snow/meta.yaml | 4 ++-- recipes/r-snowfall/meta.yaml | 4 ++-- recipes/r-soap-nmr/meta.yaml | 4 ++-- recipes/r-sparql/meta.yaml | 4 ++-- recipes/r-spdep/meta.yaml | 4 ++-- recipes/r-spp/meta.yaml | 4 ++-- recipes/r-survey/meta.yaml | 4 ++-- recipes/r-svdialogs/meta.yaml | 4 ++-- recipes/r-svgui/meta.yaml | 4 ++-- recipes/r-tfmpvalue/meta.yaml | 2 +- recipes/r-tiff/meta.yaml | 4 ++-- recipes/r-truncnorm/meta.yaml | 4 ++-- recipes/r-upsetr/meta.yaml | 4 ++-- recipes/r-vegan/2.3_0/meta.yaml | 4 ++-- recipes/r-vegan/2.3_3/meta.yaml | 4 ++-- recipes/r-venndiagram/meta.yaml | 4 ++-- recipes/r-viridis/meta.yaml | 4 ++-- recipes/r-wasabi/meta.yaml | 4 ++-- recipes/r-wrassp/meta.yaml | 4 ++-- recipes/r-writexls/meta.yaml | 4 ++-- recipes/r-xmlrpc/meta.yaml | 4 ++-- recipes/r-xnomial/meta.yaml | 4 ++-- 191 files changed, 380 insertions(+), 380 deletions(-) diff --git a/recipes/r-abind/meta.yaml b/recipes/r-abind/meta.yaml index b0cc4a90de..3053a46cee 100644 --- a/recipes/r-abind/meta.yaml +++ b/recipes/r-abind/meta.yaml @@ -18,10 +18,10 @@ build: requirements: build: - - r + - r-base run: - - r + - r-base test: commands: diff --git a/recipes/r-ada/meta.yaml b/recipes/r-ada/meta.yaml index b2d5b23266..a58d6095c6 100644 --- a/recipes/r-ada/meta.yaml +++ b/recipes/r-ada/meta.yaml @@ -17,10 +17,10 @@ build: requirements: build: - - r + - r-base - r-rpart # [not win] run: - - r + - r-base - r-rpart # [not win] test: diff --git a/recipes/r-ade4/meta.yaml b/recipes/r-ade4/meta.yaml index d76eec490a..25dfdf7112 100644 --- a/recipes/r-ade4/meta.yaml +++ b/recipes/r-ade4/meta.yaml @@ -31,10 +31,10 @@ build: # Suggests: waveslim, splancs, MASS, maptools, spdep, pixmap, ape, deldir, ade4TkGUI, adegraphics, sp, lattice requirements: build: - - r + - r-base run: - - r + - r-base test: commands: diff --git a/recipes/r-agricolae/meta.yaml b/recipes/r-agricolae/meta.yaml index a332cbaf6d..a8011351b6 100644 --- a/recipes/r-agricolae/meta.yaml +++ b/recipes/r-agricolae/meta.yaml @@ -18,7 +18,7 @@ build: # Suggests: RANN, rgeos requirements: build: - - r + - r-base - r-algdesign - r-mass - r-cluster @@ -27,7 +27,7 @@ requirements: - r-spdep run: - - r + - r-base - r-algdesign - r-mass - r-cluster diff --git a/recipes/r-amap/meta.yaml b/recipes/r-amap/meta.yaml index 2f215d509e..61a3325fb9 100644 --- a/recipes/r-amap/meta.yaml +++ b/recipes/r-amap/meta.yaml @@ -26,11 +26,11 @@ build: # Suggests: Biobase requirements: build: - - r + - r-base - gcc # [not win] run: - - r + - r-base - libgcc # [not win] test: diff --git a/recipes/r-ampvis/meta.yaml b/recipes/r-ampvis/meta.yaml index 1d4089debd..b617a2c7bb 100644 --- a/recipes/r-ampvis/meta.yaml +++ b/recipes/r-ampvis/meta.yaml @@ -20,7 +20,7 @@ build: requirements: build: - - r + - r-base - r-ggplot2 - r-ggrepel - r-reshape2 @@ -39,7 +39,7 @@ requirements: - r-gridextra - r-scales run: - - r + - r-base - r-ggplot2 - r-ggrepel - r-reshape2 diff --git a/recipes/r-aod/meta.yaml b/recipes/r-aod/meta.yaml index 78baa831de..1b02a5bb99 100644 --- a/recipes/r-aod/meta.yaml +++ b/recipes/r-aod/meta.yaml @@ -16,10 +16,10 @@ build: requirements: build: - - r + - r-base run: - - r + - r-base test: commands: diff --git a/recipes/r-argparse/meta.yaml b/recipes/r-argparse/meta.yaml index 5d8b3c8245..eb54325157 100644 --- a/recipes/r-argparse/meta.yaml +++ b/recipes/r-argparse/meta.yaml @@ -22,14 +22,14 @@ build: # Suggests: knitr, testthat requirements: build: - - r + - r-base - r-findpython - r-getopt >=1.19 - r-proto - r-rjson run: - - r + - r-base - r-findpython - r-getopt >=1.19 - r-proto diff --git a/recipes/r-aroma.affymetrix/meta.yaml b/recipes/r-aroma.affymetrix/meta.yaml index 04d8103188..41581d33fd 100644 --- a/recipes/r-aroma.affymetrix/meta.yaml +++ b/recipes/r-aroma.affymetrix/meta.yaml @@ -21,7 +21,7 @@ build: # Suggests: DBI (>= 0.3.1), gsmoothr (>= 0.1.7), RColorBrewer (>= 1.1-2), Biobase (>= 2.28.0), BiocGenerics (>= 0.14.0), affxparser (>= 1.40.0), affy (>= 1.46.0), affyPLM (>= 1.44.0), aroma.light (>= 2.4.0), gcrma (>= 2.40.0), limma (>= 3.24.1), oligo (>= 1.32.0), oligoClasses (>= 1.30.0), pdInfoBuilder (>= 1.32.0), preprocessCore (>= 1.28.0), AffymetrixDataTestFiles, dChipIO (>= 0.1.1) requirements: build: - - r + - r-base - r-mass - r-r.cache >=0.12.0 - r-r.devices >=2.13.2 @@ -36,7 +36,7 @@ requirements: - r-matrixstats >=0.50.1 run: - - r + - r-base - r-mass - r-r.cache >=0.12.0 - r-r.devices >=2.13.2 diff --git a/recipes/r-aroma.apd/meta.yaml b/recipes/r-aroma.apd/meta.yaml index fbe6dfb25b..9918c54e23 100644 --- a/recipes/r-aroma.apd/meta.yaml +++ b/recipes/r-aroma.apd/meta.yaml @@ -21,14 +21,14 @@ build: # Suggests: affxparser requirements: build: - - r + - r-base - r-r.huge >=0.9.0 - r-r.methodss3 >=1.7.0 - r-r.oo >=1.18.0 - r-r.utils >=1.34.0 run: - - r + - r-base - r-r.huge >=0.9.0 - r-r.methodss3 >=1.7.0 - r-r.oo >=1.18.0 diff --git a/recipes/r-aroma.core/meta.yaml b/recipes/r-aroma.core/meta.yaml index d6f78092ca..cf0acc9a28 100644 --- a/recipes/r-aroma.core/meta.yaml +++ b/recipes/r-aroma.core/meta.yaml @@ -21,7 +21,7 @@ build: # Suggests: png (>= 0.1-7), Cairo (>= 1.5-6), EBImage (>= 4.8.3), preprocessCore (>= 1.28.0), aroma.light (>= 2.2.1), DNAcopy (>= 1.40.0), GLAD (>= 2.30.0), sfit (>= 0.1.8), expectile (>= 0.2.5), HaarSeg (>= 0.0.2), mpcbs (>= 1.1.1) requirements: build: - - r + - r-base - r-pscbs >=0.60.0 - r-r.cache >=0.12.0 - r-r.devices >=2.13.2 @@ -36,7 +36,7 @@ requirements: - r-matrixstats >=0.50.1 run: - - r + - r-base - r-pscbs >=0.60.0 - r-r.cache >=0.12.0 - r-r.devices >=2.13.2 diff --git a/recipes/r-batch/meta.yaml b/recipes/r-batch/meta.yaml index 20898486bd..688e5994c4 100644 --- a/recipes/r-batch/meta.yaml +++ b/recipes/r-batch/meta.yaml @@ -19,10 +19,10 @@ build: # Suggests: parallel requirements: build: - - r + - r-base run: - - r + - r-base test: commands: diff --git a/recipes/r-batchjobs/meta.yaml b/recipes/r-batchjobs/meta.yaml index 910066caa4..9d249e3b76 100644 --- a/recipes/r-batchjobs/meta.yaml +++ b/recipes/r-batchjobs/meta.yaml @@ -22,7 +22,7 @@ build: # Suggests: MASS, testthat requirements: build: - - r + - r-base - r-bbmisc >=1.9 - r-dbi - r-rsqlite >=1.0.0 @@ -34,7 +34,7 @@ requirements: - r-stringr run: - - r + - r-base - r-bbmisc >=1.9 - r-dbi - r-rsqlite >=1.0.0 diff --git a/recipes/r-bbmisc/meta.yaml b/recipes/r-bbmisc/meta.yaml index c3c0f4d324..ef27abafe4 100644 --- a/recipes/r-bbmisc/meta.yaml +++ b/recipes/r-bbmisc/meta.yaml @@ -26,12 +26,12 @@ build: # Suggests: testthat, microbenchmark, codetools requirements: build: - - r + - r-base - r-checkmate - gcc # [not win] run: - - r + - r-base - r-checkmate - libgcc # [not win] diff --git a/recipes/r-beanplot/meta.yaml b/recipes/r-beanplot/meta.yaml index d2a20c63a3..23b0444b6e 100644 --- a/recipes/r-beanplot/meta.yaml +++ b/recipes/r-beanplot/meta.yaml @@ -31,10 +31,10 @@ build: # Suggests: vioplot, lattice requirements: build: - - r + - r-base run: - - r + - r-base test: commands: diff --git a/recipes/r-bh/meta.yaml b/recipes/r-bh/meta.yaml index 6d8d4ab7bb..4fbb2adf9e 100644 --- a/recipes/r-bh/meta.yaml +++ b/recipes/r-bh/meta.yaml @@ -16,9 +16,9 @@ build: - lib/ requirements: build: - - r + - r-base run: - - r + - r-base test: commands: - $R -e "library('BH')" # [not win] diff --git a/recipes/r-bigmemory.sri/meta.yaml b/recipes/r-bigmemory.sri/meta.yaml index d73c021575..e5fd759bf6 100644 --- a/recipes/r-bigmemory.sri/meta.yaml +++ b/recipes/r-bigmemory.sri/meta.yaml @@ -31,10 +31,10 @@ build: requirements: build: - - r + - r-base run: - - r + - r-base test: commands: diff --git a/recipes/r-bigmemory/meta.yaml b/recipes/r-bigmemory/meta.yaml index 7931737438..c5ca7a3134 100644 --- a/recipes/r-bigmemory/meta.yaml +++ b/recipes/r-bigmemory/meta.yaml @@ -31,14 +31,14 @@ build: # Suggests: knitr, testthat requirements: build: - - r + - r-base - r-bh - r-rcpp - r-bigmemory.sri - gcc # [not win] run: - - r + - r-base - r-bh - r-rcpp - r-bigmemory.sri diff --git a/recipes/r-bio3d/meta.yaml b/recipes/r-bio3d/meta.yaml index 38ef9bdf5f..d145d07b5d 100644 --- a/recipes/r-bio3d/meta.yaml +++ b/recipes/r-bio3d/meta.yaml @@ -32,10 +32,10 @@ build: # Suggests: XML, RCurl, lattice, ncdf, igraph, bigmemory, knitr, testthat (>= 0.9.1) requirements: build: - - r + - r-base run: - - r + - r-base test: commands: diff --git a/recipes/r-bit/meta.yaml b/recipes/r-bit/meta.yaml index bd7edfb654..4622e9b506 100644 --- a/recipes/r-bit/meta.yaml +++ b/recipes/r-bit/meta.yaml @@ -32,11 +32,11 @@ build: requirements: build: - - r + - r-base - gcc # [not win] run: - - r + - r-base - libgcc # [not win] test: diff --git a/recipes/r-bit64/meta.yaml b/recipes/r-bit64/meta.yaml index 29f63da2c9..67191ed8b0 100644 --- a/recipes/r-bit64/meta.yaml +++ b/recipes/r-bit64/meta.yaml @@ -32,12 +32,12 @@ build: requirements: build: - - r + - r-base - r-bit >=1.1_12 - gcc # [not win] run: - - r + - r-base - r-bit >=1.1_12 - libgcc # [not win] diff --git a/recipes/r-bma/meta.yaml b/recipes/r-bma/meta.yaml index aa427e07d5..6eecdbb92f 100644 --- a/recipes/r-bma/meta.yaml +++ b/recipes/r-bma/meta.yaml @@ -19,7 +19,7 @@ build: # Suggests: MASS, forward requirements: build: - - r + - r-base - r-inline - r-leaps - r-robustbase @@ -28,7 +28,7 @@ requirements: - gcc run: - - r + - r-base - r-inline - r-leaps - r-robustbase diff --git a/recipes/r-calibrate/meta.yaml b/recipes/r-calibrate/meta.yaml index 90fe6e5df0..e17f34a8fd 100644 --- a/recipes/r-calibrate/meta.yaml +++ b/recipes/r-calibrate/meta.yaml @@ -17,11 +17,11 @@ build: requirements: build: - - r + - r-base - r-mass # [not win] run: - - r + - r-base - r-mass # [not win] test: diff --git a/recipes/r-car/meta.yaml b/recipes/r-car/meta.yaml index c1853e00c7..04e2d3a522 100644 --- a/recipes/r-car/meta.yaml +++ b/recipes/r-car/meta.yaml @@ -21,7 +21,7 @@ build: # Suggests: alr4, boot, coxme, leaps, lme4, lmtest, Matrix, MatrixModels, nlme, rgl (>= 0.93.960), sandwich, SparseM, survival, survey, nloptr requirements: build: - - r + - r-base - r-mass - r-mgcv - r-nnet @@ -29,7 +29,7 @@ requirements: - r-quantreg run: - - r + - r-base - r-mass - r-mgcv - r-nnet diff --git a/recipes/r-catools/meta.yaml b/recipes/r-catools/meta.yaml index 13fefd80f4..72e0383124 100644 --- a/recipes/r-catools/meta.yaml +++ b/recipes/r-catools/meta.yaml @@ -31,12 +31,12 @@ build: # Suggests: MASS, rpart requirements: build: - - r + - r-base - r-bitops - gcc # [not win] run: - - r + - r-base - r-bitops - libgcc # [not win] diff --git a/recipes/r-cghflasso/meta.yaml b/recipes/r-cghflasso/meta.yaml index f9aa433edb..80276a340f 100644 --- a/recipes/r-cghflasso/meta.yaml +++ b/recipes/r-cghflasso/meta.yaml @@ -32,11 +32,11 @@ build: requirements: build: - - r + - r-base - gcc run: - - r + - r-base - libgcc test: diff --git a/recipes/r-chbutils/meta.yaml b/recipes/r-chbutils/meta.yaml index 3cd4c2be6c..d310b3b7e9 100644 --- a/recipes/r-chbutils/meta.yaml +++ b/recipes/r-chbutils/meta.yaml @@ -18,12 +18,12 @@ build: requirements: build: - - r + - r-base - r-mvtnorm - r-rcolorbrewer run: - - r + - r-base - r-mvtnorm - r-rcolorbrewer diff --git a/recipes/r-checkmate/meta.yaml b/recipes/r-checkmate/meta.yaml index ade7894e84..348fda42fa 100644 --- a/recipes/r-checkmate/meta.yaml +++ b/recipes/r-checkmate/meta.yaml @@ -26,12 +26,12 @@ build: # Suggests: data.table, dplyr, ggplot2, knitr, microbenchmark, testthat requirements: build: - - r + - r-base - r-backports - gcc # [not win] run: - - r + - r-base - r-backports - libgcc # [not win] diff --git a/recipes/r-cimpl/meta.yaml b/recipes/r-cimpl/meta.yaml index cc0d35a5c6..8c8abc7df9 100644 --- a/recipes/r-cimpl/meta.yaml +++ b/recipes/r-cimpl/meta.yaml @@ -11,14 +11,14 @@ build: - lib/ requirements: build: - - r + - r-base - 'r-kernsmooth' - 'r-mass' - 'r-xtable' - 'bioconductor-biomart' - 'bioconductor-biostrings' run: - - r + - r-base - 'r-kernsmooth' - 'r-mass' - 'r-xtable' diff --git a/recipes/r-circlize/meta.yaml b/recipes/r-circlize/meta.yaml index 3073d9fad3..e247b5dbb8 100644 --- a/recipes/r-circlize/meta.yaml +++ b/recipes/r-circlize/meta.yaml @@ -31,13 +31,13 @@ build: # Suggests: knitr, dendextend (>= 1.0.1) requirements: build: - - r + - r-base - r-globaloptions >=0.0.6 - r-colorspace - r-shape run: - - r + - r-base - r-globaloptions >=0.0.6 - r-colorspace - r-shape diff --git a/recipes/r-combinat/meta.yaml b/recipes/r-combinat/meta.yaml index f167356f6f..7580a5191b 100644 --- a/recipes/r-combinat/meta.yaml +++ b/recipes/r-combinat/meta.yaml @@ -17,10 +17,10 @@ build: requirements: build: - - r + - r-base run: - - r + - r-base test: commands: diff --git a/recipes/r-compute.es/meta.yaml b/recipes/r-compute.es/meta.yaml index 981642876d..be1ec4c064 100644 --- a/recipes/r-compute.es/meta.yaml +++ b/recipes/r-compute.es/meta.yaml @@ -32,10 +32,10 @@ build: requirements: build: - - r + - r-base run: - - r + - r-base test: commands: diff --git a/recipes/r-corrplot/meta.yaml b/recipes/r-corrplot/meta.yaml index 10cba79cab..6ac071710b 100644 --- a/recipes/r-corrplot/meta.yaml +++ b/recipes/r-corrplot/meta.yaml @@ -32,10 +32,10 @@ build: # Suggests: seriation, knitr requirements: build: - - r + - r-base run: - - r + - r-base test: commands: diff --git a/recipes/r-dbchip/meta.yaml b/recipes/r-dbchip/meta.yaml index 4b99d559aa..28d336068c 100644 --- a/recipes/r-dbchip/meta.yaml +++ b/recipes/r-dbchip/meta.yaml @@ -18,12 +18,12 @@ build: requirements: build: - - r + - r-base - bioconductor-deseq - bioconductor-edger run: - - r + - r-base - bioconductor-deseq - bioconductor-edger diff --git a/recipes/r-delaporte/meta.yaml b/recipes/r-delaporte/meta.yaml index 1b84b196ad..4e723fcb06 100644 --- a/recipes/r-delaporte/meta.yaml +++ b/recipes/r-delaporte/meta.yaml @@ -15,13 +15,13 @@ build: requirements: build: - - r + - r-base - r-rcpp - gcc # [linux] - llvm # [osx] run: - - r + - r-base - r-rcpp test: diff --git a/recipes/r-dendextend/meta.yaml b/recipes/r-dendextend/meta.yaml index 0b11fffdc5..d6d50ae6f9 100644 --- a/recipes/r-dendextend/meta.yaml +++ b/recipes/r-dendextend/meta.yaml @@ -31,12 +31,12 @@ build: # Suggests: dendextendRcpp (>= 0.5.0), knitr, testthat, colorspace, ggplot2, plyr, ape, profdpm, microbenchmark, gplots, NMF, d3heatmap, dynamicTreeCut, pvclust, corrplot, DendSer, MASS, cluster, circlize (>= 0.2.5), covr requirements: build: - - r + - r-base - r-magrittr >=1.0.1 - r-whisker run: - - r + - r-base - r-magrittr >=1.0.1 - r-whisker diff --git a/recipes/r-deoptimr/meta.yaml b/recipes/r-deoptimr/meta.yaml index d0ad5fb35e..5fb3f4b82b 100644 --- a/recipes/r-deoptimr/meta.yaml +++ b/recipes/r-deoptimr/meta.yaml @@ -16,9 +16,9 @@ build: - lib/ requirements: build: - - r + - r-base run: - - r + - r-base test: commands: - $R -e "library('DEoptimR')" # [not win] diff --git a/recipes/r-diagram/meta.yaml b/recipes/r-diagram/meta.yaml index f51450aed3..9c4865883b 100644 --- a/recipes/r-diagram/meta.yaml +++ b/recipes/r-diagram/meta.yaml @@ -31,11 +31,11 @@ build: requirements: build: - - r + - r-base - r-shape run: - - r + - r-base - r-shape test: diff --git a/recipes/r-discriminer/meta.yaml b/recipes/r-discriminer/meta.yaml index 62230ec7b1..4c67eaa04b 100644 --- a/recipes/r-discriminer/meta.yaml +++ b/recipes/r-discriminer/meta.yaml @@ -17,10 +17,10 @@ build: # Suggests: MASS, FactoMineR requirements: build: - - r + - r-base run: - - r + - r-base test: commands: diff --git a/recipes/r-dorng/meta.yaml b/recipes/r-dorng/meta.yaml index 5cd58dfcae..a616b383cc 100644 --- a/recipes/r-dorng/meta.yaml +++ b/recipes/r-dorng/meta.yaml @@ -31,14 +31,14 @@ build: # Suggests: doParallel, doMPI, doRedis, rbenchmark, RUnit, devtools, knitr, bibtex requirements: build: - - r + - r-base - r-foreach - r-iterators - r-pkgmaker >=0.20 - r-rngtools >=1.2.4 run: - - r + - r-base - r-foreach - r-iterators - r-pkgmaker >=0.20 diff --git a/recipes/r-dpeak/meta.yaml b/recipes/r-dpeak/meta.yaml index 94a8e2b369..8f36479cc3 100644 --- a/recipes/r-dpeak/meta.yaml +++ b/recipes/r-dpeak/meta.yaml @@ -18,7 +18,7 @@ build: requirements: build: - - r + - r-base - r-mass - bioconductor-iranges - bioconductor-bsgenome @@ -26,7 +26,7 @@ requirements: - gcc run: - - r + - r-base - r-mass - bioconductor-iranges - bioconductor-bsgenome diff --git a/recipes/r-dt/meta.yaml b/recipes/r-dt/meta.yaml index ea6052b820..cb9fea2fa7 100644 --- a/recipes/r-dt/meta.yaml +++ b/recipes/r-dt/meta.yaml @@ -29,13 +29,13 @@ build: # Suggests: jsonlite (>= 0.9.16), knitr (>= 1.8), shiny (>= 0.12.1) requirements: build: - - r + - r-base - r-htmltools >=0.3.5 - r-htmlwidgets >=0.6 - r-magrittr run: - - r + - r-base - r-htmltools >=0.3.5 - r-htmlwidgets >=0.6 - r-magrittr diff --git a/recipes/r-dunn.test/meta.yaml b/recipes/r-dunn.test/meta.yaml index 151d1d8d28..5b49c2fcd3 100644 --- a/recipes/r-dunn.test/meta.yaml +++ b/recipes/r-dunn.test/meta.yaml @@ -32,10 +32,10 @@ build: requirements: build: - - r + - r-base run: - - r + - r-base test: commands: diff --git a/recipes/r-ellipse/meta.yaml b/recipes/r-ellipse/meta.yaml index 5a519c77b1..6e2f266e2d 100644 --- a/recipes/r-ellipse/meta.yaml +++ b/recipes/r-ellipse/meta.yaml @@ -31,10 +31,10 @@ build: # Suggests: MASS requirements: build: - - r + - r-base run: - - r + - r-base test: commands: diff --git a/recipes/r-empiricalfdr.deseq2/meta.yaml b/recipes/r-empiricalfdr.deseq2/meta.yaml index de128885f6..238afcf7c3 100644 --- a/recipes/r-empiricalfdr.deseq2/meta.yaml +++ b/recipes/r-empiricalfdr.deseq2/meta.yaml @@ -13,11 +13,11 @@ build: - lib requirements: build: - - r + - r-base - bioconductor-deseq2 - bioconductor-genomicranges run: - - r + - r-base - bioconductor-deseq2 - bioconductor-genomicranges diff --git a/recipes/r-exomedepth/meta.yaml b/recipes/r-exomedepth/meta.yaml index acd08eec22..ccaa169375 100644 --- a/recipes/r-exomedepth/meta.yaml +++ b/recipes/r-exomedepth/meta.yaml @@ -16,7 +16,7 @@ build: requirements: build: - - r + - r-base - bioconductor-biostrings - bioconductor-genomicalignments - bioconductor-genomicranges >=1.23.0 @@ -28,7 +28,7 @@ requirements: - llvm # [osx] run: - - r + - r-base - bioconductor-biostrings - bioconductor-genomicalignments - bioconductor-genomicranges >=1.23.0 diff --git a/recipes/r-fail/meta.yaml b/recipes/r-fail/meta.yaml index 16247c2a78..e200395e8f 100644 --- a/recipes/r-fail/meta.yaml +++ b/recipes/r-fail/meta.yaml @@ -22,12 +22,12 @@ build: # Suggests: testthat requirements: build: - - r + - r-base - r-bbmisc - r-checkmate run: - - r + - r-base - r-bbmisc - r-checkmate diff --git a/recipes/r-fastcluster/meta.yaml b/recipes/r-fastcluster/meta.yaml index 73bd720d99..e441982282 100644 --- a/recipes/r-fastcluster/meta.yaml +++ b/recipes/r-fastcluster/meta.yaml @@ -32,11 +32,11 @@ build: requirements: build: - - r + - r-base - gcc # [not win] run: - - r + - r-base - libgcc # [not win] test: diff --git a/recipes/r-fda/meta.yaml b/recipes/r-fda/meta.yaml index 6d27f54e2b..fa2c6bfcf4 100644 --- a/recipes/r-fda/meta.yaml +++ b/recipes/r-fda/meta.yaml @@ -31,11 +31,11 @@ build: # Suggests: deSolve, R.matlab, quadprog, nlme, lattice, RCurl, zoo requirements: build: - - r + - r-base - r-matrix # [not win] run: - - r + - r-base - r-matrix # [not win] test: diff --git a/recipes/r-fdrtool/meta.yaml b/recipes/r-fdrtool/meta.yaml index f3ffda29a9..756bde25cc 100644 --- a/recipes/r-fdrtool/meta.yaml +++ b/recipes/r-fdrtool/meta.yaml @@ -31,10 +31,10 @@ build: # Suggests: graph, Rgraphviz requirements: build: - - r + - r-base run: - - r + - r-base test: commands: diff --git a/recipes/r-fftwtools/meta.yaml b/recipes/r-fftwtools/meta.yaml index 35870a3988..f0efec064a 100644 --- a/recipes/r-fftwtools/meta.yaml +++ b/recipes/r-fftwtools/meta.yaml @@ -17,12 +17,12 @@ build: requirements: build: - - r + - r-base - fftw - gcc # [not win] run: - - r + - r-base - fftw - libgcc # [not win] diff --git a/recipes/r-fitdistrplus/meta.yaml b/recipes/r-fitdistrplus/meta.yaml index 7ed24eed9c..6a7084d026 100644 --- a/recipes/r-fitdistrplus/meta.yaml +++ b/recipes/r-fitdistrplus/meta.yaml @@ -31,12 +31,12 @@ build: # Suggests: actuar, rgenoud, mc2d, gamlss.dist requirements: build: - - r + - r-base - r-mass # [not win] - r-survival # [not win] run: - - r + - r-base - r-mass # [not win] - r-survival # [not win] diff --git a/recipes/r-flowr/meta.yaml b/recipes/r-flowr/meta.yaml index 22d51b9269..0c69c1c5c5 100644 --- a/recipes/r-flowr/meta.yaml +++ b/recipes/r-flowr/meta.yaml @@ -31,13 +31,13 @@ build: # Suggests: reshape2, knitr, ggplot2, openxlsx, testthat, funr requirements: build: - - r + - r-base - r-diagram - r-params >=0.3 - r-whisker run: - - r + - r-base - r-diagram - r-params >=0.3 - r-whisker diff --git a/recipes/r-futile.logger/meta.yaml b/recipes/r-futile.logger/meta.yaml index 3f1e2b986f..c5212dd479 100644 --- a/recipes/r-futile.logger/meta.yaml +++ b/recipes/r-futile.logger/meta.yaml @@ -31,12 +31,12 @@ build: # Suggests: testthat, jsonlite requirements: build: - - r + - r-base - r-futile.options - r-lambda.r >=1.1.0 run: - - r + - r-base - r-futile.options - r-lambda.r >=1.1.0 diff --git a/recipes/r-future/0.9.0/meta.yaml b/recipes/r-future/0.9.0/meta.yaml index 14dea31e52..5299f687b0 100644 --- a/recipes/r-future/0.9.0/meta.yaml +++ b/recipes/r-future/0.9.0/meta.yaml @@ -19,12 +19,12 @@ build: # Suggests: parallel, R.rsp requirements: build: - - r + - r-base - r-globals >=0.5.0 - r-listenv run: - - r + - r-base - r-globals >=0.5.0 - r-listenv diff --git a/recipes/r-future/meta.yaml b/recipes/r-future/meta.yaml index 002f8a2cf9..beffac847a 100644 --- a/recipes/r-future/meta.yaml +++ b/recipes/r-future/meta.yaml @@ -22,13 +22,13 @@ build: # Suggests: R.rsp, markdown requirements: build: - - r + - r-base - r-digest - r-globals >=0.7.1 - r-listenv >=0.6.0 run: - - r + - r-base - r-digest - r-globals >=0.7.1 - r-listenv >=0.6.0 diff --git a/recipes/r-gam/meta.yaml b/recipes/r-gam/meta.yaml index 9009c19107..d64397998e 100644 --- a/recipes/r-gam/meta.yaml +++ b/recipes/r-gam/meta.yaml @@ -17,12 +17,12 @@ build: requirements: build: - - r + - r-base - r-foreach - gcc run: - - r + - r-base - r-foreach - libgcc # [not osx] diff --git a/recipes/r-gamlss.data/meta.yaml b/recipes/r-gamlss.data/meta.yaml index 234a2735f2..8f49a249c3 100644 --- a/recipes/r-gamlss.data/meta.yaml +++ b/recipes/r-gamlss.data/meta.yaml @@ -18,10 +18,10 @@ build: requirements: build: - - r + - r-base run: - - r + - r-base test: commands: diff --git a/recipes/r-gamlss.dist/meta.yaml b/recipes/r-gamlss.dist/meta.yaml index f95191dadb..61b57e6cb5 100644 --- a/recipes/r-gamlss.dist/meta.yaml +++ b/recipes/r-gamlss.dist/meta.yaml @@ -18,13 +18,13 @@ build: requirements: build: - - r + - r-base - r-mass - gcc # [not osx] - llvm # [osx] run: - - r + - r-base - r-mass - libgcc # [not osx] diff --git a/recipes/r-gamlss/meta.yaml b/recipes/r-gamlss/meta.yaml index bf671dc112..db58f48dc7 100644 --- a/recipes/r-gamlss/meta.yaml +++ b/recipes/r-gamlss/meta.yaml @@ -18,7 +18,7 @@ build: requirements: build: - - r + - r-base - r-mass - r-gamlss.data >=5.0_0 - r-gamlss.dist >=4.3.1 @@ -28,7 +28,7 @@ requirements: - llvm # [osx] run: - - r + - r-base - r-mass - r-gamlss.data >=5.0_0 - r-gamlss.dist >=4.3.1 diff --git a/recipes/r-genabel.data/meta.yaml b/recipes/r-genabel.data/meta.yaml index 15063fd5fd..dce875510e 100644 --- a/recipes/r-genabel.data/meta.yaml +++ b/recipes/r-genabel.data/meta.yaml @@ -20,10 +20,10 @@ build: requirements: build: - - r + - r-base run: - - r + - r-base test: commands: diff --git a/recipes/r-genenet/meta.yaml b/recipes/r-genenet/meta.yaml index f56e9cb261..9cd7b48241 100644 --- a/recipes/r-genenet/meta.yaml +++ b/recipes/r-genenet/meta.yaml @@ -31,13 +31,13 @@ build: # Suggests: graph, Rgraphviz requirements: build: - - r + - r-base - r-corpcor >=1.6.8 - r-fdrtool >=1.2.15 - r-longitudinal >=1.1.12 run: - - r + - r-base - r-corpcor >=1.6.8 - r-fdrtool >=1.2.15 - r-longitudinal >=1.1.12 diff --git a/recipes/r-geomap/meta.yaml b/recipes/r-geomap/meta.yaml index d0eab9ced3..4eae35f1f7 100644 --- a/recipes/r-geomap/meta.yaml +++ b/recipes/r-geomap/meta.yaml @@ -16,7 +16,7 @@ build: - lib/ requirements: build: - - r + - r-base - r-mba - r-rpmg - r-fields @@ -25,7 +25,7 @@ requirements: - {{native}}toolchain # [win] - gcc # [not win] run: - - r + - r-base - r-mba - r-rpmg - r-fields diff --git a/recipes/r-getopt/meta.yaml b/recipes/r-getopt/meta.yaml index 7494b2d2e2..fc32b8fd23 100644 --- a/recipes/r-getopt/meta.yaml +++ b/recipes/r-getopt/meta.yaml @@ -31,10 +31,10 @@ build: # Suggests: testthat requirements: build: - - r + - r-base run: - - r + - r-base test: commands: diff --git a/recipes/r-getoptlong/meta.yaml b/recipes/r-getoptlong/meta.yaml index 50c3564868..3151001776 100644 --- a/recipes/r-getoptlong/meta.yaml +++ b/recipes/r-getoptlong/meta.yaml @@ -31,12 +31,12 @@ build: # Suggests: testthat (>= 0.3), knitr requirements: build: - - r + - r-base - r-globaloptions >=0.0.6 - r-rjson run: - - r + - r-base - r-globaloptions >=0.0.6 - r-rjson diff --git a/recipes/r-ggally/0.5.0/meta.yaml b/recipes/r-ggally/0.5.0/meta.yaml index e6ae0de5c9..b4f86e24a1 100644 --- a/recipes/r-ggally/0.5.0/meta.yaml +++ b/recipes/r-ggally/0.5.0/meta.yaml @@ -31,7 +31,7 @@ build: # Suggests: arm (>= 1.7), intergraph (>= 2.0-0), network (>= 1.7.2), RColorBrewer (>= 1.0-5), scales (>= 0.2.3), scagnostics (>= 0.2-4), sna (>= 2.3-1), survival (>= 2.37-4), tnet (>= 3.0), roxygen2 (>= 4.0.1) requirements: build: - - r + - r-base - r-ggplot2 >=1.0.0 - r-gtable >=0.1.2 - r-plyr >=1.8 @@ -39,7 +39,7 @@ requirements: - r-stringr >=0.6.2 run: - - r + - r-base - r-ggplot2 >=1.0.0 - r-gtable >=0.1.2 - r-plyr >=1.8 diff --git a/recipes/r-ggally/meta.yaml b/recipes/r-ggally/meta.yaml index 37a0a0af85..26afabf1e7 100644 --- a/recipes/r-ggally/meta.yaml +++ b/recipes/r-ggally/meta.yaml @@ -32,7 +32,7 @@ build: # Suggests: broom (>= 0.4.0), chemometrics, geosphere (>= 1.5-1), igraph (>= 1.0.1), intergraph (>= 2.0-2), maps (>= 3.1.0), mapproj, network (>= 1.12.0), scagnostics, scales (>= 0.4.0), sna (>= 2.3-2), survival, packagedocs (>= 0.4.0), rmarkdown, roxygen2, testthat requirements: build: - - r + - r-base - r-rcolorbrewer - r-ggplot2 >=2.2.0 - r-gtable >=0.2.0 @@ -41,7 +41,7 @@ requirements: - r-reshape >=0.8.5 run: - - r + - r-base - r-rcolorbrewer - r-ggplot2 >=2.2.0 - r-gtable >=0.2.0 diff --git a/recipes/r-ggalt/meta.yaml b/recipes/r-ggalt/meta.yaml index 6b0e9e20d1..4c6eb913bc 100644 --- a/recipes/r-ggalt/meta.yaml +++ b/recipes/r-ggalt/meta.yaml @@ -19,7 +19,7 @@ build: # Suggests: testthat, gridExtra, knitr, rmarkdown, ggthemes requirements: build: - - r + - r-base - r-kernsmooth # [not win] - r-mass # [not win] - r-rcolorbrewer @@ -32,7 +32,7 @@ requirements: - r-scales run: - - r + - r-base - r-kernsmooth # [not win] - r-mass # [not win] - r-rcolorbrewer diff --git a/recipes/r-ggdendro/meta.yaml b/recipes/r-ggdendro/meta.yaml index 92ff96a432..081604cf5c 100644 --- a/recipes/r-ggdendro/meta.yaml +++ b/recipes/r-ggdendro/meta.yaml @@ -31,12 +31,12 @@ build: # Suggests: rpart(>= 4.0-0), tree, testthat, knitr, cluster requirements: build: - - r + - r-base - r-mass # [not win] - r-ggplot2 >=0.9.2 run: - - r + - r-base - r-mass # [not win] - r-ggplot2 >=0.9.2 diff --git a/recipes/r-ggrepel/meta.yaml b/recipes/r-ggrepel/meta.yaml index d197960bcb..99acb37a3f 100644 --- a/recipes/r-ggrepel/meta.yaml +++ b/recipes/r-ggrepel/meta.yaml @@ -29,13 +29,13 @@ build: # Suggests: knitr, rmarkdown requirements: build: - - r + - r-base - r-rcpp - r-ggplot2 >=2.0.0 - gcc # [not win] run: - - r + - r-base - r-rcpp - r-ggplot2 >=2.0.0 - libgcc # [not win] diff --git a/recipes/r-globals/0.6.0/meta.yaml b/recipes/r-globals/0.6.0/meta.yaml index a6991fadb6..95db478577 100644 --- a/recipes/r-globals/0.6.0/meta.yaml +++ b/recipes/r-globals/0.6.0/meta.yaml @@ -17,11 +17,11 @@ build: requirements: build: - - r + - r-base - r-codetools # [not win] run: - - r + - r-base - r-codetools # [not win] test: diff --git a/recipes/r-globals/meta.yaml b/recipes/r-globals/meta.yaml index ef188e74be..9d6438c2da 100644 --- a/recipes/r-globals/meta.yaml +++ b/recipes/r-globals/meta.yaml @@ -21,11 +21,11 @@ build: requirements: build: - - r + - r-base - r-codetools run: - - r + - r-base - r-codetools test: diff --git a/recipes/r-gmd/meta.yaml b/recipes/r-gmd/meta.yaml index fc238e5b49..2f7dae6d4e 100644 --- a/recipes/r-gmd/meta.yaml +++ b/recipes/r-gmd/meta.yaml @@ -21,11 +21,11 @@ build: # Suggests: datasets, MASS, cluster requirements: build: - - r + - r-base - r-gplots run: - - r + - r-base - r-gplots test: diff --git a/recipes/r-gmodels/meta.yaml b/recipes/r-gmodels/meta.yaml index f196df6579..e77f31b467 100644 --- a/recipes/r-gmodels/meta.yaml +++ b/recipes/r-gmodels/meta.yaml @@ -18,12 +18,12 @@ build: # Suggests: gplots, gtools, Matrix, nlme, lme4 (>= 0.999999-0) requirements: build: - - r + - r-base - r-mass - r-gdata run: - - r + - r-base - r-mass - r-gdata diff --git a/recipes/r-googlevis/meta.yaml b/recipes/r-googlevis/meta.yaml index 9a45c0242e..abb65c9fe9 100644 --- a/recipes/r-googlevis/meta.yaml +++ b/recipes/r-googlevis/meta.yaml @@ -31,11 +31,11 @@ build: # Suggests: shiny (>= 0.4.0), httpuv (>= 1.2.0), knitr (>= 1.5) requirements: build: - - r + - r-base - r-rjsonio run: - - r + - r-base - r-rjsonio test: diff --git a/recipes/r-gplots/meta.yaml b/recipes/r-gplots/meta.yaml index 6611a381fa..90ef59e4dd 100644 --- a/recipes/r-gplots/meta.yaml +++ b/recipes/r-gplots/meta.yaml @@ -32,14 +32,14 @@ build: # Suggests: grid, MASS requirements: build: - - r + - r-base - r-kernsmooth # [not win] - r-catools - r-gdata - r-gtools run: - - r + - r-base - r-kernsmooth # [not win] - r-catools - r-gdata diff --git a/recipes/r-grimport/meta.yaml b/recipes/r-grimport/meta.yaml index 03484b4521..ff2e945f1a 100644 --- a/recipes/r-grimport/meta.yaml +++ b/recipes/r-grimport/meta.yaml @@ -18,11 +18,11 @@ build: requirements: build: - - r + - r-base - r-xml run: - - r + - r-base - r-xml test: diff --git a/recipes/r-gsalib/meta.yaml b/recipes/r-gsalib/meta.yaml index 74f54e9e2c..a6c4289a9c 100644 --- a/recipes/r-gsalib/meta.yaml +++ b/recipes/r-gsalib/meta.yaml @@ -32,10 +32,10 @@ build: requirements: build: - - r + - r-base run: - - r + - r-base test: commands: diff --git a/recipes/r-gsmoothr/meta.yaml b/recipes/r-gsmoothr/meta.yaml index 11341bd18d..943a46849f 100644 --- a/recipes/r-gsmoothr/meta.yaml +++ b/recipes/r-gsmoothr/meta.yaml @@ -22,13 +22,13 @@ build: requirements: build: - - r + - r-base - posix # [win] - {{native}}toolchain # [win] - gcc # [not win] run: - - r + - r-base test: commands: diff --git a/recipes/r-htmltools/meta.yaml b/recipes/r-htmltools/meta.yaml index 8582183051..e8487a2acb 100644 --- a/recipes/r-htmltools/meta.yaml +++ b/recipes/r-htmltools/meta.yaml @@ -32,11 +32,11 @@ build: # Suggests: markdown, testthat requirements: build: - - r + - r-base - r-digest run: - - r + - r-base - r-digest test: diff --git a/recipes/r-htmlwidgets/meta.yaml b/recipes/r-htmlwidgets/meta.yaml index 91aadf2f42..b8878487cc 100644 --- a/recipes/r-htmlwidgets/meta.yaml +++ b/recipes/r-htmlwidgets/meta.yaml @@ -32,13 +32,13 @@ build: # Suggests: knitr (>= 1.8) requirements: build: - - r + - r-base - r-htmltools >=0.2.6 - r-jsonlite >=0.9.16 - r-yaml run: - - r + - r-base - r-htmltools >=0.2.6 - r-jsonlite >=0.9.16 - r-yaml diff --git a/recipes/r-hwriter/meta.yaml b/recipes/r-hwriter/meta.yaml index c076ef1fbf..7bc4d41c23 100644 --- a/recipes/r-hwriter/meta.yaml +++ b/recipes/r-hwriter/meta.yaml @@ -18,10 +18,10 @@ build: requirements: build: - - r + - r-base run: - - r + - r-base test: commands: diff --git a/recipes/r-idr/meta.yaml b/recipes/r-idr/meta.yaml index 2cf60335b9..20f6290e37 100644 --- a/recipes/r-idr/meta.yaml +++ b/recipes/r-idr/meta.yaml @@ -21,10 +21,10 @@ build: requirements: build: - - r + - r-base run: - - r + - r-base test: commands: diff --git a/recipes/r-inlinedocs/meta.yaml b/recipes/r-inlinedocs/meta.yaml index 51d850a28a..7ecb2f2932 100644 --- a/recipes/r-inlinedocs/meta.yaml +++ b/recipes/r-inlinedocs/meta.yaml @@ -20,10 +20,10 @@ build: requirements: build: - - r + - r-base run: - - r + - r-base test: commands: diff --git a/recipes/r-ipo/meta.yaml b/recipes/r-ipo/meta.yaml index e925b4a780..9986dc2fcc 100644 --- a/recipes/r-ipo/meta.yaml +++ b/recipes/r-ipo/meta.yaml @@ -20,14 +20,14 @@ build: # Suggests: parallel requirements: build: - - r + - r-base - bioconductor-xcms - r-rsm - bioconductor-camera #- libnetcdf 4.2.1.1 run: - - r + - r-base - bioconductor-xcms - r-rsm - bioconductor-camera diff --git a/recipes/r-jsonlite/meta.yaml b/recipes/r-jsonlite/meta.yaml index d468dd459a..7382eca363 100644 --- a/recipes/r-jsonlite/meta.yaml +++ b/recipes/r-jsonlite/meta.yaml @@ -32,11 +32,11 @@ build: # Suggests: curl (>= 0.5), plyr, testthat, knitr, rmarkdown, R.rsp requirements: build: - - r + - r-base - gcc # [not win] run: - - r + - r-base - libgcc # [not win] test: diff --git a/recipes/r-klar/meta.yaml b/recipes/r-klar/meta.yaml index 41d29b0862..1d717f11c0 100644 --- a/recipes/r-klar/meta.yaml +++ b/recipes/r-klar/meta.yaml @@ -18,12 +18,12 @@ build: # Suggests: scatterplot3d (>= 0.3-22), som, mlbench, rpart, e1071 requirements: build: - - r + - r-base - r-mass - r-combinat run: - - r + - r-base - r-mass - r-combinat diff --git a/recipes/r-knitr/meta.yaml b/recipes/r-knitr/meta.yaml index 2ad029f2a5..3b4077823c 100644 --- a/recipes/r-knitr/meta.yaml +++ b/recipes/r-knitr/meta.yaml @@ -16,7 +16,7 @@ build: #suggests: testit, rgl (≥ 0.95.1201), codetools, rmarkdown, tikzDevice (≥ 0.9), XML, RCurl requirements: build: - - r + - r-base - r-digest - r-evaluate >=0.8 - r-formatr @@ -26,7 +26,7 @@ requirements: - r-yaml >=2.1.5 run: - - r + - r-base - r-digest - r-evaluate >=0.8 - r-formatr diff --git a/recipes/r-knitrbootstrap/meta.yaml b/recipes/r-knitrbootstrap/meta.yaml index 667c789354..5065354938 100644 --- a/recipes/r-knitrbootstrap/meta.yaml +++ b/recipes/r-knitrbootstrap/meta.yaml @@ -32,13 +32,13 @@ build: # Suggests: testthat, roxygen2, corrplot, ggplot2, igraph, maps, mapproj, maptools, plyr, reshape2, xtable requirements: build: - - r + - r-base - r-knitr >=1.5.25 - r-markdown - r-rmarkdown run: - - r + - r-base - r-knitr >=1.5.25 - r-markdown - r-rmarkdown diff --git a/recipes/r-lambda.r/meta.yaml b/recipes/r-lambda.r/meta.yaml index 45ee61b99a..d4a698fa2b 100644 --- a/recipes/r-lambda.r/meta.yaml +++ b/recipes/r-lambda.r/meta.yaml @@ -31,10 +31,10 @@ build: # Suggests: RUnit requirements: build: - - r + - r-base run: - - r + - r-base test: commands: diff --git a/recipes/r-learnbayes/meta.yaml b/recipes/r-learnbayes/meta.yaml index 2ebfb394c3..fd1b4f5dcd 100644 --- a/recipes/r-learnbayes/meta.yaml +++ b/recipes/r-learnbayes/meta.yaml @@ -18,10 +18,10 @@ build: requirements: build: - - r + - r-base run: - - r + - r-base test: commands: diff --git a/recipes/r-listenv/0.5.0/meta.yaml b/recipes/r-listenv/0.5.0/meta.yaml index 02fb1d74ea..954f77e6d9 100644 --- a/recipes/r-listenv/0.5.0/meta.yaml +++ b/recipes/r-listenv/0.5.0/meta.yaml @@ -19,10 +19,10 @@ build: # Suggests: R.rsp requirements: build: - - r + - r-base run: - - r + - r-base test: commands: diff --git a/recipes/r-listenv/meta.yaml b/recipes/r-listenv/meta.yaml index 13d20b4b96..ecd380a498 100644 --- a/recipes/r-listenv/meta.yaml +++ b/recipes/r-listenv/meta.yaml @@ -22,10 +22,10 @@ build: # Suggests: R.utils, R.rsp requirements: build: - - r + - r-base run: - - r + - r-base test: commands: diff --git a/recipes/r-longitudinal/meta.yaml b/recipes/r-longitudinal/meta.yaml index 024a6dcd22..af11244c3d 100644 --- a/recipes/r-longitudinal/meta.yaml +++ b/recipes/r-longitudinal/meta.yaml @@ -31,11 +31,11 @@ build: # Suggests: graph, Rgraphviz requirements: build: - - r + - r-base - r-corpcor >=1.6.8 run: - - r + - r-base - r-corpcor >=1.6.8 test: diff --git a/recipes/r-lsd/meta.yaml b/recipes/r-lsd/meta.yaml index 060b671ae9..b4af7f8cd1 100644 --- a/recipes/r-lsd/meta.yaml +++ b/recipes/r-lsd/meta.yaml @@ -31,10 +31,10 @@ build: requirements: build: - - r + - r-base run: - - r + - r-base test: commands: diff --git a/recipes/r-mba/meta.yaml b/recipes/r-mba/meta.yaml index 9153406a27..4867f7e90b 100644 --- a/recipes/r-mba/meta.yaml +++ b/recipes/r-mba/meta.yaml @@ -16,14 +16,14 @@ build: - lib/ requirements: build: - - r + - r-base - r-bh - r-sp - posix # [win] - {{native}}toolchain # [win] - gcc # [not win] run: - - r + - r-base - r-bh - r-sp test: diff --git a/recipes/r-misc3d/meta.yaml b/recipes/r-misc3d/meta.yaml index a5328dc45c..deb468e7e0 100644 --- a/recipes/r-misc3d/meta.yaml +++ b/recipes/r-misc3d/meta.yaml @@ -31,10 +31,10 @@ build: # Suggests: rgl, tkrplot, MASS requirements: build: - - r + - r-base run: - - r + - r-base test: commands: diff --git a/recipes/r-mitools/meta.yaml b/recipes/r-mitools/meta.yaml index 88d5aac8d5..61413b8bef 100644 --- a/recipes/r-mitools/meta.yaml +++ b/recipes/r-mitools/meta.yaml @@ -21,10 +21,10 @@ build: # Suggests: RODBC, DBI, foreign requirements: build: - - r + - r-base run: - - r + - r-base test: commands: diff --git a/recipes/r-mmgenome/meta.yaml b/recipes/r-mmgenome/meta.yaml index 4b9b5d32b7..e2c0fc6124 100644 --- a/recipes/r-mmgenome/meta.yaml +++ b/recipes/r-mmgenome/meta.yaml @@ -20,7 +20,7 @@ build: requirements: build: - - r + - r-base - r-sp >=1.0.15 - r-gridextra >=0.9.1 - r-ggplot2 >=1.0.0 @@ -32,7 +32,7 @@ requirements: - r-dplyr >=0.4.0 run: - - r + - r-base - r-sp >=1.0.15 - r-gridextra >=0.9.1 - r-ggplot2 >=1.0.0 diff --git a/recipes/r-multitaper/meta.yaml b/recipes/r-multitaper/meta.yaml index a7d14c8a09..08ad86fbd2 100644 --- a/recipes/r-multitaper/meta.yaml +++ b/recipes/r-multitaper/meta.yaml @@ -15,10 +15,10 @@ build: requirements: build: - - r + - r-base - gcc run: - - r + - r-base - libgcc test: diff --git a/recipes/r-mutationalpatterns/meta.yaml b/recipes/r-mutationalpatterns/meta.yaml index bedd425812..28bf73c12d 100644 --- a/recipes/r-mutationalpatterns/meta.yaml +++ b/recipes/r-mutationalpatterns/meta.yaml @@ -11,7 +11,7 @@ build: - lib/ requirements: build: - - r + - r-base - bioconductor-biostrings - bioconductor-bsgenome - bioconductor-genomicranges @@ -26,7 +26,7 @@ requirements: - r-nmf - r-reshape2 run: - - r + - r-base - bioconductor-biostrings - bioconductor-bsgenome - bioconductor-genomicranges diff --git a/recipes/r-mutoss/meta.yaml b/recipes/r-mutoss/meta.yaml index 6ba2ab2c93..b6a53a1fd8 100644 --- a/recipes/r-mutoss/meta.yaml +++ b/recipes/r-mutoss/meta.yaml @@ -18,14 +18,14 @@ build: # Suggests: fdrtool, qvalue, RUnit, lattice requirements: build: - - r + - r-base - r-multcomp >=1.1_0 - bioconductor-multtest >=2.2.0 - r-mvtnorm - r-plotrix run: - - r + - r-base - r-multcomp >=1.1_0 - bioconductor-multtest >=2.2.0 - r-mvtnorm diff --git a/recipes/r-nanostringnorm/meta.yaml b/recipes/r-nanostringnorm/meta.yaml index 9decd3da67..5945c09bdb 100644 --- a/recipes/r-nanostringnorm/meta.yaml +++ b/recipes/r-nanostringnorm/meta.yaml @@ -31,7 +31,7 @@ build: # Suggests: googleVis (>= 0.2.14), lme4, RUnit (>= 0.4.26) requirements: build: - - r + - r-base - r-gdata >=2.8.2 - bioconductor-vsn >=3.22.0 - r-googlevis @@ -39,7 +39,7 @@ requirements: - r-runit run: - - r + - r-base - r-gdata >=2.8.2 - bioconductor-vsn >=3.22.0 - r-googlevis diff --git a/recipes/r-nastiseq/meta.yaml b/recipes/r-nastiseq/meta.yaml index c505d116aa..295075c4c9 100644 --- a/recipes/r-nastiseq/meta.yaml +++ b/recipes/r-nastiseq/meta.yaml @@ -18,12 +18,12 @@ build: requirements: build: - - r + - r-base - r-rocr - bioconductor-deseq run: - - r + - r-base - r-rocr - bioconductor-deseq diff --git a/recipes/r-nozzle.r1/meta.yaml b/recipes/r-nozzle.r1/meta.yaml index b7fcfc9065..ff4ad7ae57 100644 --- a/recipes/r-nozzle.r1/meta.yaml +++ b/recipes/r-nozzle.r1/meta.yaml @@ -32,10 +32,10 @@ build: requirements: build: - - r + - r-base run: - - r + - r-base test: commands: diff --git a/recipes/r-optparse/meta.yaml b/recipes/r-optparse/meta.yaml index 1ecdd63b59..de59fc6328 100644 --- a/recipes/r-optparse/meta.yaml +++ b/recipes/r-optparse/meta.yaml @@ -34,11 +34,11 @@ build: # Suggests: knitr, stringr, testthat requirements: build: - - r + - r-base - r-getopt >=1.19 run: - - r + - r-base - r-getopt >=1.19 test: diff --git a/recipes/r-outliers/meta.yaml b/recipes/r-outliers/meta.yaml index 348f33f620..90ddb065e7 100644 --- a/recipes/r-outliers/meta.yaml +++ b/recipes/r-outliers/meta.yaml @@ -18,10 +18,10 @@ build: requirements: build: - - r + - r-base run: - - r + - r-base test: commands: diff --git a/recipes/r-patpro/meta.yaml b/recipes/r-patpro/meta.yaml index b388ad73a6..db898d31c0 100644 --- a/recipes/r-patpro/meta.yaml +++ b/recipes/r-patpro/meta.yaml @@ -17,7 +17,7 @@ build: requirements: build: - - r + - r-base - r-rcolorbrewer - r-ggplot2 - r-gridextra @@ -25,7 +25,7 @@ requirements: - r-reshape2 run: - - r + - r-base - r-rcolorbrewer - r-ggplot2 - r-gridextra diff --git a/recipes/r-peer/meta.yaml b/recipes/r-peer/meta.yaml index 2465e83899..604a020d73 100644 --- a/recipes/r-peer/meta.yaml +++ b/recipes/r-peer/meta.yaml @@ -19,11 +19,11 @@ build: requirements: build: - - r + - r-base - gcc run: - - r + - r-base - libgcc test: diff --git a/recipes/r-penalized/meta.yaml b/recipes/r-penalized/meta.yaml index 829a4c57ab..1cd0bf04d6 100644 --- a/recipes/r-penalized/meta.yaml +++ b/recipes/r-penalized/meta.yaml @@ -16,11 +16,11 @@ build: requirements: build: - - r + - r-base - r-survival run: - - r + - r-base - r-survival test: diff --git a/recipes/r-permute/meta.yaml b/recipes/r-permute/meta.yaml index 2c6953538f..f80bee23e4 100644 --- a/recipes/r-permute/meta.yaml +++ b/recipes/r-permute/meta.yaml @@ -31,10 +31,10 @@ build: # Suggests: knitr (>= 1.8), rmarkdown (>= 0.6), mix requirements: build: - - r + - r-base run: - - r + - r-base test: commands: diff --git a/recipes/r-pheatmap/meta.yaml b/recipes/r-pheatmap/meta.yaml index 1eb35d3e56..9fbc9f2177 100644 --- a/recipes/r-pheatmap/meta.yaml +++ b/recipes/r-pheatmap/meta.yaml @@ -19,13 +19,13 @@ build: requirements: build: - - r + - r-base - r-rcolorbrewer - r-gtable - r-scales run: - - r + - r-base - r-rcolorbrewer - r-gtable - r-scales diff --git a/recipes/r-phonr/meta.yaml b/recipes/r-phonr/meta.yaml index 2383a51ca0..6a92e5c162 100644 --- a/recipes/r-phonr/meta.yaml +++ b/recipes/r-phonr/meta.yaml @@ -34,13 +34,13 @@ build: requirements: build: - - r + - r-base - r-deldir - r-plotrix - r-splancs run: - - r + - r-base - r-deldir - r-plotrix - r-splancs diff --git a/recipes/r-pmcmr/meta.yaml b/recipes/r-pmcmr/meta.yaml index 63aeca9fde..72a7f3d9ea 100644 --- a/recipes/r-pmcmr/meta.yaml +++ b/recipes/r-pmcmr/meta.yaml @@ -31,10 +31,10 @@ build: # Suggests: multcompView, xtable, graphics requirements: build: - - r + - r-base run: - - r + - r-base test: commands: diff --git a/recipes/r-png/meta.yaml b/recipes/r-png/meta.yaml index c277ffaedc..9baa976692 100644 --- a/recipes/r-png/meta.yaml +++ b/recipes/r-png/meta.yaml @@ -19,11 +19,11 @@ build: requirements: build: - - r + - r-base - gcc # [not win] run: - - r + - r-base - libgcc # [not win] test: diff --git a/recipes/r-pore/meta.yaml b/recipes/r-pore/meta.yaml index 5a91b135bd..e934d18e1b 100644 --- a/recipes/r-pore/meta.yaml +++ b/recipes/r-pore/meta.yaml @@ -22,7 +22,7 @@ build: requirements: build: - - r + - r-base - bioconductor-rhdf5 - r-bit64 - r-shiny @@ -30,7 +30,7 @@ requirements: - r-svdialogs run: - - r + - r-base - bioconductor-rhdf5 - r-bit64 - r-shiny diff --git a/recipes/r-pracma/meta.yaml b/recipes/r-pracma/meta.yaml index 53d26a33ee..590b8c8879 100644 --- a/recipes/r-pracma/meta.yaml +++ b/recipes/r-pracma/meta.yaml @@ -20,10 +20,10 @@ build: requirements: build: - - r + - r-base run: - - r + - r-base test: diff --git a/recipes/r-preseqr/meta.yaml b/recipes/r-preseqr/meta.yaml index 5617e30fa1..8fcd82543d 100644 --- a/recipes/r-preseqr/meta.yaml +++ b/recipes/r-preseqr/meta.yaml @@ -31,13 +31,13 @@ build: requirements: build: - - r + - r-base - r-polynom - gcc # [linux] - llvm # [osx] run: - - r + - r-base - r-polynom - libgcc # [linux] diff --git a/recipes/r-prettyunits/meta.yaml b/recipes/r-prettyunits/meta.yaml index 1f91ccec9e..d8548b76fb 100644 --- a/recipes/r-prettyunits/meta.yaml +++ b/recipes/r-prettyunits/meta.yaml @@ -34,12 +34,12 @@ build: # Suggests: testthat requirements: build: - - r + - r-base - r-assertthat - r-magrittr run: - - r + - r-base - r-assertthat - r-magrittr diff --git a/recipes/r-probmetab/1.0/meta.yaml b/recipes/r-probmetab/1.0/meta.yaml index 6d2d0431e4..451a26ebb8 100644 --- a/recipes/r-probmetab/1.0/meta.yaml +++ b/recipes/r-probmetab/1.0/meta.yaml @@ -20,7 +20,7 @@ build: # Suggests: parallel requirements: build: - - r + - r-base - bioconductor-camera - bioconductor-multtest - r-rcpparmadillo @@ -34,7 +34,7 @@ requirements: #- bioconductor-mzr run: - - r + - r-base - bioconductor-camera - bioconductor-multtest - r-rcpparmadillo diff --git a/recipes/r-probmetab/1.1/meta.yaml b/recipes/r-probmetab/1.1/meta.yaml index d286fea864..4ba7ff77c2 100644 --- a/recipes/r-probmetab/1.1/meta.yaml +++ b/recipes/r-probmetab/1.1/meta.yaml @@ -20,7 +20,7 @@ build: # Suggests: parallel requirements: build: - - r + - r-base - bioconductor-camera - bioconductor-multtest - r-rcpparmadillo @@ -34,7 +34,7 @@ requirements: #- bioconductor-mzr run: - - r + - r-base - bioconductor-camera - bioconductor-multtest - r-rcpparmadillo diff --git a/recipes/r-progress/meta.yaml b/recipes/r-progress/meta.yaml index fbaaa303b8..ae2bed4965 100644 --- a/recipes/r-progress/meta.yaml +++ b/recipes/r-progress/meta.yaml @@ -34,12 +34,12 @@ build: # Suggests: testthat requirements: build: - - r + - r-base - r-r6 - r-prettyunits run: - - r + - r-base - r-r6 - r-prettyunits diff --git a/recipes/r-proj4/meta.yaml b/recipes/r-proj4/meta.yaml index ffae5983e5..25d147857b 100644 --- a/recipes/r-proj4/meta.yaml +++ b/recipes/r-proj4/meta.yaml @@ -31,12 +31,12 @@ build: requirements: build: - - r + - r-base - gcc # [not win] - proj4 run: - - r + - r-base - libgcc # [not win] - proj4 diff --git a/recipes/r-prroc/meta.yaml b/recipes/r-prroc/meta.yaml index 7d3b8587d8..2681e77f32 100644 --- a/recipes/r-prroc/meta.yaml +++ b/recipes/r-prroc/meta.yaml @@ -21,10 +21,10 @@ build: # Suggests: testthat, ggplot2 requirements: build: - - r + - r-base run: - - r + - r-base test: commands: diff --git a/recipes/r-pscbs/meta.yaml b/recipes/r-pscbs/meta.yaml index 07aabffe63..c84b338841 100644 --- a/recipes/r-pscbs/meta.yaml +++ b/recipes/r-pscbs/meta.yaml @@ -31,7 +31,7 @@ build: # Suggests: Hmisc (>= 3.16-0), R.rsp (>= 0.20.0), R.devices (>= 2.13.1), ggplot2 (>= 1.0.1), aroma.light (>= 2.2.1) requirements: build: - - r + - r-base - bioconductor-dnacopy - r-r.cache >=0.12.0 - r-r.methodss3 >=1.7.0 @@ -42,7 +42,7 @@ requirements: - r-matrixstats >=0.15.0 run: - - r + - r-base - bioconductor-dnacopy - r-r.cache >=0.12.0 - r-r.methodss3 >=1.7.0 diff --git a/recipes/r-pscl/meta.yaml b/recipes/r-pscl/meta.yaml index c72e156766..08e522ed03 100644 --- a/recipes/r-pscl/meta.yaml +++ b/recipes/r-pscl/meta.yaml @@ -18,14 +18,14 @@ build: # Suggests: MCMCpack, car, lmtest, sandwich, zoo, coda, vcd, mvtnorm, mgcv requirements: build: - - r + - r-base - r-mass - r-lattice - gcc # [not osx] - llvm # [osx] run: - - r + - r-base - r-mass - r-lattice - libgcc # [not osx] diff --git a/recipes/r-psych/meta.yaml b/recipes/r-psych/meta.yaml index 0715969e23..9d2f5feb42 100644 --- a/recipes/r-psych/meta.yaml +++ b/recipes/r-psych/meta.yaml @@ -31,11 +31,11 @@ build: # Suggests: GPArotation, sem, lavaan, Rcsdp, graph, Rgraphviz requirements: build: - - r + - r-base - r-mnormt run: - - r + - r-base - r-mnormt test: diff --git a/recipes/r-qiimer/meta.yaml b/recipes/r-qiimer/meta.yaml index e06a19c75f..5ec927800d 100644 --- a/recipes/r-qiimer/meta.yaml +++ b/recipes/r-qiimer/meta.yaml @@ -22,11 +22,11 @@ build: # Suggests: testthat, biom requirements: build: - - r + - r-base - r-pheatmap run: - - r + - r-base - r-pheatmap test: diff --git a/recipes/r-r.cache/meta.yaml b/recipes/r-r.cache/meta.yaml index b55c710aae..f3372def2b 100644 --- a/recipes/r-r.cache/meta.yaml +++ b/recipes/r-r.cache/meta.yaml @@ -31,14 +31,14 @@ build: requirements: build: - - r + - r-base - r-r.methodss3 >=1.7.0 - r-r.oo >=1.19.0 - r-r.utils >=2.1.0 - r-digest >=0.6.8 run: - - r + - r-base - r-r.methodss3 >=1.7.0 - r-r.oo >=1.19.0 - r-r.utils >=2.1.0 diff --git a/recipes/r-r.devices/meta.yaml b/recipes/r-r.devices/meta.yaml index 037f1ba6db..2362c8b010 100644 --- a/recipes/r-r.devices/meta.yaml +++ b/recipes/r-r.devices/meta.yaml @@ -21,14 +21,14 @@ build: # Suggests: digest (>= 0.6.10), Cairo (>= 1.5-9), R.rsp (>= 0.30.0) requirements: build: - - r + - r-base - r-r.methodss3 >=1.7.1 - r-r.oo >=1.21.0 - r-r.utils >=2.5.0 - r-base64enc >=0.1_3 run: - - r + - r-base - r-r.methodss3 >=1.7.1 - r-r.oo >=1.21.0 - r-r.utils >=2.5.0 diff --git a/recipes/r-r.filesets/meta.yaml b/recipes/r-r.filesets/meta.yaml index 4fd6136df2..c8e4ee1976 100644 --- a/recipes/r-r.filesets/meta.yaml +++ b/recipes/r-r.filesets/meta.yaml @@ -21,7 +21,7 @@ build: # Suggests: BatchJobs (>= 1.6), BiocParallel (>= 1.0.3), gtools (>= 3.5.0) requirements: build: - - r + - r-base - r-r.cache >=0.12.0 - r-r.methodss3 >=1.7.0 - r-r.oo >=1.19.0 @@ -31,7 +31,7 @@ requirements: - r-listenv >=0.6.0 run: - - r + - r-base - r-r.cache >=0.12.0 - r-r.methodss3 >=1.7.0 - r-r.oo >=1.19.0 diff --git a/recipes/r-r.huge/meta.yaml b/recipes/r-r.huge/meta.yaml index 91caf0a655..f0d3f948a1 100644 --- a/recipes/r-r.huge/meta.yaml +++ b/recipes/r-r.huge/meta.yaml @@ -21,13 +21,13 @@ build: requirements: build: - - r + - r-base - r-r.methodss3 >=1.7.0 - r-r.oo >=1.18.0 - r-r.utils >=1.34.0 run: - - r + - r-base - r-r.methodss3 >=1.7.0 - r-r.oo >=1.18.0 - r-r.utils >=1.34.0 diff --git a/recipes/r-r.methodss3/1.7.0/meta.yaml b/recipes/r-r.methodss3/1.7.0/meta.yaml index de70fe8f19..67f2ab350c 100644 --- a/recipes/r-r.methodss3/1.7.0/meta.yaml +++ b/recipes/r-r.methodss3/1.7.0/meta.yaml @@ -18,10 +18,10 @@ build: requirements: build: - - r + - r-base run: - - r + - r-base test: commands: diff --git a/recipes/r-r.oo/1.19.0/meta.yaml b/recipes/r-r.oo/1.19.0/meta.yaml index b5b469d77c..bc47db5c97 100644 --- a/recipes/r-r.oo/1.19.0/meta.yaml +++ b/recipes/r-r.oo/1.19.0/meta.yaml @@ -18,11 +18,11 @@ build: # Suggests: tools requirements: build: - - r + - r-base - r-r.methodss3 >=1.7.0 run: - - r + - r-base - r-r.methodss3 >=1.7.0 test: diff --git a/recipes/r-r.oo/meta.yaml b/recipes/r-r.oo/meta.yaml index 1588378f40..b6888f6ede 100644 --- a/recipes/r-r.oo/meta.yaml +++ b/recipes/r-r.oo/meta.yaml @@ -21,11 +21,11 @@ build: # Suggests: tools requirements: build: - - r + - r-base - r-r.methodss3 >=1.7.1 run: - - r + - r-base - r-r.methodss3 >=1.7.1 test: diff --git a/recipes/r-r.rsp/meta.yaml b/recipes/r-r.rsp/meta.yaml index c03e717d7a..cd56d211c2 100644 --- a/recipes/r-r.rsp/meta.yaml +++ b/recipes/r-r.rsp/meta.yaml @@ -21,14 +21,14 @@ build: # Suggests: tcltk, digest (>= 0.6.9), ascii (>= 2.1), markdown (>= 0.7.7), knitr (>= 1.9), R.devices (>= 2.14.0), base64enc (>= 0.1-3) requirements: build: - - r + - r-base - r-r.cache >=0.12.0 - r-r.methodss3 >=1.7.1 - r-r.oo >=1.20.0 - r-r.utils run: - - r + - r-base - r-r.cache >=0.12.0 - r-r.methodss3 >=1.7.1 - r-r.oo >=1.20.0 diff --git a/recipes/r-r.utils/2.2.0/meta.yaml b/recipes/r-r.utils/2.2.0/meta.yaml index e50a6d0e2b..461fe8ca90 100644 --- a/recipes/r-r.utils/2.2.0/meta.yaml +++ b/recipes/r-r.utils/2.2.0/meta.yaml @@ -18,12 +18,12 @@ build: # Suggests: digest (>= 0.6.8) requirements: build: - - r + - r-base - r-r.methodss3 >=1.7.0 - r-r.oo >=1.19.0 run: - - r + - r-base - r-r.methodss3 >=1.7.0 - r-r.oo >=1.19.0 diff --git a/recipes/r-r.utils/meta.yaml b/recipes/r-r.utils/meta.yaml index 915d609b7a..38090cd170 100644 --- a/recipes/r-r.utils/meta.yaml +++ b/recipes/r-r.utils/meta.yaml @@ -21,12 +21,12 @@ build: # Suggests: digest (>= 0.6.10) requirements: build: - - r + - r-base - r-r.methodss3 >=1.7.1 - r-r.oo >=1.20.0 run: - - r + - r-base - r-r.methodss3 >=1.7.1 - r-r.oo >=1.20.0 diff --git a/recipes/r-rBLAST/meta.yaml b/recipes/r-rBLAST/meta.yaml index ba16408a2c..28eacddb21 100644 --- a/recipes/r-rBLAST/meta.yaml +++ b/recipes/r-rBLAST/meta.yaml @@ -12,10 +12,10 @@ build: - lib/ requirements: build: - - r + - r-base - bioconductor-biostrings run: - - r + - r-base - bioconductor-biostrings - blast test: diff --git a/recipes/r-rainbow/meta.yaml b/recipes/r-rainbow/meta.yaml index 712df2b0be..57d7240a96 100644 --- a/recipes/r-rainbow/meta.yaml +++ b/recipes/r-rainbow/meta.yaml @@ -32,7 +32,7 @@ build: # Suggests: forecast requirements: build: - - r + - r-base - r-mass # [not win] - r-cluster # [not win] - r-colorspace @@ -41,7 +41,7 @@ requirements: - r-pcapp run: - - r + - r-base - r-mass # [not win] - r-cluster # [not win] - r-colorspace diff --git a/recipes/r-rcircos/1.1.3/meta.yaml b/recipes/r-rcircos/1.1.3/meta.yaml index b8b85d0262..5f498f48d0 100644 --- a/recipes/r-rcircos/1.1.3/meta.yaml +++ b/recipes/r-rcircos/1.1.3/meta.yaml @@ -32,10 +32,10 @@ build: requirements: build: - - r + - r-base run: - - r + - r-base test: commands: diff --git a/recipes/r-rcircos/meta.yaml b/recipes/r-rcircos/meta.yaml index 3555b55f2b..09b30b2b6d 100644 --- a/recipes/r-rcircos/meta.yaml +++ b/recipes/r-rcircos/meta.yaml @@ -23,10 +23,10 @@ build: requirements: build: - - r + - r-base run: - - r + - r-base test: commands: diff --git a/recipes/r-rcppparallel/meta.yaml b/recipes/r-rcppparallel/meta.yaml index fa0b8a7a4f..2d2deadb46 100644 --- a/recipes/r-rcppparallel/meta.yaml +++ b/recipes/r-rcppparallel/meta.yaml @@ -19,10 +19,10 @@ requirements: - r-bh >=1.60.0_1 - gcc # [linux] - llvm # [osx] - - r + - r-base run: - - r + - r-base - r-bh >=1.60.0_1 - libgcc # [linux] diff --git a/recipes/r-readbrukerflexdata/meta.yaml b/recipes/r-readbrukerflexdata/meta.yaml index 215291315b..ce7c524aa2 100644 --- a/recipes/r-readbrukerflexdata/meta.yaml +++ b/recipes/r-readbrukerflexdata/meta.yaml @@ -21,10 +21,10 @@ build: requirements: build: - - r + - r-base run: - - r + - r-base test: commands: diff --git a/recipes/r-readmzxmldata/meta.yaml b/recipes/r-readmzxmldata/meta.yaml index 080d99030a..7704f350ca 100644 --- a/recipes/r-readmzxmldata/meta.yaml +++ b/recipes/r-readmzxmldata/meta.yaml @@ -22,13 +22,13 @@ build: requirements: build: - - r + - r-base - r-xml - r-base64enc - r-digest run: - - r + - r-base - r-xml - r-base64enc - r-digest diff --git a/recipes/r-readr/meta.yaml b/recipes/r-readr/meta.yaml index d4e24d6826..41aac43be8 100644 --- a/recipes/r-readr/meta.yaml +++ b/recipes/r-readr/meta.yaml @@ -21,7 +21,7 @@ build: # Suggests: testthat, knitr, rmarkdown, stringi requirements: build: - - r + - r-base - r-bh - r-rcpp - r-curl @@ -29,7 +29,7 @@ requirements: - llvm # [osx] run: - - r + - r-base - r-bh - r-rcpp - r-curl diff --git a/recipes/r-relaimpo/meta.yaml b/recipes/r-relaimpo/meta.yaml index dd0cbf20f5..00715fe47b 100644 --- a/recipes/r-relaimpo/meta.yaml +++ b/recipes/r-relaimpo/meta.yaml @@ -21,7 +21,7 @@ build: requirements: build: - - r + - r-base - r-mass - r-boot - r-corpcor @@ -29,7 +29,7 @@ requirements: - r-survey run: - - r + - r-base - r-mass - r-boot - r-corpcor diff --git a/recipes/r-rfoc/meta.yaml b/recipes/r-rfoc/meta.yaml index 403496988b..d548377283 100644 --- a/recipes/r-rfoc/meta.yaml +++ b/recipes/r-rfoc/meta.yaml @@ -15,14 +15,14 @@ build: - lib/ requirements: build: - - r + - r-base - r-geomap - r-mass - r-rpmg - r-rseis - r-splancs run: - - r + - r-base - r-geomap - r-mass - r-rpmg diff --git a/recipes/r-rgraphics/meta.yaml b/recipes/r-rgraphics/meta.yaml index 6af1aa8d00..dc4856ef26 100644 --- a/recipes/r-rgraphics/meta.yaml +++ b/recipes/r-rgraphics/meta.yaml @@ -34,12 +34,12 @@ build: # Suggests: agricolae, animation, CircStats, circular, cluster, colorspace, diagram, dichromat, gplots, graph, gridBase, gridExtra, gridSVG, grImport, gWidgets, gWidgetsRGtk2, hexbin, Hmisc, hyperdraw, hypergraph, igraph, iplots, ipred, latticeExtra, mapdata, maps, maptools, MASS, misc3d, munsell, network, openair, oz, party, pixmap, playwith, plotrix, pmg, png, quantmod, raster, Rcmdr, RColorBrewer, rgdal, rggobi, rgl, RGraphics, Rgraphviz, scatterplot3d, soiltexture, sp, SVGAnnotation, symbols, TeachingDemos, tools, vcd, vcdExtra, venneuler, vrmlgen, XML requirements: build: - - r + - r-base - r-ggplot2 - r-lattice run: - - r + - r-base - r-ggplot2 - r-lattice diff --git a/recipes/r-rmarkdown/meta.yaml b/recipes/r-rmarkdown/meta.yaml index 5b3be03dd5..f3a37a3a38 100644 --- a/recipes/r-rmarkdown/meta.yaml +++ b/recipes/r-rmarkdown/meta.yaml @@ -16,14 +16,14 @@ build: # Suggests: shiny (>= 0.11), testthat, digest requirements: build: - - r + - r-base - r-catools - r-htmltools >=0.2.4 - r-knitr >=1.12.3 - r-yaml >=2.1.5 run: - - r + - r-base - r-catools - r-htmltools >=0.2.4 - r-knitr >=1.12.3 diff --git a/recipes/r-rniftyreg/meta.yaml b/recipes/r-rniftyreg/meta.yaml index 1346faf9e8..ca95394de6 100644 --- a/recipes/r-rniftyreg/meta.yaml +++ b/recipes/r-rniftyreg/meta.yaml @@ -18,14 +18,14 @@ build: requirements: build: - - r + - r-base - r-rcpp - r-rcppeigen - r-ore - gcc # [not win] run: - - r + - r-base - r-rcpp - r-rcppeigen - r-ore diff --git a/recipes/r-robustrankaggreg/meta.yaml b/recipes/r-robustrankaggreg/meta.yaml index 091c3921d3..0a8107aaf6 100644 --- a/recipes/r-robustrankaggreg/meta.yaml +++ b/recipes/r-robustrankaggreg/meta.yaml @@ -16,12 +16,12 @@ build: requirements: build: - - r + - r-base - gcc # [linux] - llvm # [osx] run: - - r + - r-base - libgcc # [linux] test: diff --git a/recipes/r-rocr/meta.yaml b/recipes/r-rocr/meta.yaml index 73813fac54..182dc89373 100644 --- a/recipes/r-rocr/meta.yaml +++ b/recipes/r-rocr/meta.yaml @@ -21,7 +21,7 @@ build: requirements: build: - - r + - r-base - r-gplots run: diff --git a/recipes/r-rpmg/meta.yaml b/recipes/r-rpmg/meta.yaml index 4768ca60fd..5c2a329afe 100644 --- a/recipes/r-rpmg/meta.yaml +++ b/recipes/r-rpmg/meta.yaml @@ -16,9 +16,9 @@ build: - lib/ requirements: build: - - r + - r-base run: - - r + - r-base test: commands: - $R -e "library('RPMG')" # [not win] diff --git a/recipes/r-rrcov/meta.yaml b/recipes/r-rrcov/meta.yaml index 81342c2fb7..e21f1039c4 100644 --- a/recipes/r-rrcov/meta.yaml +++ b/recipes/r-rrcov/meta.yaml @@ -16,7 +16,7 @@ build: - lib/ requirements: build: - - r + - r-base - r-cluster - r-lattice - r-mvtnorm @@ -26,7 +26,7 @@ requirements: - {{native}}toolchain # [win] - gcc # [not win] run: - - r + - r-base - r-cluster - r-lattice - r-mvtnorm diff --git a/recipes/r-rseis/meta.yaml b/recipes/r-rseis/meta.yaml index 9aed07dab5..ae220b230f 100644 --- a/recipes/r-rseis/meta.yaml +++ b/recipes/r-rseis/meta.yaml @@ -16,14 +16,14 @@ build: - lib/ requirements: build: - - r + - r-base - r-rpmg - r-rwave - posix # [win] - {{native}}toolchain # [win] - gcc # [not win] run: - - r + - r-base - r-rpmg - r-rwave test: diff --git a/recipes/r-rsm/meta.yaml b/recipes/r-rsm/meta.yaml index 05d5ef64f0..4ff61c493f 100644 --- a/recipes/r-rsm/meta.yaml +++ b/recipes/r-rsm/meta.yaml @@ -31,10 +31,10 @@ build: # Suggests: Vdgraph, conf.design, DoE.base, FrF2 requirements: build: - - r + - r-base run: - - r + - r-base test: commands: diff --git a/recipes/r-rsolnp/meta.yaml b/recipes/r-rsolnp/meta.yaml index 3d45235446..be549922b6 100644 --- a/recipes/r-rsolnp/meta.yaml +++ b/recipes/r-rsolnp/meta.yaml @@ -20,11 +20,11 @@ build: requirements: build: - - r + - r-base - r-truncnorm run: - - r + - r-base - r-truncnorm test: diff --git a/recipes/r-runit/meta.yaml b/recipes/r-runit/meta.yaml index 9e0e8725ca..d6b362eea8 100644 --- a/recipes/r-runit/meta.yaml +++ b/recipes/r-runit/meta.yaml @@ -31,10 +31,10 @@ build: # Suggests: XML (>= 3.1.0) requirements: build: - - r + - r-base run: - - r + - r-base test: commands: diff --git a/recipes/r-rwave/meta.yaml b/recipes/r-rwave/meta.yaml index 873fc65db9..e226a7c02c 100644 --- a/recipes/r-rwave/meta.yaml +++ b/recipes/r-rwave/meta.yaml @@ -16,12 +16,12 @@ build: - lib/ requirements: build: - - r + - r-base - posix # [win] - {{native}}toolchain # [win] - gcc # [not win] run: - - r + - r-base test: commands: - $R -e "library('Rwave')" # [not win] diff --git a/recipes/r-sartools/1.2.0/meta.yaml b/recipes/r-sartools/1.2.0/meta.yaml index 9ed158cce7..0867c78d22 100644 --- a/recipes/r-sartools/1.2.0/meta.yaml +++ b/recipes/r-sartools/1.2.0/meta.yaml @@ -19,13 +19,13 @@ build: # Suggests: parallel requirements: build: - - r + - r-base - r-knitr - bioconductor-deseq2 - bioconductor-edger run: - - r + - r-base - r-knitr - bioconductor-deseq2 - bioconductor-edger diff --git a/recipes/r-sartools/1.3.2/meta.yaml b/recipes/r-sartools/1.3.2/meta.yaml index 6d31e61727..1c330718b3 100644 --- a/recipes/r-sartools/1.3.2/meta.yaml +++ b/recipes/r-sartools/1.3.2/meta.yaml @@ -19,13 +19,13 @@ build: # Suggests: parallel requirements: build: - - r + - r-base - r-knitr - bioconductor-deseq2 - bioconductor-edger run: - - r + - r-base - r-knitr - bioconductor-deseq2 - bioconductor-edger diff --git a/recipes/r-scales/meta.yaml b/recipes/r-scales/meta.yaml index f6e2b5141f..a165bde86c 100644 --- a/recipes/r-scales/meta.yaml +++ b/recipes/r-scales/meta.yaml @@ -35,7 +35,7 @@ build: # Suggests: testthat (>= 0.8), covr, hms requirements: build: - - r + - r-base - r-rcolorbrewer - r-rcpp - r-dichromat @@ -47,7 +47,7 @@ requirements: - gcc # [not win] run: - - r + - r-base - r-rcolorbrewer - r-rcpp - r-dichromat diff --git a/recipes/r-sendmailr/meta.yaml b/recipes/r-sendmailr/meta.yaml index be54b9e5ce..aaafdc709c 100644 --- a/recipes/r-sendmailr/meta.yaml +++ b/recipes/r-sendmailr/meta.yaml @@ -21,11 +21,11 @@ build: requirements: build: - - r + - r-base - r-base64enc run: - - r + - r-base - r-base64enc test: diff --git a/recipes/r-seqinr/meta.yaml b/recipes/r-seqinr/meta.yaml index 468016eb03..0eb3750db5 100644 --- a/recipes/r-seqinr/meta.yaml +++ b/recipes/r-seqinr/meta.yaml @@ -31,11 +31,11 @@ build: # Suggests: segmented requirements: build: - - r + - r-base - r-ade4 run: - - r + - r-base - r-ade4 test: diff --git a/recipes/r-shape/meta.yaml b/recipes/r-shape/meta.yaml index 50859248f5..0991eff6ee 100644 --- a/recipes/r-shape/meta.yaml +++ b/recipes/r-shape/meta.yaml @@ -31,10 +31,10 @@ build: requirements: build: - - r + - r-base run: - - r + - r-base test: commands: diff --git a/recipes/r-signal/meta.yaml b/recipes/r-signal/meta.yaml index 5e6df0b6cb..a85bc69c54 100644 --- a/recipes/r-signal/meta.yaml +++ b/recipes/r-signal/meta.yaml @@ -32,12 +32,12 @@ build: # Suggests: pracma requirements: build: - - r + - r-base - r-mass # [not win] - gcc # [not win] run: - - r + - r-base - r-mass # [not win] - libgcc # [not win] diff --git a/recipes/r-skellam/meta.yaml b/recipes/r-skellam/meta.yaml index f99288c566..ea8ee4b317 100644 --- a/recipes/r-skellam/meta.yaml +++ b/recipes/r-skellam/meta.yaml @@ -19,11 +19,11 @@ build: # Suggests: knitr, VGAM requirements: build: - - r + - r-base - gcc # [not win] run: - - r + - r-base - libgcc # [not win] test: diff --git a/recipes/r-sleuth/meta.yaml b/recipes/r-sleuth/meta.yaml index 0e145fc69b..3fc05f72ff 100644 --- a/recipes/r-sleuth/meta.yaml +++ b/recipes/r-sleuth/meta.yaml @@ -10,7 +10,7 @@ build: - lib/ requirements: build: - - r + - r-base - bioconductor-rhdf5 - r-ggplot2 - r-dplyr @@ -18,7 +18,7 @@ requirements: - r-shiny - r-data.table run: - - r + - r-base - bioconductor-rhdf5 - r-ggplot2 - r-dplyr diff --git a/recipes/r-snow/meta.yaml b/recipes/r-snow/meta.yaml index 20488a0ed4..a970e773d2 100644 --- a/recipes/r-snow/meta.yaml +++ b/recipes/r-snow/meta.yaml @@ -32,10 +32,10 @@ build: # Suggests: Rmpi,rlecuyer,nws requirements: build: - - r + - r-base run: - - r + - r-base test: commands: diff --git a/recipes/r-snowfall/meta.yaml b/recipes/r-snowfall/meta.yaml index 6adb6b3c53..adde732af7 100644 --- a/recipes/r-snowfall/meta.yaml +++ b/recipes/r-snowfall/meta.yaml @@ -31,13 +31,13 @@ build: # Suggests: Rmpi requirements: build: - - r + - r-base - r-snow - gcc # [linux] - llvm # [osx] run: - - r + - r-base - r-snow test: diff --git a/recipes/r-soap-nmr/meta.yaml b/recipes/r-soap-nmr/meta.yaml index dbdc6348ce..9f93aa4473 100644 --- a/recipes/r-soap-nmr/meta.yaml +++ b/recipes/r-soap-nmr/meta.yaml @@ -12,7 +12,7 @@ build: - lib/ requirements: build: - - r + - r-base - r-matrix - r-ptw - r-ggplot2 @@ -20,7 +20,7 @@ requirements: - r-matrixstats - r-reshape2 run: - - r + - r-base - r-matrix - r-ptw - r-ggplot2 diff --git a/recipes/r-sparql/meta.yaml b/recipes/r-sparql/meta.yaml index 7412afb826..cfc585db5f 100644 --- a/recipes/r-sparql/meta.yaml +++ b/recipes/r-sparql/meta.yaml @@ -16,11 +16,11 @@ build: - lib/ requirements: build: - - r + - r-base - r-rcurl - r-xml run: - - r + - r-base - r-rcurl - r-xml test: diff --git a/recipes/r-spdep/meta.yaml b/recipes/r-spdep/meta.yaml index 924705c44b..8c60df5a88 100644 --- a/recipes/r-spdep/meta.yaml +++ b/recipes/r-spdep/meta.yaml @@ -18,7 +18,7 @@ build: # Suggests: parallel, spam(>= 0.13-1), RANN, rgeos, RColorBrewer, lattice, xtable, maptools (>= 0.5-4), foreign, igraph, knitr requirements: build: - - r + - r-base - r-learnbayes - r-mass - r-matrix >=1.0.12 @@ -32,7 +32,7 @@ requirements: - llvm # [osx] run: - - r + - r-base - r-learnbayes - r-mass - r-matrix >=1.0.12 diff --git a/recipes/r-spp/meta.yaml b/recipes/r-spp/meta.yaml index 20fe08c104..c52f9d977d 100644 --- a/recipes/r-spp/meta.yaml +++ b/recipes/r-spp/meta.yaml @@ -18,7 +18,7 @@ build: requirements: build: - - r + - r-base - boost {{CONDA_BOOST}}* - r-catools - bioconductor-rsamtools @@ -28,7 +28,7 @@ requirements: - bzip2 run: - - r + - r-base - boost {{CONDA_BOOST}}* - r-catools - bioconductor-rsamtools diff --git a/recipes/r-survey/meta.yaml b/recipes/r-survey/meta.yaml index 1daccf6dfe..ee79e39a73 100644 --- a/recipes/r-survey/meta.yaml +++ b/recipes/r-survey/meta.yaml @@ -20,13 +20,13 @@ build: # Suggests: foreign, MASS, KernSmooth, hexbin, mitools, RSQLite, RODBC, quantreg, parallel, CompQuadForm, DBI requirements: build: - - r + - r-base - r-matrix - r-lattice - r-survival run: - - r + - r-base - r-matrix - r-lattice - r-survival diff --git a/recipes/r-svdialogs/meta.yaml b/recipes/r-svdialogs/meta.yaml index d66518ed76..e8befdbafc 100644 --- a/recipes/r-svdialogs/meta.yaml +++ b/recipes/r-svdialogs/meta.yaml @@ -32,11 +32,11 @@ build: requirements: build: - - r + - r-base - r-svgui >=0.9_52 run: - - r + - r-base - r-svgui >=0.9_52 test: diff --git a/recipes/r-svgui/meta.yaml b/recipes/r-svgui/meta.yaml index a800770a0a..4ca4517f37 100644 --- a/recipes/r-svgui/meta.yaml +++ b/recipes/r-svgui/meta.yaml @@ -32,10 +32,10 @@ build: requirements: build: - - r + - r-base run: - - r + - r-base test: commands: diff --git a/recipes/r-tfmpvalue/meta.yaml b/recipes/r-tfmpvalue/meta.yaml index 062e6cc501..0953106a13 100644 --- a/recipes/r-tfmpvalue/meta.yaml +++ b/recipes/r-tfmpvalue/meta.yaml @@ -22,7 +22,7 @@ requirements: - llvm # [osx] run: - - r + - r-base - r-rcpp - libgcc # [not osx] diff --git a/recipes/r-tiff/meta.yaml b/recipes/r-tiff/meta.yaml index 85eb25e6d1..bfaff5b9df 100644 --- a/recipes/r-tiff/meta.yaml +++ b/recipes/r-tiff/meta.yaml @@ -17,13 +17,13 @@ build: requirements: build: - - r + - r-base - libtiff - jpeg - gcc # [not win] run: - - r + - r-base - libgcc # [not win] - libtiff - jpeg diff --git a/recipes/r-truncnorm/meta.yaml b/recipes/r-truncnorm/meta.yaml index 33092e4760..7573c72ea6 100644 --- a/recipes/r-truncnorm/meta.yaml +++ b/recipes/r-truncnorm/meta.yaml @@ -21,10 +21,10 @@ build: # Suggests: digest (>= 0.6.10), Cairo (>= 1.5-9), R.rsp (>= 0.30.0) requirements: build: - - r + - r-base run: - - r + - r-base test: commands: diff --git a/recipes/r-upsetr/meta.yaml b/recipes/r-upsetr/meta.yaml index 83b0e496e7..396a298d2c 100644 --- a/recipes/r-upsetr/meta.yaml +++ b/recipes/r-upsetr/meta.yaml @@ -21,13 +21,13 @@ build: # Suggests: knitr requirements: build: - - r + - r-base - r-ggplot2 - r-gridextra - r-plyr run: - - r + - r-base - r-ggplot2 - r-gridextra - r-plyr diff --git a/recipes/r-vegan/2.3_0/meta.yaml b/recipes/r-vegan/2.3_0/meta.yaml index 3dab681e46..08d4534e6f 100644 --- a/recipes/r-vegan/2.3_0/meta.yaml +++ b/recipes/r-vegan/2.3_0/meta.yaml @@ -21,7 +21,7 @@ build: # Suggests: parallel, tcltk requirements: build: - - r + - r-base - r-mass # [not win] - r-cluster # [not win] - r-lattice # [not win] @@ -30,7 +30,7 @@ requirements: - gcc # [not win] run: - - r + - r-base - r-mass # [not win] - r-cluster # [not win] - r-lattice # [not win] diff --git a/recipes/r-vegan/2.3_3/meta.yaml b/recipes/r-vegan/2.3_3/meta.yaml index e457f6575c..99b3b8bce6 100644 --- a/recipes/r-vegan/2.3_3/meta.yaml +++ b/recipes/r-vegan/2.3_3/meta.yaml @@ -31,7 +31,7 @@ build: # Suggests: parallel, tcltk requirements: build: - - r + - r-base - r-mass # [not win] - r-cluster # [not win] - r-lattice # [not win] @@ -40,7 +40,7 @@ requirements: - gcc # [not win] run: - - r + - r-base - r-mass # [not win] - r-cluster # [not win] - r-lattice # [not win] diff --git a/recipes/r-venndiagram/meta.yaml b/recipes/r-venndiagram/meta.yaml index 80d1f3d3a5..0232455a9c 100644 --- a/recipes/r-venndiagram/meta.yaml +++ b/recipes/r-venndiagram/meta.yaml @@ -30,11 +30,11 @@ build: # Suggests: testthat requirements: build: - - r + - r-base - r-futile.logger run: - - r + - r-base - r-futile.logger test: diff --git a/recipes/r-viridis/meta.yaml b/recipes/r-viridis/meta.yaml index 8936630439..c9c91d9e45 100644 --- a/recipes/r-viridis/meta.yaml +++ b/recipes/r-viridis/meta.yaml @@ -17,12 +17,12 @@ build: # Suggests: hexbin (>= 1.27.0), scales, MASS, knitr, dichromat, colorspace, rasterVis, httr, mapproj requirements: build: - - r + - r-base - r-ggplot2 >=1.0.1 - r-gridextra run: - - r + - r-base - r-ggplot2 >=1.0.1 - r-gridextra diff --git a/recipes/r-wasabi/meta.yaml b/recipes/r-wasabi/meta.yaml index c3357a8697..4570974a7e 100644 --- a/recipes/r-wasabi/meta.yaml +++ b/recipes/r-wasabi/meta.yaml @@ -12,12 +12,12 @@ build: - lib/ requirements: build: - - r + - r-base - bioconductor-rhdf5 - r-data.table - r-rjson run: - - r + - r-base - bioconductor-rhdf5 - r-data.table - r-rjson diff --git a/recipes/r-wrassp/meta.yaml b/recipes/r-wrassp/meta.yaml index 0074226856..d6688a9835 100644 --- a/recipes/r-wrassp/meta.yaml +++ b/recipes/r-wrassp/meta.yaml @@ -18,13 +18,13 @@ build: # Suggests: compare(>= 0.2.4), rmarkdown, knitr, testthat(>= 0.7.1) requirements: build: - - r + - r-base - posix # [win] - {{native}}toolchain # [win] - gcc # [not win] run: - - r + - r-base - libgcc # [linux] test: diff --git a/recipes/r-writexls/meta.yaml b/recipes/r-writexls/meta.yaml index 2686e97814..704b87cfec 100644 --- a/recipes/r-writexls/meta.yaml +++ b/recipes/r-writexls/meta.yaml @@ -32,10 +32,10 @@ build: requirements: build: - - r + - r-base run: - - r + - r-base test: commands: diff --git a/recipes/r-xmlrpc/meta.yaml b/recipes/r-xmlrpc/meta.yaml index 83c74f0d0f..6ce4d135d7 100644 --- a/recipes/r-xmlrpc/meta.yaml +++ b/recipes/r-xmlrpc/meta.yaml @@ -30,12 +30,12 @@ build: # Suggests: parallel requirements: build: - - r + - r-base - r-rcurl - r-xml run: - - r + - r-base - r-rcurl - r-xml diff --git a/recipes/r-xnomial/meta.yaml b/recipes/r-xnomial/meta.yaml index 29444ff54c..8a435aee35 100644 --- a/recipes/r-xnomial/meta.yaml +++ b/recipes/r-xnomial/meta.yaml @@ -15,9 +15,9 @@ build: requirements: build: - - r + - r-base run: - - r + - r-base test: commands: From 3f266029d8f80c5a832848a6538569693eb2a035 Mon Sep 17 00:00:00 2001 From: Bjoern Gruening Date: Sat, 3 Jun 2017 21:05:38 +0200 Subject: [PATCH 015/116] change r to r-base --- recipes/bioconductor-affy/meta.yaml | 4 ++-- recipes/bioconductor-affyio/meta.yaml | 4 ++-- recipes/bioconductor-alpine/meta.yaml | 4 ++-- recipes/bioconductor-annotate/meta.yaml | 4 ++-- recipes/bioconductor-annotationforge/meta.yaml | 4 ++-- recipes/bioconductor-annotationhub/meta.yaml | 4 ++-- recipes/bioconductor-aroma.light/meta.yaml | 4 ++-- recipes/bioconductor-ballgown/meta.yaml | 4 ++-- recipes/bioconductor-basic4cseq/meta.yaml | 4 ++-- recipes/bioconductor-biocinstaller/meta.yaml | 4 ++-- recipes/bioconductor-biocparallel/meta.yaml | 4 ++-- recipes/bioconductor-biocstyle/meta.yaml | 4 ++-- recipes/bioconductor-biomart/meta.yaml | 4 ++-- recipes/bioconductor-biomformat/meta.yaml | 4 ++-- recipes/bioconductor-bionet/meta.yaml | 4 ++-- recipes/bioconductor-biosigner/meta.yaml | 4 ++-- recipes/bioconductor-biovizbase/meta.yaml | 4 ++-- recipes/bioconductor-bsgenome.celegans.ucsc.ce10/meta.yaml | 4 ++-- recipes/bioconductor-bsgenome.celegans.ucsc.ce6/meta.yaml | 4 ++-- recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm3/meta.yaml | 4 ++-- recipes/bioconductor-bsgenome.ecoli.ncbi.20080805/meta.yaml | 4 ++-- recipes/bioconductor-bsgenome.hsapiens.ucsc.hg19/meta.yaml | 4 ++-- recipes/bioconductor-bsgenome.mmusculus.ucsc.mm10/meta.yaml | 4 ++-- recipes/bioconductor-bsgenome.mmusculus.ucsc.mm9/meta.yaml | 4 ++-- recipes/bioconductor-bubbletree/meta.yaml | 4 ++-- recipes/bioconductor-bumphunter/meta.yaml | 4 ++-- recipes/bioconductor-camera/1.22.0/meta.yaml | 4 ++-- recipes/bioconductor-camera/1.26.0/meta.yaml | 4 ++-- recipes/bioconductor-camera/meta.yaml | 4 ++-- recipes/bioconductor-cardinal/meta.yaml | 4 ++-- recipes/bioconductor-category/meta.yaml | 4 ++-- recipes/bioconductor-cexor/meta.yaml | 4 ++-- recipes/bioconductor-cghbase/meta.yaml | 4 ++-- recipes/bioconductor-cghcall/meta.yaml | 4 ++-- recipes/bioconductor-chicago/meta.yaml | 4 ++-- recipes/bioconductor-chipcomp/meta.yaml | 4 ++-- recipes/bioconductor-chipseeker/meta.yaml | 4 ++-- recipes/bioconductor-clusterprofiler/meta.yaml | 4 ++-- recipes/bioconductor-cn.mops/meta.yaml | 4 ++-- recipes/bioconductor-complexheatmap/meta.yaml | 4 ++-- recipes/bioconductor-csaw/meta.yaml | 4 ++-- recipes/bioconductor-cummerbund/2.12.1/meta.yaml | 4 ++-- recipes/bioconductor-cummerbund/2.8.2/meta.yaml | 4 ++-- recipes/bioconductor-cummerbund/meta.yaml | 4 ++-- recipes/bioconductor-dada2/meta.yaml | 4 ++-- recipes/bioconductor-deepsnv/meta.yaml | 4 ++-- recipes/bioconductor-degreport/meta.yaml | 4 ++-- recipes/bioconductor-deseq/meta.yaml | 4 ++-- recipes/bioconductor-deseq2/1.10.1/meta.yaml | 4 ++-- recipes/bioconductor-dexseq/1.18.4/meta.yaml | 4 ++-- recipes/bioconductor-diffbind/meta.yaml | 4 ++-- recipes/bioconductor-dnacopy/meta.yaml | 4 ++-- recipes/bioconductor-do.db/meta.yaml | 4 ++-- recipes/bioconductor-dose/meta.yaml | 4 ++-- recipes/bioconductor-ebimage/meta.yaml | 4 ++-- recipes/bioconductor-edaseq/meta.yaml | 4 ++-- recipes/bioconductor-edger/3.12.1/meta.yaml | 4 ++-- recipes/bioconductor-ensembldb/meta.yaml | 4 ++-- recipes/bioconductor-fastseg/meta.yaml | 4 ++-- recipes/bioconductor-flowai/meta.yaml | 4 ++-- recipes/bioconductor-flowcore/meta.yaml | 4 ++-- recipes/bioconductor-flowdensity/meta.yaml | 4 ++-- recipes/bioconductor-flowfp/meta.yaml | 4 ++-- recipes/bioconductor-flowviz/meta.yaml | 4 ++-- recipes/bioconductor-fourcseq/meta.yaml | 4 ++-- recipes/bioconductor-gage/meta.yaml | 4 ++-- recipes/bioconductor-gagedata/meta.yaml | 4 ++-- recipes/bioconductor-genebreak/meta.yaml | 4 ++-- recipes/bioconductor-genefilter/meta.yaml | 4 ++-- recipes/bioconductor-genelendatabase/1.6.0/meta.yaml | 4 ++-- recipes/bioconductor-genelendatabase/meta.yaml | 4 ++-- recipes/bioconductor-geneplotter/meta.yaml | 4 ++-- recipes/bioconductor-geoquery/meta.yaml | 4 ++-- recipes/bioconductor-ggbio/meta.yaml | 4 ++-- recipes/bioconductor-ggtree/meta.yaml | 4 ++-- recipes/bioconductor-gosemsim/meta.yaml | 4 ++-- recipes/bioconductor-gostats/meta.yaml | 4 ++-- recipes/bioconductor-gothic/meta.yaml | 4 ++-- recipes/bioconductor-graph/meta.yaml | 4 ++-- recipes/bioconductor-graphite/meta.yaml | 4 ++-- recipes/bioconductor-gseabase/meta.yaml | 4 ++-- recipes/bioconductor-gviz/meta.yaml | 4 ++-- recipes/bioconductor-heatplus/meta.yaml | 4 ++-- recipes/bioconductor-hom.hs.inp.db/meta.yaml | 4 ++-- recipes/bioconductor-ihw/meta.yaml | 4 ++-- recipes/bioconductor-illuminaio/meta.yaml | 4 ++-- recipes/bioconductor-illuminamousev2.db/meta.yaml | 4 ++-- recipes/bioconductor-interactivedisplaybase/meta.yaml | 4 ++-- recipes/bioconductor-iranges/2.4.6/meta.yaml | 4 ++-- recipes/bioconductor-iranges/2.4.7/meta.yaml | 4 ++-- recipes/bioconductor-isomirs/meta.yaml | 4 ++-- recipes/bioconductor-jmosaics/meta.yaml | 4 ++-- recipes/bioconductor-kcsmart/meta.yaml | 4 ++-- recipes/bioconductor-kegg.db/meta.yaml | 4 ++-- recipes/bioconductor-kegggraph/meta.yaml | 4 ++-- recipes/bioconductor-keggrest/meta.yaml | 4 ++-- recipes/bioconductor-limma/3.26.7/meta.yaml | 4 ++-- recipes/bioconductor-limma/3.28.2/meta.yaml | 4 ++-- recipes/bioconductor-limma/3.28.6/meta.yaml | 4 ++-- recipes/bioconductor-lpsymphony/meta.yaml | 4 ++-- recipes/bioconductor-made4/meta.yaml | 4 ++-- recipes/bioconductor-marray/meta.yaml | 4 ++-- recipes/bioconductor-masigpro/meta.yaml | 4 ++-- recipes/bioconductor-medips/meta.yaml | 4 ++-- recipes/bioconductor-metagenomeseq/meta.yaml | 4 ++-- recipes/bioconductor-metams/meta.yaml | 4 ++-- recipes/bioconductor-methylkit/meta.yaml | 4 ++-- recipes/bioconductor-mgug4122a.db/meta.yaml | 4 ++-- recipes/bioconductor-minfi/meta.yaml | 4 ++-- recipes/bioconductor-mmdiff/meta.yaml | 4 ++-- recipes/bioconductor-mosaics/meta.yaml | 4 ++-- recipes/bioconductor-motifbreakr/meta.yaml | 4 ++-- recipes/bioconductor-motifdb/meta.yaml | 4 ++-- recipes/bioconductor-motifstack/meta.yaml | 4 ++-- recipes/bioconductor-motiv/meta.yaml | 4 ++-- recipes/bioconductor-multtest/meta.yaml | 4 ++-- recipes/bioconductor-mzr/meta.yaml | 4 ++-- recipes/bioconductor-noiseq/meta.yaml | 4 ++-- recipes/bioconductor-org.ce.eg.db/meta.yaml | 4 ++-- recipes/bioconductor-org.hs.eg.db/meta.yaml | 4 ++-- recipes/bioconductor-org.mm.eg.db/3.3.0/meta.yaml | 4 ++-- recipes/bioconductor-org.mm.eg.db/meta.yaml | 4 ++-- recipes/bioconductor-organismdbi/meta.yaml | 4 ++-- recipes/bioconductor-pathview/meta.yaml | 4 ++-- recipes/bioconductor-pcamethods/meta.yaml | 4 ++-- recipes/bioconductor-pchicdata/meta.yaml | 4 ++-- recipes/bioconductor-phyloseq/meta.yaml | 4 ++-- recipes/bioconductor-preprocesscore/meta.yaml | 4 ++-- recipes/bioconductor-probamr/meta.yaml | 4 ++-- recipes/bioconductor-protgenerics/meta.yaml | 4 ++-- recipes/bioconductor-qdnaseq.mm10/1.4.0/meta.yaml | 4 ++-- recipes/bioconductor-qdnaseq/meta.yaml | 4 ++-- recipes/bioconductor-rbgl/meta.yaml | 4 ++-- recipes/bioconductor-rcas/meta.yaml | 4 ++-- recipes/bioconductor-rcytoscape/meta.yaml | 4 ++-- recipes/bioconductor-regioner/meta.yaml | 4 ++-- recipes/bioconductor-repitools/meta.yaml | 4 ++-- recipes/bioconductor-rgadem/meta.yaml | 4 ++-- recipes/bioconductor-rgalaxy/meta.yaml | 4 ++-- recipes/bioconductor-rgraphviz/2.13.0/meta.yaml | 4 ++-- recipes/bioconductor-rgraphviz/meta.yaml | 4 ++-- recipes/bioconductor-rhdf5/meta.yaml | 4 ++-- recipes/bioconductor-rhtslib/meta.yaml | 4 ++-- recipes/bioconductor-ringo/meta.yaml | 4 ++-- recipes/bioconductor-rnaseqpower/meta.yaml | 4 ++-- recipes/bioconductor-roar/meta.yaml | 4 ++-- recipes/bioconductor-ropls/1.2.14/meta.yaml | 4 ++-- recipes/bioconductor-ropls/meta.yaml | 4 ++-- recipes/bioconductor-rots/meta.yaml | 4 ++-- recipes/bioconductor-rsamtools/meta.yaml | 4 ++-- recipes/bioconductor-rsubread/meta.yaml | 4 ++-- recipes/bioconductor-s4vectors/0.8.11/meta.yaml | 4 ++-- recipes/bioconductor-seqlogo/meta.yaml | 4 ++-- recipes/bioconductor-shortread/meta.yaml | 4 ++-- recipes/bioconductor-siggenes/meta.yaml | 4 ++-- recipes/bioconductor-sradb/meta.yaml | 4 ++-- recipes/bioconductor-summarizedexperiment/1.0.2/meta.yaml | 4 ++-- recipes/bioconductor-sva/meta.yaml | 4 ++-- recipes/bioconductor-systempiper/meta.yaml | 4 ++-- recipes/bioconductor-topgo/meta.yaml | 4 ++-- recipes/bioconductor-txdb.dmelanogaster.ucsc.dm3.ensgene/meta.yaml | 4 ++-- recipes/bioconductor-txdb.hsapiens.ucsc.hg19.knowngene/meta.yaml | 4 ++-- recipes/bioconductor-txdb.mmusculus.ucsc.mm10.ensgene/meta.yaml | 4 ++-- recipes/bioconductor-tximport/meta.yaml | 4 ++-- recipes/bioconductor-variantannotation/meta.yaml | 4 ++-- recipes/bioconductor-vsn/meta.yaml | 4 ++-- recipes/bioconductor-xcms/1.44.0/meta.yaml | 4 ++-- recipes/bioconductor-xcms/1.46.0/meta.yaml | 4 ++-- recipes/bioconductor-xcms/1.48.0/meta.yaml | 4 ++-- recipes/bioconductor-xcms/meta.yaml | 4 ++-- recipes/bioconductor-zlibbioc/meta.yaml | 4 ++-- 171 files changed, 342 insertions(+), 342 deletions(-) diff --git a/recipes/bioconductor-affy/meta.yaml b/recipes/bioconductor-affy/meta.yaml index 9001c71a59..283483b38c 100644 --- a/recipes/bioconductor-affy/meta.yaml +++ b/recipes/bioconductor-affy/meta.yaml @@ -18,7 +18,7 @@ requirements: - bioconductor-biocinstaller - bioconductor-preprocesscore - bioconductor-zlibbioc - - r + - r-base run: - 'bioconductor-affyio >=1.13.3' - 'bioconductor-biobase >=2.5.5' @@ -26,7 +26,7 @@ requirements: - bioconductor-biocinstaller - bioconductor-preprocesscore - bioconductor-zlibbioc - - r + - r-base test: commands: - '$R -e "library(''affy'')"' diff --git a/recipes/bioconductor-affyio/meta.yaml b/recipes/bioconductor-affyio/meta.yaml index 50e7288a40..2992d805fa 100644 --- a/recipes/bioconductor-affyio/meta.yaml +++ b/recipes/bioconductor-affyio/meta.yaml @@ -13,10 +13,10 @@ build: requirements: build: - bioconductor-zlibbioc - - r + - r-base run: - bioconductor-zlibbioc - - r + - r-base test: commands: - '$R -e "library(''affyio'')"' diff --git a/recipes/bioconductor-alpine/meta.yaml b/recipes/bioconductor-alpine/meta.yaml index 34133269b5..d1dc5e111b 100644 --- a/recipes/bioconductor-alpine/meta.yaml +++ b/recipes/bioconductor-alpine/meta.yaml @@ -23,7 +23,7 @@ requirements: - bioconductor-rsamtools - bioconductor-s4vectors - bioconductor-summarizedexperiment - - r + - r-base - r-speedglm - r-stringr run: @@ -38,7 +38,7 @@ requirements: - bioconductor-rsamtools - bioconductor-s4vectors - bioconductor-summarizedexperiment - - r + - r-base - r-speedglm - r-stringr test: diff --git a/recipes/bioconductor-annotate/meta.yaml b/recipes/bioconductor-annotate/meta.yaml index 21d3c234ea..bb391961f9 100644 --- a/recipes/bioconductor-annotate/meta.yaml +++ b/recipes/bioconductor-annotate/meta.yaml @@ -15,7 +15,7 @@ requirements: - 'bioconductor-annotationdbi >=1.27.5' - bioconductor-biobase - 'bioconductor-biocgenerics >=0.13.8' - - r + - r-base - r-dbi - r-xml - r-xtable @@ -23,7 +23,7 @@ requirements: - 'bioconductor-annotationdbi >=1.27.5' - bioconductor-biobase - 'bioconductor-biocgenerics >=0.13.8' - - r + - r-base - r-dbi - r-xml - r-xtable diff --git a/recipes/bioconductor-annotationforge/meta.yaml b/recipes/bioconductor-annotationforge/meta.yaml index bd49fb4dd3..014881e626 100644 --- a/recipes/bioconductor-annotationforge/meta.yaml +++ b/recipes/bioconductor-annotationforge/meta.yaml @@ -16,7 +16,7 @@ requirements: - 'bioconductor-biobase >=1.17.0' - 'bioconductor-biocgenerics >=0.15.10' - bioconductor-s4vectors - - r + - r-base - r-dbi - r-rsqlite - r-xml @@ -25,7 +25,7 @@ requirements: - 'bioconductor-biobase >=1.17.0' - 'bioconductor-biocgenerics >=0.15.10' - bioconductor-s4vectors - - r + - r-base - r-dbi - r-rsqlite - r-xml diff --git a/recipes/bioconductor-annotationhub/meta.yaml b/recipes/bioconductor-annotationhub/meta.yaml index f302a695d5..008e5ba1c8 100644 --- a/recipes/bioconductor-annotationhub/meta.yaml +++ b/recipes/bioconductor-annotationhub/meta.yaml @@ -17,7 +17,7 @@ requirements: - bioconductor-biocinstaller - bioconductor-interactivedisplaybase - bioconductor-s4vectors - - r + - r-base - r-httr - r-rsqlite run: @@ -26,7 +26,7 @@ requirements: - bioconductor-biocinstaller - bioconductor-interactivedisplaybase - bioconductor-s4vectors - - r + - r-base - r-httr - r-rsqlite test: diff --git a/recipes/bioconductor-aroma.light/meta.yaml b/recipes/bioconductor-aroma.light/meta.yaml index de623da53c..fb83e2165c 100644 --- a/recipes/bioconductor-aroma.light/meta.yaml +++ b/recipes/bioconductor-aroma.light/meta.yaml @@ -15,13 +15,13 @@ build: requirements: build: - - r + - r-base - 'r-matrixstats >=0.50.2' - 'r-r.methodss3 >=1.7.1' - 'r-r.oo >=1.20.0' - 'r-r.utils >=2.4.0' run: - - r + - r-base - 'r-matrixstats >=0.50.2' - 'r-r.methodss3 >=1.7.1' - 'r-r.oo >=1.20.0' diff --git a/recipes/bioconductor-ballgown/meta.yaml b/recipes/bioconductor-ballgown/meta.yaml index e4f4782817..f2c24e86df 100644 --- a/recipes/bioconductor-ballgown/meta.yaml +++ b/recipes/bioconductor-ballgown/meta.yaml @@ -20,7 +20,7 @@ requirements: - bioconductor-rtracklayer - bioconductor-s4vectors - bioconductor-sva - - r + - r-base - r-rcolorbrewer run: - bioconductor-biobase @@ -31,7 +31,7 @@ requirements: - bioconductor-rtracklayer - bioconductor-s4vectors - bioconductor-sva - - r + - r-base - r-rcolorbrewer test: commands: diff --git a/recipes/bioconductor-basic4cseq/meta.yaml b/recipes/bioconductor-basic4cseq/meta.yaml index b61cf875a1..324b36dec1 100644 --- a/recipes/bioconductor-basic4cseq/meta.yaml +++ b/recipes/bioconductor-basic4cseq/meta.yaml @@ -16,7 +16,7 @@ requirements: - bioconductor-bsgenome.ecoli.ncbi.20080805 - bioconductor-genomicalignments - bioconductor-genomicranges - - r + - r-base - r-catools - r-rcircos run: @@ -24,7 +24,7 @@ requirements: - bioconductor-bsgenome.ecoli.ncbi.20080805 - bioconductor-genomicalignments - bioconductor-genomicranges - - r + - r-base - r-catools - r-rcircos test: diff --git a/recipes/bioconductor-biocinstaller/meta.yaml b/recipes/bioconductor-biocinstaller/meta.yaml index 6e37cc68cc..9f4b18756a 100644 --- a/recipes/bioconductor-biocinstaller/meta.yaml +++ b/recipes/bioconductor-biocinstaller/meta.yaml @@ -12,9 +12,9 @@ build: - lib/ requirements: build: - - r + - r-base run: - - r + - r-base test: commands: - '$R -e "library(''BiocInstaller'')"' diff --git a/recipes/bioconductor-biocparallel/meta.yaml b/recipes/bioconductor-biocparallel/meta.yaml index 6fe42a0a69..2daa17a027 100644 --- a/recipes/bioconductor-biocparallel/meta.yaml +++ b/recipes/bioconductor-biocparallel/meta.yaml @@ -12,11 +12,11 @@ build: - lib/ requirements: build: - - r + - r-base - r-futile.logger - r-snow run: - - r + - r-base - r-futile.logger - r-snow test: diff --git a/recipes/bioconductor-biocstyle/meta.yaml b/recipes/bioconductor-biocstyle/meta.yaml index 26b1470aed..74606ba6ba 100644 --- a/recipes/bioconductor-biocstyle/meta.yaml +++ b/recipes/bioconductor-biocstyle/meta.yaml @@ -12,9 +12,9 @@ build: - lib/ requirements: build: - - r + - r-base run: - - r + - r-base test: commands: - '$R -e "library(''BiocStyle'')"' diff --git a/recipes/bioconductor-biomart/meta.yaml b/recipes/bioconductor-biomart/meta.yaml index 9ea2f79906..efc1a59360 100644 --- a/recipes/bioconductor-biomart/meta.yaml +++ b/recipes/bioconductor-biomart/meta.yaml @@ -13,12 +13,12 @@ build: requirements: build: - bioconductor-annotationdbi - - r + - r-base - r-rcurl - r-xml run: - bioconductor-annotationdbi - - r + - r-base - r-rcurl - r-xml test: diff --git a/recipes/bioconductor-biomformat/meta.yaml b/recipes/bioconductor-biomformat/meta.yaml index 9be7272faf..004fa7ef44 100644 --- a/recipes/bioconductor-biomformat/meta.yaml +++ b/recipes/bioconductor-biomformat/meta.yaml @@ -13,12 +13,12 @@ build: requirements: build: - bioconductor-rhdf5 - - r + - r-base - 'r-jsonlite >=0.9.16' - 'r-plyr >=1.8' run: - bioconductor-rhdf5 - - r + - r-base - 'r-jsonlite >=0.9.16' - 'r-plyr >=1.8' test: diff --git a/recipes/bioconductor-bionet/meta.yaml b/recipes/bioconductor-bionet/meta.yaml index 8d6d4c2e37..1699a17b68 100644 --- a/recipes/bioconductor-bionet/meta.yaml +++ b/recipes/bioconductor-bionet/meta.yaml @@ -16,14 +16,14 @@ requirements: - bioconductor-biobase - bioconductor-graph - bioconductor-rbgl - - r + - r-base - r-igraph >=1.0.1 run: - bioconductor-annotationdbi - bioconductor-biobase - bioconductor-graph - bioconductor-rbgl - - r + - r-base - r-igraph >=1.0.1 test: commands: diff --git a/recipes/bioconductor-biosigner/meta.yaml b/recipes/bioconductor-biosigner/meta.yaml index bac5d49146..0692754bb4 100644 --- a/recipes/bioconductor-biosigner/meta.yaml +++ b/recipes/bioconductor-biosigner/meta.yaml @@ -14,13 +14,13 @@ requirements: build: - bioconductor-ropls - bioconductor-biobase - - r + - r-base - r-e1071 - r-randomforest run: - bioconductor-ropls - bioconductor-biobase - - r + - r-base - r-e1071 - r-randomforest test: diff --git a/recipes/bioconductor-biovizbase/meta.yaml b/recipes/bioconductor-biovizbase/meta.yaml index d86e40c3e9..cf1a5d5617 100644 --- a/recipes/bioconductor-biovizbase/meta.yaml +++ b/recipes/bioconductor-biovizbase/meta.yaml @@ -25,7 +25,7 @@ requirements: - 'bioconductor-s4vectors >=0.9.25' - bioconductor-summarizedexperiment - 'bioconductor-variantannotation >=1.11.4' - - r + - r-base - r-dichromat - r-hmisc - r-rcolorbrewer @@ -44,7 +44,7 @@ requirements: - 'bioconductor-s4vectors >=0.9.25' - bioconductor-summarizedexperiment - 'bioconductor-variantannotation >=1.11.4' - - r + - r-base - r-dichromat - r-hmisc - r-rcolorbrewer diff --git a/recipes/bioconductor-bsgenome.celegans.ucsc.ce10/meta.yaml b/recipes/bioconductor-bsgenome.celegans.ucsc.ce10/meta.yaml index 4c191556dc..1b6e74f2d0 100644 --- a/recipes/bioconductor-bsgenome.celegans.ucsc.ce10/meta.yaml +++ b/recipes/bioconductor-bsgenome.celegans.ucsc.ce10/meta.yaml @@ -13,10 +13,10 @@ build: requirements: build: - 'bioconductor-bsgenome >=1.33.5' - - r + - r-base run: - 'bioconductor-bsgenome >=1.33.5' - - r + - r-base test: commands: - '$R -e "library(''BSgenome.Celegans.UCSC.ce10'')"' diff --git a/recipes/bioconductor-bsgenome.celegans.ucsc.ce6/meta.yaml b/recipes/bioconductor-bsgenome.celegans.ucsc.ce6/meta.yaml index c80f48ea53..7f781c66a3 100644 --- a/recipes/bioconductor-bsgenome.celegans.ucsc.ce6/meta.yaml +++ b/recipes/bioconductor-bsgenome.celegans.ucsc.ce6/meta.yaml @@ -16,10 +16,10 @@ build: requirements: build: - bioconductor-bsgenome >=1.33.5 - - r + - r-base run: - bioconductor-bsgenome >=1.33.5 - - r + - r-base test: commands: diff --git a/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm3/meta.yaml b/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm3/meta.yaml index 5c0de7ad38..1af730d498 100644 --- a/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm3/meta.yaml +++ b/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm3/meta.yaml @@ -16,10 +16,10 @@ build: requirements: build: - bioconductor-bsgenome >=1.33.5 - - r + - r-base run: - bioconductor-bsgenome >=1.33.5 - - r + - r-base test: commands: diff --git a/recipes/bioconductor-bsgenome.ecoli.ncbi.20080805/meta.yaml b/recipes/bioconductor-bsgenome.ecoli.ncbi.20080805/meta.yaml index 5a06446c91..96d15324e3 100644 --- a/recipes/bioconductor-bsgenome.ecoli.ncbi.20080805/meta.yaml +++ b/recipes/bioconductor-bsgenome.ecoli.ncbi.20080805/meta.yaml @@ -13,10 +13,10 @@ build: requirements: build: - 'bioconductor-bsgenome >=1.33.5' - - r + - r-base run: - 'bioconductor-bsgenome >=1.33.5' - - r + - r-base test: commands: - '$R -e "library(''BSgenome.Ecoli.NCBI.20080805'')"' diff --git a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg19/meta.yaml b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg19/meta.yaml index bf2b5fb27a..e97314030c 100644 --- a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg19/meta.yaml +++ b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg19/meta.yaml @@ -13,10 +13,10 @@ build: requirements: build: - 'bioconductor-bsgenome >=1.33.5' - - r + - r-base run: - 'bioconductor-bsgenome >=1.33.5' - - r + - r-base test: commands: - '$R -e "library(''BSgenome.Hsapiens.UCSC.hg19'')"' diff --git a/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm10/meta.yaml b/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm10/meta.yaml index cd301ee9fb..283d78b581 100644 --- a/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm10/meta.yaml +++ b/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm10/meta.yaml @@ -13,10 +13,10 @@ build: requirements: build: - 'bioconductor-bsgenome >=1.33.5' - - r + - r-base run: - 'bioconductor-bsgenome >=1.33.5' - - r + - r-base test: commands: - '$R -e "library(''BSgenome.Mmusculus.UCSC.mm10'')"' diff --git a/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm9/meta.yaml b/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm9/meta.yaml index d5d75a4cf1..f29efa944f 100644 --- a/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm9/meta.yaml +++ b/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm9/meta.yaml @@ -13,10 +13,10 @@ build: requirements: build: - 'bioconductor-bsgenome >=1.33.5' - - r + - r-base run: - 'bioconductor-bsgenome >=1.33.5' - - r + - r-base test: commands: - '$R -e "library(''BSgenome.Mmusculus.UCSC.mm9'')"' diff --git a/recipes/bioconductor-bubbletree/meta.yaml b/recipes/bioconductor-bubbletree/meta.yaml index 2b38dc79bc..3c2a206736 100644 --- a/recipes/bioconductor-bubbletree/meta.yaml +++ b/recipes/bioconductor-bubbletree/meta.yaml @@ -19,7 +19,7 @@ requirements: - bioconductor-genomicranges - bioconductor-iranges - bioconductor-limma - - r + - r-base - r-dplyr - r-e1071 - r-ggplot2 @@ -41,7 +41,7 @@ requirements: - bioconductor-genomicranges - bioconductor-iranges - bioconductor-limma - - r + - r-base - r-dplyr - r-e1071 - r-ggplot2 diff --git a/recipes/bioconductor-bumphunter/meta.yaml b/recipes/bioconductor-bumphunter/meta.yaml index cf90837c67..e8f75909a0 100644 --- a/recipes/bioconductor-bumphunter/meta.yaml +++ b/recipes/bioconductor-bumphunter/meta.yaml @@ -20,7 +20,7 @@ requirements: - 'bioconductor-iranges >=2.3.23' - bioconductor-limma - 'bioconductor-s4vectors >=0.9.25' - - r + - r-base - r-dorng - r-foreach - r-iterators @@ -35,7 +35,7 @@ requirements: - 'bioconductor-iranges >=2.3.23' - bioconductor-limma - 'bioconductor-s4vectors >=0.9.25' - - r + - r-base - r-dorng - r-foreach - r-iterators diff --git a/recipes/bioconductor-camera/1.22.0/meta.yaml b/recipes/bioconductor-camera/1.22.0/meta.yaml index 1f75bf85b9..f96c7dde2a 100644 --- a/recipes/bioconductor-camera/1.22.0/meta.yaml +++ b/recipes/bioconductor-camera/1.22.0/meta.yaml @@ -17,7 +17,7 @@ requirements: - bioconductor-graph - bioconductor-rbgl - 'bioconductor-xcms >=1.13.5' - - r + - r-base - r-hmisc - gmp - r-igraph @@ -26,7 +26,7 @@ requirements: - bioconductor-graph - bioconductor-rbgl - 'bioconductor-xcms >=1.13.5' - - r + - r-base - r-hmisc - gmp - r-igraph diff --git a/recipes/bioconductor-camera/1.26.0/meta.yaml b/recipes/bioconductor-camera/1.26.0/meta.yaml index 82c2f90ae9..734e4d9869 100644 --- a/recipes/bioconductor-camera/1.26.0/meta.yaml +++ b/recipes/bioconductor-camera/1.26.0/meta.yaml @@ -17,7 +17,7 @@ requirements: - bioconductor-graph - bioconductor-rbgl - 'bioconductor-xcms >=1.13.5' - - r + - r-base - r-hmisc - gmp - r-igraph @@ -26,7 +26,7 @@ requirements: - bioconductor-graph - bioconductor-rbgl - 'bioconductor-xcms >=1.13.5' - - r + - r-base - r-hmisc - gmp - r-igraph diff --git a/recipes/bioconductor-camera/meta.yaml b/recipes/bioconductor-camera/meta.yaml index 060b24c348..3e9d0acd8e 100644 --- a/recipes/bioconductor-camera/meta.yaml +++ b/recipes/bioconductor-camera/meta.yaml @@ -17,7 +17,7 @@ requirements: - bioconductor-graph - bioconductor-rbgl - 'bioconductor-xcms >=1.13.5' - - r + - r-base - r-hmisc - r-igraph run: @@ -25,7 +25,7 @@ requirements: - bioconductor-graph - bioconductor-rbgl - 'bioconductor-xcms >=1.13.5' - - r + - r-base - r-hmisc - r-igraph test: diff --git a/recipes/bioconductor-cardinal/meta.yaml b/recipes/bioconductor-cardinal/meta.yaml index e4d2f1e157..115c312cf3 100644 --- a/recipes/bioconductor-cardinal/meta.yaml +++ b/recipes/bioconductor-cardinal/meta.yaml @@ -18,7 +18,7 @@ requirements: - bioconductor-biobase - bioconductor-biocgenerics - bioconductor-protgenerics - - r + - r-base - r-irlba - r-signal - r-sp @@ -26,7 +26,7 @@ requirements: - bioconductor-biobase - bioconductor-biocgenerics - bioconductor-protgenerics - - r + - r-base - r-irlba - r-signal - r-sp diff --git a/recipes/bioconductor-category/meta.yaml b/recipes/bioconductor-category/meta.yaml index be52a1221b..5af5d80e16 100644 --- a/recipes/bioconductor-category/meta.yaml +++ b/recipes/bioconductor-category/meta.yaml @@ -20,7 +20,7 @@ requirements: - bioconductor-graph - bioconductor-gseabase - bioconductor-rbgl - - r + - r-base - r-rsqlite run: - bioconductor-annotate @@ -31,7 +31,7 @@ requirements: - bioconductor-graph - bioconductor-gseabase - bioconductor-rbgl - - r + - r-base - r-rsqlite test: commands: diff --git a/recipes/bioconductor-cexor/meta.yaml b/recipes/bioconductor-cexor/meta.yaml index f73243c8bc..5b7d1babae 100644 --- a/recipes/bioconductor-cexor/meta.yaml +++ b/recipes/bioconductor-cexor/meta.yaml @@ -19,7 +19,7 @@ requirements: - bioconductor-rsamtools - bioconductor-rtracklayer - bioconductor-s4vectors - - r + - r-base - r-idr - r-rcolorbrewer run: @@ -30,7 +30,7 @@ requirements: - bioconductor-rsamtools - bioconductor-rtracklayer - bioconductor-s4vectors - - r + - r-base - r-idr - r-rcolorbrewer test: diff --git a/recipes/bioconductor-cghbase/meta.yaml b/recipes/bioconductor-cghbase/meta.yaml index 35cb28e728..12b8ee9b65 100644 --- a/recipes/bioconductor-cghbase/meta.yaml +++ b/recipes/bioconductor-cghbase/meta.yaml @@ -14,11 +14,11 @@ requirements: build: - 'bioconductor-biobase >=2.5.5' - bioconductor-marray - - r + - r-base run: - 'bioconductor-biobase >=2.5.5' - bioconductor-marray - - r + - r-base test: commands: - '$R -e "library(''CGHbase'')"' diff --git a/recipes/bioconductor-cghcall/meta.yaml b/recipes/bioconductor-cghcall/meta.yaml index a7fe690f30..bee8dee0b4 100644 --- a/recipes/bioconductor-cghcall/meta.yaml +++ b/recipes/bioconductor-cghcall/meta.yaml @@ -16,14 +16,14 @@ requirements: - 'bioconductor-cghbase >=1.15.1' - 'bioconductor-dnacopy >=1.6.0' - 'bioconductor-impute >=1.8.0' - - r + - r-base - r-snowfall run: - bioconductor-biobase - 'bioconductor-cghbase >=1.15.1' - 'bioconductor-dnacopy >=1.6.0' - 'bioconductor-impute >=1.8.0' - - r + - r-base - r-snowfall test: commands: diff --git a/recipes/bioconductor-chicago/meta.yaml b/recipes/bioconductor-chicago/meta.yaml index 4121ece4fc..225c6abd42 100644 --- a/recipes/bioconductor-chicago/meta.yaml +++ b/recipes/bioconductor-chicago/meta.yaml @@ -12,13 +12,13 @@ build: - lib/ requirements: build: - - r + - r-base - r-data.table - r-delaporte - r-hmisc - r-matrixstats run: - - r + - r-base - r-data.table - r-delaporte - r-hmisc diff --git a/recipes/bioconductor-chipcomp/meta.yaml b/recipes/bioconductor-chipcomp/meta.yaml index 4216149281..64e0fc6a74 100644 --- a/recipes/bioconductor-chipcomp/meta.yaml +++ b/recipes/bioconductor-chipcomp/meta.yaml @@ -16,7 +16,7 @@ build: requirements: build: - - r + - r-base - bioconductor-genomicranges - bioconductor-iranges - bioconductor-rtracklayer @@ -29,7 +29,7 @@ requirements: - bioconductor-bsgenome.hsapiens.ucsc.hg19 run: - - r + - r-base - bioconductor-genomicranges - bioconductor-iranges - bioconductor-rtracklayer diff --git a/recipes/bioconductor-chipseeker/meta.yaml b/recipes/bioconductor-chipseeker/meta.yaml index f957d97feb..67021afd08 100644 --- a/recipes/bioconductor-chipseeker/meta.yaml +++ b/recipes/bioconductor-chipseeker/meta.yaml @@ -22,7 +22,7 @@ requirements: - bioconductor-rtracklayer - 'bioconductor-s4vectors >=0.9.25' - bioconductor-txdb.hsapiens.ucsc.hg19.knowngene - - r + - r-base - r-dplyr - r-ggplot2 - r-gplots @@ -43,7 +43,7 @@ requirements: - bioconductor-rtracklayer - 'bioconductor-s4vectors >=0.9.25' - bioconductor-txdb.hsapiens.ucsc.hg19.knowngene - - r + - r-base - r-dplyr - r-ggplot2 - r-gplots diff --git a/recipes/bioconductor-clusterprofiler/meta.yaml b/recipes/bioconductor-clusterprofiler/meta.yaml index e27032afe1..e87313c96e 100644 --- a/recipes/bioconductor-clusterprofiler/meta.yaml +++ b/recipes/bioconductor-clusterprofiler/meta.yaml @@ -20,7 +20,7 @@ requirements: - bioconductor-gseabase - bioconductor-qvalue - bioconductor-topgo - - r + - r-base - r-ggplot2 - r-magrittr - r-plyr @@ -34,7 +34,7 @@ requirements: - bioconductor-gseabase - bioconductor-qvalue - bioconductor-topgo - - r + - r-base - r-ggplot2 - r-magrittr - r-plyr diff --git a/recipes/bioconductor-cn.mops/meta.yaml b/recipes/bioconductor-cn.mops/meta.yaml index 1bed5e5be6..3da4f4353a 100644 --- a/recipes/bioconductor-cn.mops/meta.yaml +++ b/recipes/bioconductor-cn.mops/meta.yaml @@ -17,7 +17,7 @@ requirements: - bioconductor-genomicranges - bioconductor-iranges - bioconductor-rsamtools - - r + - r-base - gcc # [linux] - llvm # [osx] run: @@ -26,7 +26,7 @@ requirements: - bioconductor-genomicranges - bioconductor-iranges - bioconductor-rsamtools - - r + - r-base - libgcc # [linux] test: commands: diff --git a/recipes/bioconductor-complexheatmap/meta.yaml b/recipes/bioconductor-complexheatmap/meta.yaml index 8fb58266a1..7114633c15 100644 --- a/recipes/bioconductor-complexheatmap/meta.yaml +++ b/recipes/bioconductor-complexheatmap/meta.yaml @@ -14,7 +14,7 @@ build: - lib/ requirements: build: - - r + - r-base - 'r-circlize >=0.3.1' - r-colorspace - 'r-dendextend >=1.0.1' @@ -22,7 +22,7 @@ requirements: - 'r-globaloptions >=0.0.6' - r-rcolorbrewer run: - - r + - r-base - 'r-circlize >=0.3.1' - r-colorspace - 'r-dendextend >=1.0.1' diff --git a/recipes/bioconductor-csaw/meta.yaml b/recipes/bioconductor-csaw/meta.yaml index e88648977d..7217ceed82 100644 --- a/recipes/bioconductor-csaw/meta.yaml +++ b/recipes/bioconductor-csaw/meta.yaml @@ -24,7 +24,7 @@ requirements: - bioconductor-s4vectors - bioconductor-summarizedexperiment - bioconductor-rhtslib - - r + - r-base run: - bioconductor-annotationdbi - bioconductor-edger @@ -38,7 +38,7 @@ requirements: - bioconductor-s4vectors - bioconductor-summarizedexperiment - bioconductor-rhtslib - - r + - r-base test: commands: - '$R -e "library(''csaw'')"' diff --git a/recipes/bioconductor-cummerbund/2.12.1/meta.yaml b/recipes/bioconductor-cummerbund/2.12.1/meta.yaml index 36496718d5..1fd204a342 100644 --- a/recipes/bioconductor-cummerbund/2.12.1/meta.yaml +++ b/recipes/bioconductor-cummerbund/2.12.1/meta.yaml @@ -18,7 +18,7 @@ requirements: - bioconductor-gviz - bioconductor-rtracklayer - bioconductor-s4vectors - - r + - r-base - r-fastcluster - r-ggplot2 - r-plyr @@ -30,7 +30,7 @@ requirements: - bioconductor-gviz - bioconductor-rtracklayer - bioconductor-s4vectors - - r + - r-base - r-fastcluster - r-ggplot2 - r-plyr diff --git a/recipes/bioconductor-cummerbund/2.8.2/meta.yaml b/recipes/bioconductor-cummerbund/2.8.2/meta.yaml index e2d7e0b95b..3c886aae44 100644 --- a/recipes/bioconductor-cummerbund/2.8.2/meta.yaml +++ b/recipes/bioconductor-cummerbund/2.8.2/meta.yaml @@ -18,7 +18,7 @@ requirements: - bioconductor-gviz - bioconductor-rtracklayer - bioconductor-s4vectors - - r + - r-base - r-fastcluster - r-ggplot2 - r-plyr @@ -30,7 +30,7 @@ requirements: - bioconductor-gviz - bioconductor-rtracklayer - bioconductor-s4vectors - - r + - r-base - r-fastcluster - r-ggplot2 - r-plyr diff --git a/recipes/bioconductor-cummerbund/meta.yaml b/recipes/bioconductor-cummerbund/meta.yaml index 9bef6fd3a5..a14b9d05ef 100644 --- a/recipes/bioconductor-cummerbund/meta.yaml +++ b/recipes/bioconductor-cummerbund/meta.yaml @@ -17,7 +17,7 @@ requirements: - bioconductor-gviz - bioconductor-rtracklayer - 'bioconductor-s4vectors >=0.9.25' - - r + - r-base - r-fastcluster - r-ggplot2 - r-plyr @@ -29,7 +29,7 @@ requirements: - bioconductor-gviz - bioconductor-rtracklayer - 'bioconductor-s4vectors >=0.9.25' - - r + - r-base - r-fastcluster - r-ggplot2 - r-plyr diff --git a/recipes/bioconductor-dada2/meta.yaml b/recipes/bioconductor-dada2/meta.yaml index d4c98361df..3044102e41 100644 --- a/recipes/bioconductor-dada2/meta.yaml +++ b/recipes/bioconductor-dada2/meta.yaml @@ -16,7 +16,7 @@ requirements: build: - 'bioconductor-biostrings >=2.32.1' - 'bioconductor-shortread >=1.24.0' - - r + - r-base - 'r-data.table >=1.9.4' - 'r-ggplot2 >=1.0' - 'r-rcpp >=0.11.2' @@ -27,7 +27,7 @@ requirements: run: - 'bioconductor-biostrings >=2.32.1' - 'bioconductor-shortread >=1.24.0' - - r + - r-base - 'r-data.table >=1.9.4' - 'r-ggplot2 >=1.0' - 'r-rcpp >=0.11.2' diff --git a/recipes/bioconductor-deepsnv/meta.yaml b/recipes/bioconductor-deepsnv/meta.yaml index 16708f3553..1cd0ea2457 100644 --- a/recipes/bioconductor-deepsnv/meta.yaml +++ b/recipes/bioconductor-deepsnv/meta.yaml @@ -18,7 +18,7 @@ requirements: - bioconductor-rhtslib - bioconductor-summarizedexperiment - bioconductor-variantannotation >=1.13.44 - - r + - r-base - r-vgam run: - bioconductor-biostrings @@ -27,7 +27,7 @@ requirements: - bioconductor-rhtslib - bioconductor-summarizedexperiment - bioconductor-variantannotation >=1.13.44 - - r + - r-base - r-vgam test: commands: diff --git a/recipes/bioconductor-degreport/meta.yaml b/recipes/bioconductor-degreport/meta.yaml index d0a1a8c2d0..2d1edaa53a 100644 --- a/recipes/bioconductor-degreport/meta.yaml +++ b/recipes/bioconductor-degreport/meta.yaml @@ -14,13 +14,13 @@ requirements: build: - bioconductor-biocgenerics - bioconductor-edger - - r + - r-base - r-ggplot2 - r-plyr run: - bioconductor-biocgenerics - bioconductor-edger - - r + - r-base - r-ggplot2 - r-plyr test: diff --git a/recipes/bioconductor-deseq/meta.yaml b/recipes/bioconductor-deseq/meta.yaml index fddb9a4147..bb83de79ae 100644 --- a/recipes/bioconductor-deseq/meta.yaml +++ b/recipes/bioconductor-deseq/meta.yaml @@ -16,7 +16,7 @@ requirements: - 'bioconductor-biocgenerics >=0.7.5' - bioconductor-genefilter - bioconductor-geneplotter - - r + - r-base - r-locfit - r-rcolorbrewer run: @@ -24,7 +24,7 @@ requirements: - 'bioconductor-biocgenerics >=0.7.5' - bioconductor-genefilter - bioconductor-geneplotter - - r + - r-base - r-locfit - r-rcolorbrewer test: diff --git a/recipes/bioconductor-deseq2/1.10.1/meta.yaml b/recipes/bioconductor-deseq2/1.10.1/meta.yaml index e01836bb90..af621a1bd9 100644 --- a/recipes/bioconductor-deseq2/1.10.1/meta.yaml +++ b/recipes/bioconductor-deseq2/1.10.1/meta.yaml @@ -21,7 +21,7 @@ requirements: - bioconductor-iranges - bioconductor-s4vectors - 'bioconductor-summarizedexperiment >=0.2.0' - - r + - r-base - r-ggplot2 - r-hmisc - r-locfit @@ -37,7 +37,7 @@ requirements: - bioconductor-iranges - bioconductor-s4vectors - 'bioconductor-summarizedexperiment >=0.2.0' - - r + - r-base - r-ggplot2 - r-hmisc - r-locfit diff --git a/recipes/bioconductor-dexseq/1.18.4/meta.yaml b/recipes/bioconductor-dexseq/1.18.4/meta.yaml index efee167a07..37ab0d7083 100644 --- a/recipes/bioconductor-dexseq/1.18.4/meta.yaml +++ b/recipes/bioconductor-dexseq/1.18.4/meta.yaml @@ -26,7 +26,7 @@ requirements: - bioconductor-rsamtools - bioconductor-s4vectors - bioconductor-summarizedexperiment - - r + - r-base - r-hwriter - r-rcolorbrewer - r-statmod @@ -45,7 +45,7 @@ requirements: - bioconductor-rsamtools - bioconductor-s4vectors - bioconductor-summarizedexperiment - - r + - r-base - r-hwriter - r-rcolorbrewer - r-statmod diff --git a/recipes/bioconductor-diffbind/meta.yaml b/recipes/bioconductor-diffbind/meta.yaml index 909dd7a9f0..2552d2c16d 100644 --- a/recipes/bioconductor-diffbind/meta.yaml +++ b/recipes/bioconductor-diffbind/meta.yaml @@ -30,7 +30,7 @@ requirements: - bioconductor-summarizedexperiment - bioconductor-systempiper - bioconductor-zlibbioc - - r + - r-base - r-amap - r-dplyr - r-gplots @@ -52,7 +52,7 @@ requirements: - bioconductor-summarizedexperiment - bioconductor-systempiper - bioconductor-zlibbioc - - r + - r-base - r-amap - r-dplyr - r-gplots diff --git a/recipes/bioconductor-dnacopy/meta.yaml b/recipes/bioconductor-dnacopy/meta.yaml index 046d5e8872..e5a86d1447 100644 --- a/recipes/bioconductor-dnacopy/meta.yaml +++ b/recipes/bioconductor-dnacopy/meta.yaml @@ -12,10 +12,10 @@ build: - lib/ requirements: build: - - r + - r-base - gcc run: - - r + - r-base test: commands: - '$R -e "library(''DNAcopy'')"' diff --git a/recipes/bioconductor-do.db/meta.yaml b/recipes/bioconductor-do.db/meta.yaml index 1d1368062a..380920b584 100644 --- a/recipes/bioconductor-do.db/meta.yaml +++ b/recipes/bioconductor-do.db/meta.yaml @@ -13,10 +13,10 @@ build: requirements: build: - 'bioconductor-annotationdbi >=1.9.7' - - r + - r-base run: - 'bioconductor-annotationdbi >=1.9.7' - - r + - r-base test: commands: - '$R -e "library(''DO.db'')"' diff --git a/recipes/bioconductor-dose/meta.yaml b/recipes/bioconductor-dose/meta.yaml index 62791575a4..feb46b61b0 100644 --- a/recipes/bioconductor-dose/meta.yaml +++ b/recipes/bioconductor-dose/meta.yaml @@ -16,7 +16,7 @@ requirements: - bioconductor-do.db - bioconductor-gosemsim - bioconductor-qvalue - - r + - r-base - r-ggplot2 - r-igraph - r-plyr @@ -28,7 +28,7 @@ requirements: - bioconductor-do.db - bioconductor-gosemsim - bioconductor-qvalue - - r + - r-base - r-ggplot2 - r-igraph - r-plyr diff --git a/recipes/bioconductor-ebimage/meta.yaml b/recipes/bioconductor-ebimage/meta.yaml index 27d2b77cf5..32362e67be 100644 --- a/recipes/bioconductor-ebimage/meta.yaml +++ b/recipes/bioconductor-ebimage/meta.yaml @@ -15,7 +15,7 @@ build: requirements: build: - 'bioconductor-biocgenerics >=0.7.1' - - r + - r-base - r-abind - r-fftwtools - r-jpeg @@ -24,7 +24,7 @@ requirements: - r-tiff run: - 'bioconductor-biocgenerics >=0.7.1' - - r + - r-base - r-abind - r-fftwtools - r-jpeg diff --git a/recipes/bioconductor-edaseq/meta.yaml b/recipes/bioconductor-edaseq/meta.yaml index cfc108287e..7aef919035 100644 --- a/recipes/bioconductor-edaseq/meta.yaml +++ b/recipes/bioconductor-edaseq/meta.yaml @@ -27,7 +27,7 @@ requirements: - 'bioconductor-iranges >=1.13.9' - 'bioconductor-rsamtools >=1.5.75' - 'bioconductor-shortread >=1.11.42' - - r + - r-base run: - bioconductor-annotationdbi - bioconductor-aroma.light @@ -41,7 +41,7 @@ requirements: - 'bioconductor-iranges >=1.13.9' - 'bioconductor-rsamtools >=1.5.75' - 'bioconductor-shortread >=1.11.42' - - r + - r-base test: commands: diff --git a/recipes/bioconductor-edger/3.12.1/meta.yaml b/recipes/bioconductor-edger/3.12.1/meta.yaml index fe6edc8af2..127f1c2395 100644 --- a/recipes/bioconductor-edger/3.12.1/meta.yaml +++ b/recipes/bioconductor-edger/3.12.1/meta.yaml @@ -13,10 +13,10 @@ build: requirements: build: - bioconductor-limma - - r + - r-base run: - bioconductor-limma - - r + - r-base test: commands: - '$R -e "library(''edgeR'')"' diff --git a/recipes/bioconductor-ensembldb/meta.yaml b/recipes/bioconductor-ensembldb/meta.yaml index 9904287d60..749ee812fd 100644 --- a/recipes/bioconductor-ensembldb/meta.yaml +++ b/recipes/bioconductor-ensembldb/meta.yaml @@ -23,7 +23,7 @@ requirements: - bioconductor-rsamtools - bioconductor-rtracklayer - bioconductor-s4vectors - - r + - r-base - r-dbi - r-rsqlite run: @@ -38,7 +38,7 @@ requirements: - bioconductor-rsamtools - bioconductor-rtracklayer - bioconductor-s4vectors - - r + - r-base - r-dbi - r-rsqlite test: diff --git a/recipes/bioconductor-fastseg/meta.yaml b/recipes/bioconductor-fastseg/meta.yaml index b3d96c45a1..9eca234a01 100644 --- a/recipes/bioconductor-fastseg/meta.yaml +++ b/recipes/bioconductor-fastseg/meta.yaml @@ -17,14 +17,14 @@ requirements: - bioconductor-genomicranges - bioconductor-iranges - bioconductor-s4vectors - - r + - r-base run: - bioconductor-biobase - bioconductor-biocgenerics - bioconductor-genomicranges - bioconductor-iranges - bioconductor-s4vectors - - r + - r-base test: commands: - '$R -e "library(''fastseg'')"' diff --git a/recipes/bioconductor-flowai/meta.yaml b/recipes/bioconductor-flowai/meta.yaml index bd56384914..cc3e4d2fdc 100644 --- a/recipes/bioconductor-flowai/meta.yaml +++ b/recipes/bioconductor-flowai/meta.yaml @@ -13,7 +13,7 @@ build: requirements: build: - bioconductor-flowcore - - r + - r-base - r-changepoint - r-ggplot2 - r-knitr @@ -23,7 +23,7 @@ requirements: - r-scales run: - bioconductor-flowcore - - r + - r-base - r-changepoint - r-ggplot2 - r-knitr diff --git a/recipes/bioconductor-flowcore/meta.yaml b/recipes/bioconductor-flowcore/meta.yaml index ddf67e5e53..97f7aaf699 100644 --- a/recipes/bioconductor-flowcore/meta.yaml +++ b/recipes/bioconductor-flowcore/meta.yaml @@ -15,7 +15,7 @@ requirements: - bioconductor-biobase - 'bioconductor-biocgenerics >=0.1.14' - bioconductor-graph - - r + - r-base - r-corpcor - r-matrixstats - r-rcpp @@ -27,7 +27,7 @@ requirements: - bioconductor-biobase - 'bioconductor-biocgenerics >=0.1.14' - bioconductor-graph - - r + - r-base - r-corpcor - r-matrixstats - r-bh diff --git a/recipes/bioconductor-flowdensity/meta.yaml b/recipes/bioconductor-flowdensity/meta.yaml index b0a8486eaa..8a192333fd 100644 --- a/recipes/bioconductor-flowdensity/meta.yaml +++ b/recipes/bioconductor-flowdensity/meta.yaml @@ -13,14 +13,14 @@ build: requirements: build: - bioconductor-flowcore - - r + - r-base - r-car - r-geomap - r-gplots - r-rfoc run: - bioconductor-flowcore - - r + - r-base - r-car - r-geomap - r-gplots diff --git a/recipes/bioconductor-flowfp/meta.yaml b/recipes/bioconductor-flowfp/meta.yaml index bfd195aa98..ab6c05e8ce 100644 --- a/recipes/bioconductor-flowfp/meta.yaml +++ b/recipes/bioconductor-flowfp/meta.yaml @@ -16,13 +16,13 @@ requirements: - 'bioconductor-biocgenerics >=0.1.6' - bioconductor-flowcore - bioconductor-flowviz - - r + - r-base run: - bioconductor-biobase - 'bioconductor-biocgenerics >=0.1.6' - bioconductor-flowcore - bioconductor-flowviz - - r + - r-base test: commands: - '$R -e "library(''flowFP'')"' diff --git a/recipes/bioconductor-flowviz/meta.yaml b/recipes/bioconductor-flowviz/meta.yaml index a2be0766ec..1e84fa03fe 100644 --- a/recipes/bioconductor-flowviz/meta.yaml +++ b/recipes/bioconductor-flowviz/meta.yaml @@ -14,7 +14,7 @@ requirements: build: - bioconductor-biobase - bioconductor-flowcore - - r + - r-base - r-hexbin - r-idpmisc - r-latticeextra @@ -22,7 +22,7 @@ requirements: run: - bioconductor-biobase - bioconductor-flowcore - - r + - r-base - r-hexbin - r-idpmisc - r-latticeextra diff --git a/recipes/bioconductor-fourcseq/meta.yaml b/recipes/bioconductor-fourcseq/meta.yaml index 9a2a3f8380..6b44959020 100644 --- a/recipes/bioconductor-fourcseq/meta.yaml +++ b/recipes/bioconductor-fourcseq/meta.yaml @@ -21,7 +21,7 @@ requirements: - bioconductor-rsamtools - bioconductor-rtracklayer - bioconductor-summarizedexperiment - - r + - r-base - r-fda - r-ggplot2 - r-gtools @@ -37,7 +37,7 @@ requirements: - bioconductor-rsamtools - bioconductor-rtracklayer - bioconductor-summarizedexperiment - - r + - r-base - r-fda - r-ggplot2 - r-gtools diff --git a/recipes/bioconductor-gage/meta.yaml b/recipes/bioconductor-gage/meta.yaml index ad73ea02ab..f2be2bd72f 100644 --- a/recipes/bioconductor-gage/meta.yaml +++ b/recipes/bioconductor-gage/meta.yaml @@ -16,12 +16,12 @@ requirements: - bioconductor-annotationdbi - bioconductor-graph - bioconductor-keggrest - - r + - r-base run: - bioconductor-annotationdbi - bioconductor-graph - bioconductor-keggrest - - r + - r-base test: commands: - '$R -e "library(''gage'')"' diff --git a/recipes/bioconductor-gagedata/meta.yaml b/recipes/bioconductor-gagedata/meta.yaml index f8970dd94a..47decde094 100644 --- a/recipes/bioconductor-gagedata/meta.yaml +++ b/recipes/bioconductor-gagedata/meta.yaml @@ -12,9 +12,9 @@ build: - lib/ requirements: build: - - r + - r-base run: - - r + - r-base test: commands: - '$R -e "library(''gageData'')"' diff --git a/recipes/bioconductor-genebreak/meta.yaml b/recipes/bioconductor-genebreak/meta.yaml index 26b50da174..3d2f5b2fbe 100644 --- a/recipes/bioconductor-genebreak/meta.yaml +++ b/recipes/bioconductor-genebreak/meta.yaml @@ -16,13 +16,13 @@ requirements: - bioconductor-cghcall - bioconductor-genomicranges - bioconductor-qdnaseq - - r + - r-base run: - bioconductor-cghbase - bioconductor-cghcall - bioconductor-genomicranges - bioconductor-qdnaseq - - r + - r-base test: commands: - '$R -e "library(''GeneBreak'')"' diff --git a/recipes/bioconductor-genefilter/meta.yaml b/recipes/bioconductor-genefilter/meta.yaml index b6f0ead6ab..9c7eecfb5d 100644 --- a/recipes/bioconductor-genefilter/meta.yaml +++ b/recipes/bioconductor-genefilter/meta.yaml @@ -17,14 +17,14 @@ requirements: - bioconductor-annotationdbi - bioconductor-biobase - 'bioconductor-s4vectors >=0.9.42' - - r + - r-base run: - libgcc - bioconductor-annotate - bioconductor-annotationdbi - bioconductor-biobase - 'bioconductor-s4vectors >=0.9.42' - - r + - r-base test: commands: - '$R -e "library(''genefilter'')"' diff --git a/recipes/bioconductor-genelendatabase/1.6.0/meta.yaml b/recipes/bioconductor-genelendatabase/1.6.0/meta.yaml index 8d8ae00665..5ccaefb233 100644 --- a/recipes/bioconductor-genelendatabase/1.6.0/meta.yaml +++ b/recipes/bioconductor-genelendatabase/1.6.0/meta.yaml @@ -15,11 +15,11 @@ requirements: build: - 'bioconductor-genomicfeatures >=1.3.15' - bioconductor-rtracklayer - - r + - r-base run: - 'bioconductor-genomicfeatures >=1.3.15' - bioconductor-rtracklayer - - r + - r-base test: commands: - '$R -e "library(''geneLenDataBase'')"' diff --git a/recipes/bioconductor-genelendatabase/meta.yaml b/recipes/bioconductor-genelendatabase/meta.yaml index bb0eb6ee68..1e1a879894 100644 --- a/recipes/bioconductor-genelendatabase/meta.yaml +++ b/recipes/bioconductor-genelendatabase/meta.yaml @@ -14,11 +14,11 @@ requirements: build: - 'bioconductor-genomicfeatures >=1.3.15' - bioconductor-rtracklayer - - r + - r-base run: - 'bioconductor-genomicfeatures >=1.3.15' - bioconductor-rtracklayer - - r + - r-base test: commands: - '$R -e "library(''geneLenDataBase'')"' diff --git a/recipes/bioconductor-geneplotter/meta.yaml b/recipes/bioconductor-geneplotter/meta.yaml index 5ac813412e..6eba0e08ca 100644 --- a/recipes/bioconductor-geneplotter/meta.yaml +++ b/recipes/bioconductor-geneplotter/meta.yaml @@ -16,14 +16,14 @@ requirements: - bioconductor-annotationdbi - bioconductor-biobase - bioconductor-biocgenerics - - r + - r-base - r-rcolorbrewer run: - bioconductor-annotate - bioconductor-annotationdbi - bioconductor-biobase - bioconductor-biocgenerics - - r + - r-base - r-rcolorbrewer test: commands: diff --git a/recipes/bioconductor-geoquery/meta.yaml b/recipes/bioconductor-geoquery/meta.yaml index a03d3be2fb..6ea101717a 100644 --- a/recipes/bioconductor-geoquery/meta.yaml +++ b/recipes/bioconductor-geoquery/meta.yaml @@ -13,13 +13,13 @@ build: requirements: build: - bioconductor-biobase - - r + - r-base - r-httr - r-rcurl - r-xml run: - bioconductor-biobase - - r + - r-base - r-httr - r-rcurl - r-xml diff --git a/recipes/bioconductor-ggbio/meta.yaml b/recipes/bioconductor-ggbio/meta.yaml index 0b4e3dcfe6..8a427cf32a 100644 --- a/recipes/bioconductor-ggbio/meta.yaml +++ b/recipes/bioconductor-ggbio/meta.yaml @@ -30,7 +30,7 @@ requirements: - 'bioconductor-s4vectors >=0.9.25' - bioconductor-summarizedexperiment - 'bioconductor-variantannotation >=1.11.4' - - r + - r-base - r-ggally - 'r-ggplot2 >=1.0.0' - r-gridextra @@ -57,7 +57,7 @@ requirements: - 'bioconductor-s4vectors >=0.9.25' - bioconductor-summarizedexperiment - 'bioconductor-variantannotation >=1.11.4' - - r + - r-base - r-ggally - 'r-ggplot2 >=1.0.0' - r-gridextra diff --git a/recipes/bioconductor-ggtree/meta.yaml b/recipes/bioconductor-ggtree/meta.yaml index 9fff7ef6ba..0f1d324c01 100644 --- a/recipes/bioconductor-ggtree/meta.yaml +++ b/recipes/bioconductor-ggtree/meta.yaml @@ -12,14 +12,14 @@ build: - lib/ requirements: build: - - r + - r-base - r-ape - 'r-ggplot2 >=2.0.0' - r-jsonlite - r-magrittr - r-tidyr run: - - r + - r-base - r-ape - 'r-ggplot2 >=2.0.0' - r-jsonlite diff --git a/recipes/bioconductor-gosemsim/meta.yaml b/recipes/bioconductor-gosemsim/meta.yaml index f390e58909..e0cd9c049d 100644 --- a/recipes/bioconductor-gosemsim/meta.yaml +++ b/recipes/bioconductor-gosemsim/meta.yaml @@ -14,14 +14,14 @@ requirements: build: - bioconductor-annotationdbi - bioconductor-go.db - - r + - r-base - r-rcpp - gcc # [linux] - llvm # [osx] run: - bioconductor-annotationdbi - bioconductor-go.db - - r + - r-base - r-rcpp - libgcc # [linux] test: diff --git a/recipes/bioconductor-gostats/meta.yaml b/recipes/bioconductor-gostats/meta.yaml index 726204ba85..d235e009b0 100644 --- a/recipes/bioconductor-gostats/meta.yaml +++ b/recipes/bioconductor-gostats/meta.yaml @@ -20,7 +20,7 @@ requirements: - 'bioconductor-go.db >=1.13.0' - 'bioconductor-graph >=1.15.15' - bioconductor-rbgl - - r + - r-base run: - 'bioconductor-annotate >=1.13.2' - 'bioconductor-annotationdbi >=0.0.89' @@ -30,7 +30,7 @@ requirements: - 'bioconductor-go.db >=1.13.0' - 'bioconductor-graph >=1.15.15' - bioconductor-rbgl - - r + - r-base test: commands: - '$R -e "library(''GOstats'')"' diff --git a/recipes/bioconductor-gothic/meta.yaml b/recipes/bioconductor-gothic/meta.yaml index f511de09ac..e72d52c05f 100644 --- a/recipes/bioconductor-gothic/meta.yaml +++ b/recipes/bioconductor-gothic/meta.yaml @@ -21,7 +21,7 @@ requirements: - bioconductor-rtracklayer - 'bioconductor-s4vectors >=0.9.38' - bioconductor-shortread - - r + - r-base - r-data.table - r-ggplot2 run: @@ -34,7 +34,7 @@ requirements: - bioconductor-rtracklayer - 'bioconductor-s4vectors >=0.9.38' - bioconductor-shortread - - r + - r-base - r-data.table - r-ggplot2 test: diff --git a/recipes/bioconductor-graph/meta.yaml b/recipes/bioconductor-graph/meta.yaml index ca829151bf..018846ab30 100644 --- a/recipes/bioconductor-graph/meta.yaml +++ b/recipes/bioconductor-graph/meta.yaml @@ -17,10 +17,10 @@ build: requirements: build: - 'bioconductor-biocgenerics >=0.13.11' - - r + - r-base run: - 'bioconductor-biocgenerics >=0.13.11' - - r + - r-base test: commands: diff --git a/recipes/bioconductor-graphite/meta.yaml b/recipes/bioconductor-graphite/meta.yaml index 6e348fc7b7..512504402e 100644 --- a/recipes/bioconductor-graphite/meta.yaml +++ b/recipes/bioconductor-graphite/meta.yaml @@ -15,13 +15,13 @@ requirements: - bioconductor-annotationdbi - bioconductor-biocgenerics - bioconductor-graph - - r + - r-base - r-rappdirs run: - bioconductor-annotationdbi - bioconductor-biocgenerics - bioconductor-graph - - r + - r-base - r-rappdirs test: commands: diff --git a/recipes/bioconductor-gseabase/meta.yaml b/recipes/bioconductor-gseabase/meta.yaml index 7ce36b5db3..1ed1e0d7b6 100644 --- a/recipes/bioconductor-gseabase/meta.yaml +++ b/recipes/bioconductor-gseabase/meta.yaml @@ -17,7 +17,7 @@ requirements: - 'bioconductor-biobase >=2.17.8' - 'bioconductor-biocgenerics >=0.13.8' - 'bioconductor-graph >=1.37.2' - - r + - r-base - r-xml run: - 'bioconductor-annotate >=1.45.3' @@ -25,7 +25,7 @@ requirements: - 'bioconductor-biobase >=2.17.8' - 'bioconductor-biocgenerics >=0.13.8' - 'bioconductor-graph >=1.37.2' - - r + - r-base - r-xml test: commands: diff --git a/recipes/bioconductor-gviz/meta.yaml b/recipes/bioconductor-gviz/meta.yaml index de16ea0db8..ba0dc797c1 100644 --- a/recipes/bioconductor-gviz/meta.yaml +++ b/recipes/bioconductor-gviz/meta.yaml @@ -28,7 +28,7 @@ requirements: - 'bioconductor-rtracklayer >=1.25.13' - 'bioconductor-s4vectors >=0.9.25' - 'bioconductor-xvector >=0.5.7' - - r + - r-base - 'r-digest >=0.6.8' - 'r-latticeextra >=0.6_26' - 'r-matrixstats >=0.8.14' @@ -50,7 +50,7 @@ requirements: - 'bioconductor-rtracklayer >=1.25.13' - 'bioconductor-s4vectors >=0.9.25' - 'bioconductor-xvector >=0.5.7' - - r + - r-base - 'r-digest >=0.6.8' - 'r-latticeextra >=0.6_26' - 'r-matrixstats >=0.8.14' diff --git a/recipes/bioconductor-heatplus/meta.yaml b/recipes/bioconductor-heatplus/meta.yaml index 2b447fc3f0..281c24d0ff 100644 --- a/recipes/bioconductor-heatplus/meta.yaml +++ b/recipes/bioconductor-heatplus/meta.yaml @@ -12,10 +12,10 @@ build: - lib/ requirements: build: - - r + - r-base - r-rcolorbrewer run: - - r + - r-base - r-rcolorbrewer test: commands: diff --git a/recipes/bioconductor-hom.hs.inp.db/meta.yaml b/recipes/bioconductor-hom.hs.inp.db/meta.yaml index 82a49ee97f..8648f41817 100644 --- a/recipes/bioconductor-hom.hs.inp.db/meta.yaml +++ b/recipes/bioconductor-hom.hs.inp.db/meta.yaml @@ -13,10 +13,10 @@ build: requirements: build: - 'bioconductor-annotationdbi >=1.29.20' - - r + - r-base run: - 'bioconductor-annotationdbi >=1.29.20' - - r + - r-base test: commands: - '$R -e "library(''hom.Hs.inp.db'')"' diff --git a/recipes/bioconductor-ihw/meta.yaml b/recipes/bioconductor-ihw/meta.yaml index 30b13c1e36..0a3defb76a 100644 --- a/recipes/bioconductor-ihw/meta.yaml +++ b/recipes/bioconductor-ihw/meta.yaml @@ -14,13 +14,13 @@ requirements: build: - bioconductor-biocgenerics - bioconductor-lpsymphony - - r + - r-base - r-fdrtool - r-slam run: - bioconductor-biocgenerics - bioconductor-lpsymphony - - r + - r-base - r-fdrtool - r-slam test: diff --git a/recipes/bioconductor-illuminaio/meta.yaml b/recipes/bioconductor-illuminaio/meta.yaml index 12d9996336..0892858415 100644 --- a/recipes/bioconductor-illuminaio/meta.yaml +++ b/recipes/bioconductor-illuminaio/meta.yaml @@ -12,10 +12,10 @@ build: - lib/ requirements: build: - - r + - r-base - r-base64 run: - - r + - r-base - r-base64 test: commands: diff --git a/recipes/bioconductor-illuminamousev2.db/meta.yaml b/recipes/bioconductor-illuminamousev2.db/meta.yaml index 274b51cea4..d2a6d62f9e 100644 --- a/recipes/bioconductor-illuminamousev2.db/meta.yaml +++ b/recipes/bioconductor-illuminamousev2.db/meta.yaml @@ -15,11 +15,11 @@ requirements: build: - 'bioconductor-annotationdbi >=1.29.20' - 'bioconductor-org.mm.eg.db >=3.1.2' - - r + - r-base run: - 'bioconductor-annotationdbi >=1.29.20' - 'bioconductor-org.mm.eg.db >=3.1.2' - - r + - r-base test: commands: - '$R -e "library(''illuminaMousev2.db'')"' diff --git a/recipes/bioconductor-interactivedisplaybase/meta.yaml b/recipes/bioconductor-interactivedisplaybase/meta.yaml index 7cbdb69f69..68749e27c4 100644 --- a/recipes/bioconductor-interactivedisplaybase/meta.yaml +++ b/recipes/bioconductor-interactivedisplaybase/meta.yaml @@ -13,11 +13,11 @@ build: requirements: build: - bioconductor-biocgenerics - - r + - r-base - r-shiny run: - bioconductor-biocgenerics - - r + - r-base - r-shiny test: commands: diff --git a/recipes/bioconductor-iranges/2.4.6/meta.yaml b/recipes/bioconductor-iranges/2.4.6/meta.yaml index 457ebe3c8d..e6acec73dd 100644 --- a/recipes/bioconductor-iranges/2.4.6/meta.yaml +++ b/recipes/bioconductor-iranges/2.4.6/meta.yaml @@ -16,11 +16,11 @@ requirements: build: - 'bioconductor-biocgenerics >=0.15.10' - 'bioconductor-s4vectors >=0.8.4' - - r + - r-base run: - 'bioconductor-biocgenerics >=0.15.10' - 'bioconductor-s4vectors >=0.8.4' - - r + - r-base test: commands: - '$R -e "library(''IRanges'')"' diff --git a/recipes/bioconductor-iranges/2.4.7/meta.yaml b/recipes/bioconductor-iranges/2.4.7/meta.yaml index 080891ccdc..518bef3941 100644 --- a/recipes/bioconductor-iranges/2.4.7/meta.yaml +++ b/recipes/bioconductor-iranges/2.4.7/meta.yaml @@ -14,11 +14,11 @@ requirements: build: - bioconductor-biocgenerics >=0.15.10 - bioconductor-s4vectors >=0.8.4 - - r + - r-base run: - bioconductor-biocgenerics >=0.15.10 - bioconductor-s4vectors >=0.8.4 - - r + - r-base test: commands: - $R -e "library('IRanges')" diff --git a/recipes/bioconductor-isomirs/meta.yaml b/recipes/bioconductor-isomirs/meta.yaml index 74cb583f73..a1294cad58 100644 --- a/recipes/bioconductor-isomirs/meta.yaml +++ b/recipes/bioconductor-isomirs/meta.yaml @@ -18,7 +18,7 @@ requirements: - bioconductor-iranges - bioconductor-s4vectors - 'bioconductor-summarizedexperiment >=0.2.0' - - r + - r-base - r-discriminer - r-dplyr - r-ggally @@ -33,7 +33,7 @@ requirements: - bioconductor-iranges - bioconductor-s4vectors - 'bioconductor-summarizedexperiment >=0.2.0' - - r + - r-base - r-discriminer - r-dplyr - r-ggally diff --git a/recipes/bioconductor-jmosaics/meta.yaml b/recipes/bioconductor-jmosaics/meta.yaml index 81b9a4cf07..f1954b29d5 100644 --- a/recipes/bioconductor-jmosaics/meta.yaml +++ b/recipes/bioconductor-jmosaics/meta.yaml @@ -16,10 +16,10 @@ build: requirements: build: - bioconductor-mosaics - - r + - r-base run: - bioconductor-mosaics - - r + - r-base test: commands: diff --git a/recipes/bioconductor-kcsmart/meta.yaml b/recipes/bioconductor-kcsmart/meta.yaml index 37a3977a57..6f81229184 100644 --- a/recipes/bioconductor-kcsmart/meta.yaml +++ b/recipes/bioconductor-kcsmart/meta.yaml @@ -15,12 +15,12 @@ requirements: - bioconductor-biocgenerics - bioconductor-multtest - bioconductor-siggenes - - r + - r-base run: - bioconductor-biocgenerics - bioconductor-multtest - bioconductor-siggenes - - r + - r-base test: commands: - '$R -e "library(''KCsmart'')"' diff --git a/recipes/bioconductor-kegg.db/meta.yaml b/recipes/bioconductor-kegg.db/meta.yaml index 0a4627220c..3adb7fe437 100644 --- a/recipes/bioconductor-kegg.db/meta.yaml +++ b/recipes/bioconductor-kegg.db/meta.yaml @@ -13,10 +13,10 @@ build: requirements: build: - 'bioconductor-annotationdbi >=1.34.3' - - r + - r-base run: - 'bioconductor-annotationdbi >=1.34.3' - - r + - r-base test: commands: - '$R -e "library(''KEGG.db'')"' diff --git a/recipes/bioconductor-kegggraph/meta.yaml b/recipes/bioconductor-kegggraph/meta.yaml index 43876d85df..74d7822acd 100644 --- a/recipes/bioconductor-kegggraph/meta.yaml +++ b/recipes/bioconductor-kegggraph/meta.yaml @@ -13,11 +13,11 @@ build: requirements: build: - bioconductor-graph - - r + - r-base - 'r-xml >=2.3-0' run: - bioconductor-graph - - r + - r-base - 'r-xml >=2.3-0' test: commands: diff --git a/recipes/bioconductor-keggrest/meta.yaml b/recipes/bioconductor-keggrest/meta.yaml index 84e2b55802..330c8dc432 100644 --- a/recipes/bioconductor-keggrest/meta.yaml +++ b/recipes/bioconductor-keggrest/meta.yaml @@ -13,12 +13,12 @@ build: requirements: build: - bioconductor-biostrings - - r + - r-base - r-httr - r-png run: - bioconductor-biostrings - - r + - r-base - r-httr - r-png test: diff --git a/recipes/bioconductor-limma/3.26.7/meta.yaml b/recipes/bioconductor-limma/3.26.7/meta.yaml index 42990abeac..aad2b2bfe5 100644 --- a/recipes/bioconductor-limma/3.26.7/meta.yaml +++ b/recipes/bioconductor-limma/3.26.7/meta.yaml @@ -12,9 +12,9 @@ build: - lib/ requirements: build: - - r + - r-base run: - - r + - r-base test: commands: - '$R -e "library(''limma'')"' diff --git a/recipes/bioconductor-limma/3.28.2/meta.yaml b/recipes/bioconductor-limma/3.28.2/meta.yaml index 610d768419..6bcc9a550e 100644 --- a/recipes/bioconductor-limma/3.28.2/meta.yaml +++ b/recipes/bioconductor-limma/3.28.2/meta.yaml @@ -12,9 +12,9 @@ build: - lib/ requirements: build: - - r + - r-base run: - - r + - r-base test: commands: - '$R -e "library(''limma'')"' diff --git a/recipes/bioconductor-limma/3.28.6/meta.yaml b/recipes/bioconductor-limma/3.28.6/meta.yaml index 987071ec93..06875fa695 100644 --- a/recipes/bioconductor-limma/3.28.6/meta.yaml +++ b/recipes/bioconductor-limma/3.28.6/meta.yaml @@ -12,9 +12,9 @@ build: - lib/ requirements: build: - - r + - r-base run: - - r + - r-base test: commands: - '$R -e "library(''limma'')"' diff --git a/recipes/bioconductor-lpsymphony/meta.yaml b/recipes/bioconductor-lpsymphony/meta.yaml index fa38aa24a4..142ee98dd0 100644 --- a/recipes/bioconductor-lpsymphony/meta.yaml +++ b/recipes/bioconductor-lpsymphony/meta.yaml @@ -13,9 +13,9 @@ build: requirements: build: - gcc - - r + - r-base run: - - r + - r-base test: commands: - '$R -e "library(''lpsymphony'')"' diff --git a/recipes/bioconductor-made4/meta.yaml b/recipes/bioconductor-made4/meta.yaml index ac73561e2b..dfe97c653e 100644 --- a/recipes/bioconductor-made4/meta.yaml +++ b/recipes/bioconductor-made4/meta.yaml @@ -12,13 +12,13 @@ build: - lib/ requirements: build: - - r + - r-base - r-ade4 - r-rcolorbrewer - r-gplots - r-scatterplot3d run: - - r + - r-base - r-ade4 - r-rcolorbrewer - r-gplots diff --git a/recipes/bioconductor-marray/meta.yaml b/recipes/bioconductor-marray/meta.yaml index 2df71300fd..551345eb59 100644 --- a/recipes/bioconductor-marray/meta.yaml +++ b/recipes/bioconductor-marray/meta.yaml @@ -13,10 +13,10 @@ build: requirements: build: - bioconductor-limma - - r + - r-base run: - bioconductor-limma - - r + - r-base test: commands: - '$R -e "library(''marray'')"' diff --git a/recipes/bioconductor-masigpro/meta.yaml b/recipes/bioconductor-masigpro/meta.yaml index 1e2ef5f8d5..016b5a5a08 100644 --- a/recipes/bioconductor-masigpro/meta.yaml +++ b/recipes/bioconductor-masigpro/meta.yaml @@ -13,12 +13,12 @@ build: requirements: build: - bioconductor-biobase - - r + - r-base - r-mclust - r-venn run: - bioconductor-biobase - - r + - r-base - r-mclust - r-venn test: diff --git a/recipes/bioconductor-medips/meta.yaml b/recipes/bioconductor-medips/meta.yaml index cb579e5b9c..891ef924f1 100644 --- a/recipes/bioconductor-medips/meta.yaml +++ b/recipes/bioconductor-medips/meta.yaml @@ -22,7 +22,7 @@ requirements: - bioconductor-preprocesscore - bioconductor-rsamtools - bioconductor-rtracklayer - - r + - r-base - r-gtools run: - bioconductor-biomart @@ -35,7 +35,7 @@ requirements: - bioconductor-preprocesscore - bioconductor-rsamtools - bioconductor-rtracklayer - - r + - r-base - r-gtools test: commands: diff --git a/recipes/bioconductor-metagenomeseq/meta.yaml b/recipes/bioconductor-metagenomeseq/meta.yaml index 4af9cdd078..0ce646b633 100644 --- a/recipes/bioconductor-metagenomeseq/meta.yaml +++ b/recipes/bioconductor-metagenomeseq/meta.yaml @@ -14,7 +14,7 @@ requirements: build: - bioconductor-biobase - bioconductor-limma - - r + - r-base - r-foreach - r-glmnet - r-gplots @@ -23,7 +23,7 @@ requirements: run: - bioconductor-biobase - bioconductor-limma - - r + - r-base - r-foreach - r-glmnet - r-gplots diff --git a/recipes/bioconductor-metams/meta.yaml b/recipes/bioconductor-metams/meta.yaml index 88256f07f5..75368e38c7 100644 --- a/recipes/bioconductor-metams/meta.yaml +++ b/recipes/bioconductor-metams/meta.yaml @@ -16,13 +16,13 @@ requirements: - bioconductor-biocgenerics - bioconductor-camera - 'bioconductor-xcms >=1.35' - - r + - r-base - r-robustbase run: - bioconductor-biocgenerics - bioconductor-camera - 'bioconductor-xcms >=1.35' - - r + - r-base - r-robustbase test: commands: diff --git a/recipes/bioconductor-methylkit/meta.yaml b/recipes/bioconductor-methylkit/meta.yaml index 7d3c0aca37..9d748a6b2c 100644 --- a/recipes/bioconductor-methylkit/meta.yaml +++ b/recipes/bioconductor-methylkit/meta.yaml @@ -28,7 +28,7 @@ requirements: - bioconductor-s4vectors - bioconductor-rhtslib - bioconductor-zlibbioc - - r + - r-base - 'r-data.table >=1.9.6' - r-emdbook - r-gtools @@ -50,7 +50,7 @@ requirements: - bioconductor-s4vectors - bioconductor-rhtslib - bioconductor-zlibbioc - - r + - r-base - 'r-data.table >=1.9.6' - r-emdbook - r-gtools diff --git a/recipes/bioconductor-mgug4122a.db/meta.yaml b/recipes/bioconductor-mgug4122a.db/meta.yaml index 0faf046ca3..6aed14ee58 100644 --- a/recipes/bioconductor-mgug4122a.db/meta.yaml +++ b/recipes/bioconductor-mgug4122a.db/meta.yaml @@ -14,11 +14,11 @@ requirements: build: - 'bioconductor-annotationdbi >=1.34.3' - 'bioconductor-org.mm.eg.db >=3.3.0' - - r + - r-base run: - 'bioconductor-annotationdbi >=1.34.3' - 'bioconductor-org.mm.eg.db >=3.3.0' - - r + - r-base test: commands: - '$R -e "library(''mgug4122a.db'')"' diff --git a/recipes/bioconductor-minfi/meta.yaml b/recipes/bioconductor-minfi/meta.yaml index 136918cda6..67d1182058 100644 --- a/recipes/bioconductor-minfi/meta.yaml +++ b/recipes/bioconductor-minfi/meta.yaml @@ -27,7 +27,7 @@ requirements: - bioconductor-s4vectors - bioconductor-siggenes - 'bioconductor-summarizedexperiment >=1.1.6' - - r + - r-base - r-beanplot - r-data.table - 'r-matrixstats >=0.50.0' @@ -52,7 +52,7 @@ requirements: - bioconductor-s4vectors - bioconductor-siggenes - 'bioconductor-summarizedexperiment >=1.1.6' - - r + - r-base - r-beanplot - r-data.table - 'r-matrixstats >=0.50.0' diff --git a/recipes/bioconductor-mmdiff/meta.yaml b/recipes/bioconductor-mmdiff/meta.yaml index 2e57fa060c..5ea08247bf 100644 --- a/recipes/bioconductor-mmdiff/meta.yaml +++ b/recipes/bioconductor-mmdiff/meta.yaml @@ -16,7 +16,7 @@ build: requirements: build: - - r + - r-base - bioconductor-genomicranges - bioconductor-diffbind - r-gmd @@ -24,7 +24,7 @@ requirements: - bioconductor-iranges - bioconductor-biobase run: - - r + - r-base - bioconductor-genomicranges - bioconductor-diffbind - r-gmd diff --git a/recipes/bioconductor-mosaics/meta.yaml b/recipes/bioconductor-mosaics/meta.yaml index 69808c8347..80936128e0 100644 --- a/recipes/bioconductor-mosaics/meta.yaml +++ b/recipes/bioconductor-mosaics/meta.yaml @@ -21,7 +21,7 @@ requirements: - bioconductor-iranges - bioconductor-rsamtools - bioconductor-s4vectors - - r + - r-base - r-rcpp - gcc # [linux] - llvm # [osx] @@ -32,7 +32,7 @@ requirements: - bioconductor-iranges - bioconductor-rsamtools - bioconductor-s4vectors - - r + - r-base - r-rcpp - libgcc # [linux] diff --git a/recipes/bioconductor-motifbreakr/meta.yaml b/recipes/bioconductor-motifbreakr/meta.yaml index 84e1dda6fb..691d3e0bde 100644 --- a/recipes/bioconductor-motifbreakr/meta.yaml +++ b/recipes/bioconductor-motifbreakr/meta.yaml @@ -25,7 +25,7 @@ requirements: - bioconductor-rtracklayer - 'bioconductor-s4vectors >=0.9.25' - bioconductor-variantannotation - - r + - r-base - r-grimport - r-matrixstats - r-stringr @@ -44,7 +44,7 @@ requirements: - bioconductor-rtracklayer - 'bioconductor-s4vectors >=0.9.25' - bioconductor-variantannotation - - r + - r-base - r-grimport - r-matrixstats - r-stringr diff --git a/recipes/bioconductor-motifdb/meta.yaml b/recipes/bioconductor-motifdb/meta.yaml index 5794c0a7dd..eaa22e3b53 100644 --- a/recipes/bioconductor-motifdb/meta.yaml +++ b/recipes/bioconductor-motifdb/meta.yaml @@ -17,14 +17,14 @@ requirements: - bioconductor-iranges - bioconductor-rtracklayer - bioconductor-s4vectors - - r + - r-base run: - bioconductor-biocgenerics - bioconductor-biostrings - bioconductor-iranges - bioconductor-rtracklayer - bioconductor-s4vectors - - r + - r-base test: commands: - '$R -e "library(''MotifDb'')"' diff --git a/recipes/bioconductor-motifstack/meta.yaml b/recipes/bioconductor-motifstack/meta.yaml index 57db2ab951..b86dc8433c 100644 --- a/recipes/bioconductor-motifstack/meta.yaml +++ b/recipes/bioconductor-motifstack/meta.yaml @@ -14,7 +14,7 @@ requirements: build: - bioconductor-biostrings - bioconductor-motiv - - r + - r-base - r-ade4 - r-grimport - r-scales @@ -22,7 +22,7 @@ requirements: run: - bioconductor-biostrings - bioconductor-motiv - - r + - r-base - r-ade4 - r-grimport - r-scales diff --git a/recipes/bioconductor-motiv/meta.yaml b/recipes/bioconductor-motiv/meta.yaml index 3d169d701d..dd8c653813 100644 --- a/recipes/bioconductor-motiv/meta.yaml +++ b/recipes/bioconductor-motiv/meta.yaml @@ -19,7 +19,7 @@ requirements: - 'bioconductor-iranges >=1.13.5' - bioconductor-rgadem - bioconductor-s4vectors - - r + - r-base - gsl {{CONDA_GSL}}* run: @@ -28,7 +28,7 @@ requirements: - 'bioconductor-iranges >=1.13.5' - bioconductor-rgadem - bioconductor-s4vectors - - r + - r-base - gsl {{CONDA_GSL}}* test: commands: diff --git a/recipes/bioconductor-multtest/meta.yaml b/recipes/bioconductor-multtest/meta.yaml index f638d96063..6bc02f2f8c 100644 --- a/recipes/bioconductor-multtest/meta.yaml +++ b/recipes/bioconductor-multtest/meta.yaml @@ -14,11 +14,11 @@ requirements: build: - bioconductor-biobase - bioconductor-biocgenerics - - r + - r-base run: - bioconductor-biobase - bioconductor-biocgenerics - - r + - r-base test: commands: - '$R -e "library(''multtest'')"' diff --git a/recipes/bioconductor-mzr/meta.yaml b/recipes/bioconductor-mzr/meta.yaml index 9371bc2e01..09d4a09d4e 100644 --- a/recipes/bioconductor-mzr/meta.yaml +++ b/recipes/bioconductor-mzr/meta.yaml @@ -17,7 +17,7 @@ requirements: - 'bioconductor-biocgenerics >=0.13.6' - bioconductor-protgenerics - bioconductor-zlibbioc - - r + - r-base - 'r-rcpp >=0.10.1' - 'libnetcdf ==4.3.3.1' - gcc @@ -26,7 +26,7 @@ requirements: - 'bioconductor-biocgenerics >=0.13.6' - bioconductor-protgenerics - bioconductor-zlibbioc - - r + - r-base - 'r-rcpp >=0.10.1' - 'libnetcdf ==4.3.3.1' - libgcc diff --git a/recipes/bioconductor-noiseq/meta.yaml b/recipes/bioconductor-noiseq/meta.yaml index c5d1039981..1972a81536 100644 --- a/recipes/bioconductor-noiseq/meta.yaml +++ b/recipes/bioconductor-noiseq/meta.yaml @@ -13,10 +13,10 @@ build: requirements: build: - 'bioconductor-biobase >=2.13.11' - - r + - r-base run: - 'bioconductor-biobase >=2.13.11' - - r + - r-base test: commands: - '$R -e "library(''NOISeq'')"' diff --git a/recipes/bioconductor-org.ce.eg.db/meta.yaml b/recipes/bioconductor-org.ce.eg.db/meta.yaml index cdd6546d5e..7a55dc1a77 100644 --- a/recipes/bioconductor-org.ce.eg.db/meta.yaml +++ b/recipes/bioconductor-org.ce.eg.db/meta.yaml @@ -16,10 +16,10 @@ build: requirements: build: - bioconductor-annotationdbi >=1.31.19 - - r + - r-base run: - bioconductor-annotationdbi >=1.31.19 - - r + - r-base test: commands: diff --git a/recipes/bioconductor-org.hs.eg.db/meta.yaml b/recipes/bioconductor-org.hs.eg.db/meta.yaml index a02810d3a8..be92d8bb92 100644 --- a/recipes/bioconductor-org.hs.eg.db/meta.yaml +++ b/recipes/bioconductor-org.hs.eg.db/meta.yaml @@ -13,10 +13,10 @@ build: requirements: build: - 'bioconductor-annotationdbi >=1.33.10' - - r + - r-base run: - 'bioconductor-annotationdbi >=1.33.10' - - r + - r-base test: commands: - '$R -e "library(''org.Hs.eg.db'')"' diff --git a/recipes/bioconductor-org.mm.eg.db/3.3.0/meta.yaml b/recipes/bioconductor-org.mm.eg.db/3.3.0/meta.yaml index d89154fd3d..c2d0a061e5 100644 --- a/recipes/bioconductor-org.mm.eg.db/3.3.0/meta.yaml +++ b/recipes/bioconductor-org.mm.eg.db/3.3.0/meta.yaml @@ -13,10 +13,10 @@ build: requirements: build: - 'bioconductor-annotationdbi >=1.33.10' - - r + - r-base run: - 'bioconductor-annotationdbi >=1.33.10' - - r + - r-base test: commands: - '$R -e "library(''org.Mm.eg.db'')"' diff --git a/recipes/bioconductor-org.mm.eg.db/meta.yaml b/recipes/bioconductor-org.mm.eg.db/meta.yaml index 1c6d8bb150..f78eac381d 100644 --- a/recipes/bioconductor-org.mm.eg.db/meta.yaml +++ b/recipes/bioconductor-org.mm.eg.db/meta.yaml @@ -13,10 +13,10 @@ build: requirements: build: - bioconductor-annotationdbi >=1.35.4 - - r + - r-base run: - bioconductor-annotationdbi >=1.35.4 - - r + - r-base test: commands: - $R -e "library('org.Mm.eg.db')" diff --git a/recipes/bioconductor-organismdbi/meta.yaml b/recipes/bioconductor-organismdbi/meta.yaml index b78d994dc6..bf57316422 100644 --- a/recipes/bioconductor-organismdbi/meta.yaml +++ b/recipes/bioconductor-organismdbi/meta.yaml @@ -22,7 +22,7 @@ requirements: - bioconductor-iranges - bioconductor-rbgl - 'bioconductor-s4vectors >=0.9.25' - - r + - r-base - r-rsqlite run: - 'bioconductor-annotationdbi >=1.33.15' @@ -35,7 +35,7 @@ requirements: - bioconductor-iranges - bioconductor-rbgl - 'bioconductor-s4vectors >=0.9.25' - - r + - r-base - r-rsqlite test: commands: diff --git a/recipes/bioconductor-pathview/meta.yaml b/recipes/bioconductor-pathview/meta.yaml index 962f01bf32..0a3c390b94 100644 --- a/recipes/bioconductor-pathview/meta.yaml +++ b/recipes/bioconductor-pathview/meta.yaml @@ -20,7 +20,7 @@ requirements: - bioconductor-keggrest - bioconductor-org.hs.eg.db - bioconductor-rgraphviz - - r + - r-base - r-png - r-xml run: @@ -30,7 +30,7 @@ requirements: - bioconductor-keggrest - bioconductor-org.hs.eg.db - bioconductor-rgraphviz - - r + - r-base - r-png - r-xml test: diff --git a/recipes/bioconductor-pcamethods/meta.yaml b/recipes/bioconductor-pcamethods/meta.yaml index e1dc664d68..d814ff2cf2 100644 --- a/recipes/bioconductor-pcamethods/meta.yaml +++ b/recipes/bioconductor-pcamethods/meta.yaml @@ -14,14 +14,14 @@ requirements: build: - bioconductor-biobase - bioconductor-biocgenerics - - r + - r-base - 'r-rcpp >=0.11.3' - gcc # [linux] - llvm # [osx] run: - bioconductor-biobase - bioconductor-biocgenerics - - r + - r-base - 'r-rcpp >=0.11.3' test: commands: diff --git a/recipes/bioconductor-pchicdata/meta.yaml b/recipes/bioconductor-pchicdata/meta.yaml index 2cec3a785d..3915982cca 100644 --- a/recipes/bioconductor-pchicdata/meta.yaml +++ b/recipes/bioconductor-pchicdata/meta.yaml @@ -13,10 +13,10 @@ build: requirements: build: - bioconductor-chicago - - r + - r-base run: - bioconductor-chicago - - r + - r-base test: commands: - '$R -e "library(''PCHiCdata'')"' diff --git a/recipes/bioconductor-phyloseq/meta.yaml b/recipes/bioconductor-phyloseq/meta.yaml index d605e78948..9a59043d74 100644 --- a/recipes/bioconductor-phyloseq/meta.yaml +++ b/recipes/bioconductor-phyloseq/meta.yaml @@ -17,7 +17,7 @@ requirements: - 'bioconductor-biomformat >=0.4.0' - 'bioconductor-biostrings >=2.28.0' - 'bioconductor-multtest >=2.16.0' - - r + - r-base - 'r-ade4 >=1.7.2' - 'r-ape >=3.1.1' - 'r-data.table >=1.9.6' @@ -35,7 +35,7 @@ requirements: - 'bioconductor-biomformat >=0.4.0' - 'bioconductor-biostrings >=2.28.0' - 'bioconductor-multtest >=2.16.0' - - r + - r-base - 'r-ade4 >=1.7.2' - 'r-ape >=3.1.1' - 'r-data.table >=1.9.6' diff --git a/recipes/bioconductor-preprocesscore/meta.yaml b/recipes/bioconductor-preprocesscore/meta.yaml index 4dd611cba2..216b1e3a50 100644 --- a/recipes/bioconductor-preprocesscore/meta.yaml +++ b/recipes/bioconductor-preprocesscore/meta.yaml @@ -12,9 +12,9 @@ build: - lib/ requirements: build: - - r + - r-base run: - - r + - r-base test: commands: - '$R -e "library(''preprocessCore'')"' diff --git a/recipes/bioconductor-probamr/meta.yaml b/recipes/bioconductor-probamr/meta.yaml index 4dab23af67..1a31e13012 100644 --- a/recipes/bioconductor-probamr/meta.yaml +++ b/recipes/bioconductor-probamr/meta.yaml @@ -18,7 +18,7 @@ requirements: - bioconductor-genomicranges - bioconductor-iranges - bioconductor-rtracklayer - - r + - r-base run: - bioconductor-annotationdbi - bioconductor-biostrings @@ -26,7 +26,7 @@ requirements: - bioconductor-genomicranges - bioconductor-iranges - bioconductor-rtracklayer - - r + - r-base test: commands: - '$R -e "library(''proBAMr'')"' diff --git a/recipes/bioconductor-protgenerics/meta.yaml b/recipes/bioconductor-protgenerics/meta.yaml index 5398890151..21005e061c 100644 --- a/recipes/bioconductor-protgenerics/meta.yaml +++ b/recipes/bioconductor-protgenerics/meta.yaml @@ -12,9 +12,9 @@ build: - lib/ requirements: build: - - r + - r-base run: - - r + - r-base test: commands: - '$R -e "library(''ProtGenerics'')"' diff --git a/recipes/bioconductor-qdnaseq.mm10/1.4.0/meta.yaml b/recipes/bioconductor-qdnaseq.mm10/1.4.0/meta.yaml index f89ae82838..46f9920a49 100644 --- a/recipes/bioconductor-qdnaseq.mm10/1.4.0/meta.yaml +++ b/recipes/bioconductor-qdnaseq.mm10/1.4.0/meta.yaml @@ -13,10 +13,10 @@ build: requirements: build: - bioconductor-qdnaseq - - r + - r-base run: - bioconductor-qdnaseq - - r + - r-base test: commands: - '$R -e "library(''QDNAseq.mm10'')"' diff --git a/recipes/bioconductor-qdnaseq/meta.yaml b/recipes/bioconductor-qdnaseq/meta.yaml index 5a3c6bd803..60bf4daab4 100644 --- a/recipes/bioconductor-qdnaseq/meta.yaml +++ b/recipes/bioconductor-qdnaseq/meta.yaml @@ -19,7 +19,7 @@ requirements: - 'bioconductor-genomicranges >=1.20' - 'bioconductor-iranges >=2.2' - 'bioconductor-rsamtools >=1.20' - - r + - r-base - 'r-matrixstats >=0.50.2' - 'r-r.utils >=2.3.0' run: @@ -30,7 +30,7 @@ requirements: - 'bioconductor-genomicranges >=1.20' - 'bioconductor-iranges >=2.2' - 'bioconductor-rsamtools >=1.20' - - r + - r-base - 'r-matrixstats >=0.50.2' - 'r-r.utils >=2.3.0' test: diff --git a/recipes/bioconductor-rbgl/meta.yaml b/recipes/bioconductor-rbgl/meta.yaml index 0ddc936bcd..6ae1aef7d5 100644 --- a/recipes/bioconductor-rbgl/meta.yaml +++ b/recipes/bioconductor-rbgl/meta.yaml @@ -13,10 +13,10 @@ build: requirements: build: - bioconductor-graph - - r + - r-base run: - bioconductor-graph - - r + - r-base test: commands: - '$R -e "library(''RBGL'')"' diff --git a/recipes/bioconductor-rcas/meta.yaml b/recipes/bioconductor-rcas/meta.yaml index f131d52b78..5b7ad3a7bd 100644 --- a/recipes/bioconductor-rcas/meta.yaml +++ b/recipes/bioconductor-rcas/meta.yaml @@ -18,7 +18,7 @@ build: # testthat requirements: build: - - r + - r-base - bioconductor-biomart - bioconductor-topgo - bioconductor-genomicfeatures @@ -41,7 +41,7 @@ requirements: - r-knitr >=1.12.3 - r-plotrix run: - - r + - r-base - bioconductor-biomart - bioconductor-topgo - bioconductor-genomicfeatures diff --git a/recipes/bioconductor-rcytoscape/meta.yaml b/recipes/bioconductor-rcytoscape/meta.yaml index 923f76187a..abf89b6c3b 100644 --- a/recipes/bioconductor-rcytoscape/meta.yaml +++ b/recipes/bioconductor-rcytoscape/meta.yaml @@ -14,12 +14,12 @@ requirements: build: - bioconductor-biocgenerics - 'bioconductor-graph >=1.31.0' - - r + - r-base - 'r-xmlrpc >=0.2.4' run: - bioconductor-biocgenerics - 'bioconductor-graph >=1.31.0' - - r + - r-base - 'r-xmlrpc >=0.2.4' test: commands: diff --git a/recipes/bioconductor-regioner/meta.yaml b/recipes/bioconductor-regioner/meta.yaml index e59d89634d..37c252c52e 100644 --- a/recipes/bioconductor-regioner/meta.yaml +++ b/recipes/bioconductor-regioner/meta.yaml @@ -17,7 +17,7 @@ requirements: - bioconductor-genomicranges - bioconductor-iranges - bioconductor-rtracklayer - - r + - r-base - r-memoise run: - bioconductor-bsgenome @@ -25,7 +25,7 @@ requirements: - bioconductor-genomicranges - bioconductor-iranges - bioconductor-rtracklayer - - r + - r-base - r-memoise test: commands: diff --git a/recipes/bioconductor-repitools/meta.yaml b/recipes/bioconductor-repitools/meta.yaml index f25129300f..d4ad6a9ae7 100644 --- a/recipes/bioconductor-repitools/meta.yaml +++ b/recipes/bioconductor-repitools/meta.yaml @@ -25,7 +25,7 @@ requirements: - bioconductor-rsamtools - bioconductor-rtracklayer - 'bioconductor-s4vectors >=0.9.25' - - r + - r-base - r-aroma.affymetrix - r-gplots - r-gsmoothr @@ -44,7 +44,7 @@ requirements: - bioconductor-rsamtools - bioconductor-rtracklayer - 'bioconductor-s4vectors >=0.9.25' - - r + - r-base - r-aroma.affymetrix - r-gplots - r-gsmoothr diff --git a/recipes/bioconductor-rgadem/meta.yaml b/recipes/bioconductor-rgadem/meta.yaml index 1e284e3ed2..90c72ebbbf 100644 --- a/recipes/bioconductor-rgadem/meta.yaml +++ b/recipes/bioconductor-rgadem/meta.yaml @@ -16,13 +16,13 @@ requirements: - bioconductor-bsgenome - bioconductor-iranges - bioconductor-seqlogo - - r + - r-base run: - bioconductor-biostrings - bioconductor-bsgenome - bioconductor-iranges - bioconductor-seqlogo - - r + - r-base test: commands: - '$R -e "library(''rGADEM'')"' diff --git a/recipes/bioconductor-rgalaxy/meta.yaml b/recipes/bioconductor-rgalaxy/meta.yaml index 299309ba32..c636756a36 100644 --- a/recipes/bioconductor-rgalaxy/meta.yaml +++ b/recipes/bioconductor-rgalaxy/meta.yaml @@ -14,7 +14,7 @@ requirements: build: - bioconductor-biobase - bioconductor-biocgenerics - - r + - r-base - r-digest - r-optparse - r-roxygen2 @@ -22,7 +22,7 @@ requirements: run: - bioconductor-biobase - bioconductor-biocgenerics - - r + - r-base - r-digest - r-optparse - r-roxygen2 diff --git a/recipes/bioconductor-rgraphviz/2.13.0/meta.yaml b/recipes/bioconductor-rgraphviz/2.13.0/meta.yaml index 1d6fcdae8f..a9bf441047 100644 --- a/recipes/bioconductor-rgraphviz/2.13.0/meta.yaml +++ b/recipes/bioconductor-rgraphviz/2.13.0/meta.yaml @@ -15,10 +15,10 @@ build: requirements: build: - bioconductor-graph - - r + - r-base run: - bioconductor-graph - - r + - r-base test: commands: - '$R -e "library(''Rgraphviz'')"' diff --git a/recipes/bioconductor-rgraphviz/meta.yaml b/recipes/bioconductor-rgraphviz/meta.yaml index e7e2742e11..6447360882 100644 --- a/recipes/bioconductor-rgraphviz/meta.yaml +++ b/recipes/bioconductor-rgraphviz/meta.yaml @@ -16,12 +16,12 @@ build: requirements: build: - bioconductor-graph - - r + - r-base - gcc # [linux] - llvm # [osx] run: - bioconductor-graph - - r + - r-base - libgcc # [linux] test: commands: diff --git a/recipes/bioconductor-rhdf5/meta.yaml b/recipes/bioconductor-rhdf5/meta.yaml index 426518a13f..07c04087fa 100644 --- a/recipes/bioconductor-rhdf5/meta.yaml +++ b/recipes/bioconductor-rhdf5/meta.yaml @@ -15,12 +15,12 @@ build: requirements: build: - bioconductor-zlibbioc - - r + - r-base - gcc # [linux] - llvm # [osx] run: - bioconductor-zlibbioc - - r + - r-base - libgcc # [linux] test: commands: diff --git a/recipes/bioconductor-rhtslib/meta.yaml b/recipes/bioconductor-rhtslib/meta.yaml index 836c75c062..0764e9934b 100644 --- a/recipes/bioconductor-rhtslib/meta.yaml +++ b/recipes/bioconductor-rhtslib/meta.yaml @@ -19,13 +19,13 @@ build: #for each dependency, the used version for building the package is in comment requirements: build: - - r + - r-base - bioconductor-zlibbioc # 1.18.0 - autoconf 2.69 pl5.20.3.1_4 - gcc # [linux] - llvm # [osx] run: - - r + - r-base - bioconductor-zlibbioc # 1.18.0 - libgcc # [linux] diff --git a/recipes/bioconductor-ringo/meta.yaml b/recipes/bioconductor-ringo/meta.yaml index 6b02ff5ed4..02590f5b7f 100644 --- a/recipes/bioconductor-ringo/meta.yaml +++ b/recipes/bioconductor-ringo/meta.yaml @@ -17,7 +17,7 @@ requirements: - bioconductor-genefilter - bioconductor-limma - bioconductor-vsn - - r + - r-base - r-rcolorbrewer run: - 'bioconductor-biobase >=1.14.1' @@ -25,7 +25,7 @@ requirements: - bioconductor-genefilter - bioconductor-limma - bioconductor-vsn - - r + - r-base - r-rcolorbrewer test: commands: diff --git a/recipes/bioconductor-rnaseqpower/meta.yaml b/recipes/bioconductor-rnaseqpower/meta.yaml index 48ad913ec9..984c439254 100644 --- a/recipes/bioconductor-rnaseqpower/meta.yaml +++ b/recipes/bioconductor-rnaseqpower/meta.yaml @@ -15,9 +15,9 @@ build: requirements: build: - - r + - r-base run: - - r + - r-base test: commands: diff --git a/recipes/bioconductor-roar/meta.yaml b/recipes/bioconductor-roar/meta.yaml index 132e0c8d9c..8ed5f1a584 100644 --- a/recipes/bioconductor-roar/meta.yaml +++ b/recipes/bioconductor-roar/meta.yaml @@ -20,7 +20,7 @@ requirements: - bioconductor-rtracklayer - bioconductor-s4vectors - bioconductor-summarizedexperiment - - r + - r-base run: - bioconductor-biocgenerics - bioconductor-genomeinfodb @@ -30,7 +30,7 @@ requirements: - bioconductor-rtracklayer - bioconductor-s4vectors - bioconductor-summarizedexperiment - - r + - r-base test: commands: - '$R -e "library(''roar'')"' diff --git a/recipes/bioconductor-ropls/1.2.14/meta.yaml b/recipes/bioconductor-ropls/1.2.14/meta.yaml index 5b36fcb039..d8fc86c913 100644 --- a/recipes/bioconductor-ropls/1.2.14/meta.yaml +++ b/recipes/bioconductor-ropls/1.2.14/meta.yaml @@ -12,9 +12,9 @@ build: - lib/ requirements: build: - - r + - r-base run: - - r + - r-base test: commands: - '$R -e "library(''ropls'')"' diff --git a/recipes/bioconductor-ropls/meta.yaml b/recipes/bioconductor-ropls/meta.yaml index fabbbffbc9..c7508c5c38 100644 --- a/recipes/bioconductor-ropls/meta.yaml +++ b/recipes/bioconductor-ropls/meta.yaml @@ -12,9 +12,9 @@ build: - lib/ requirements: build: - - r + - r-base run: - - r + - r-base test: commands: - '$R -e "library(''ropls'')"' diff --git a/recipes/bioconductor-rots/meta.yaml b/recipes/bioconductor-rots/meta.yaml index 87d2996414..4efa6fe4db 100644 --- a/recipes/bioconductor-rots/meta.yaml +++ b/recipes/bioconductor-rots/meta.yaml @@ -13,13 +13,13 @@ build: requirements: build: - bioconductor-biobase - - r + - r-base - r-rcpp - gcc # [linux] - llvm # [osx] run: - bioconductor-biobase - - r + - r-base - r-rcpp test: commands: diff --git a/recipes/bioconductor-rsamtools/meta.yaml b/recipes/bioconductor-rsamtools/meta.yaml index 3df3f33965..6e77a7b512 100644 --- a/recipes/bioconductor-rsamtools/meta.yaml +++ b/recipes/bioconductor-rsamtools/meta.yaml @@ -31,7 +31,7 @@ requirements: - bioconductor-s4vectors 0.12.0 #>=0.7.11 - bioconductor-xvector 0.12.1 #>=0.9.1 - bioconductor-zlibbioc 1.18.0 - - r + - r-base - r-bitops 1.0_6 run: - bioconductor-biocgenerics 0.20.0 #>=0.1.3 @@ -43,7 +43,7 @@ requirements: - bioconductor-s4vectors 0.12.0 #>=0.7.11 - bioconductor-xvector 0.12.1 #>=0.9.1 - bioconductor-zlibbioc 1.18.0 - - r + - r-base - r-bitops 1.0_6 test: diff --git a/recipes/bioconductor-rsubread/meta.yaml b/recipes/bioconductor-rsubread/meta.yaml index 711648b399..d84333de7e 100644 --- a/recipes/bioconductor-rsubread/meta.yaml +++ b/recipes/bioconductor-rsubread/meta.yaml @@ -12,9 +12,9 @@ build: - lib/ requirements: build: - - r + - r-base run: - - r + - r-base test: commands: - '$R -e "library(''Rsubread'')"' diff --git a/recipes/bioconductor-s4vectors/0.8.11/meta.yaml b/recipes/bioconductor-s4vectors/0.8.11/meta.yaml index 2fed3b67c4..f9d6490679 100644 --- a/recipes/bioconductor-s4vectors/0.8.11/meta.yaml +++ b/recipes/bioconductor-s4vectors/0.8.11/meta.yaml @@ -15,10 +15,10 @@ build: requirements: build: - 'bioconductor-biocgenerics >=0.15.10' - - r + - r-base run: - 'bioconductor-biocgenerics >=0.15.10' - - r + - r-base test: commands: - '$R -e "library(''S4Vectors'')"' diff --git a/recipes/bioconductor-seqlogo/meta.yaml b/recipes/bioconductor-seqlogo/meta.yaml index f84033cc70..133879fa9f 100644 --- a/recipes/bioconductor-seqlogo/meta.yaml +++ b/recipes/bioconductor-seqlogo/meta.yaml @@ -12,9 +12,9 @@ build: - lib/ requirements: build: - - r + - r-base run: - - r + - r-base test: commands: - '$R -e "library(''seqLogo'')"' diff --git a/recipes/bioconductor-shortread/meta.yaml b/recipes/bioconductor-shortread/meta.yaml index 33fbd190b5..fb57978dd5 100644 --- a/recipes/bioconductor-shortread/meta.yaml +++ b/recipes/bioconductor-shortread/meta.yaml @@ -23,7 +23,7 @@ requirements: - 'bioconductor-rsamtools >=1.21.4' - 'bioconductor-s4vectors >=0.7.1' - bioconductor-zlibbioc - - r + - r-base - r-hwriter - r-latticeextra @@ -39,7 +39,7 @@ requirements: - 'bioconductor-rsamtools >=1.21.4' - 'bioconductor-s4vectors >=0.7.1' - bioconductor-zlibbioc - - r + - r-base - r-hwriter - r-latticeextra diff --git a/recipes/bioconductor-siggenes/meta.yaml b/recipes/bioconductor-siggenes/meta.yaml index 1b4844f1a2..38f6008bc9 100644 --- a/recipes/bioconductor-siggenes/meta.yaml +++ b/recipes/bioconductor-siggenes/meta.yaml @@ -14,11 +14,11 @@ requirements: build: - bioconductor-biobase - bioconductor-multtest - - r + - r-base run: - bioconductor-biobase - bioconductor-multtest - - r + - r-base test: commands: - '$R -e "library(''siggenes'')"' diff --git a/recipes/bioconductor-sradb/meta.yaml b/recipes/bioconductor-sradb/meta.yaml index a7847f5152..eabc04643b 100644 --- a/recipes/bioconductor-sradb/meta.yaml +++ b/recipes/bioconductor-sradb/meta.yaml @@ -14,13 +14,13 @@ requirements: build: - bioconductor-geoquery - bioconductor-graph - - r + - r-base - r-rcurl - r-rsqlite run: - bioconductor-geoquery - bioconductor-graph - - r + - r-base - r-rcurl - r-rsqlite test: diff --git a/recipes/bioconductor-summarizedexperiment/1.0.2/meta.yaml b/recipes/bioconductor-summarizedexperiment/1.0.2/meta.yaml index 194bd7c6aa..8b3b6c97a8 100644 --- a/recipes/bioconductor-summarizedexperiment/1.0.2/meta.yaml +++ b/recipes/bioconductor-summarizedexperiment/1.0.2/meta.yaml @@ -18,7 +18,7 @@ requirements: - 'bioconductor-genomicranges >=1.22.1' - bioconductor-iranges - 'bioconductor-s4vectors >=0.7.11' - - r + - r-base run: - bioconductor-biobase - 'bioconductor-biocgenerics >=0.15.3' @@ -26,7 +26,7 @@ requirements: - 'bioconductor-genomicranges >=1.22.1' - bioconductor-iranges - 'bioconductor-s4vectors >=0.7.11' - - r + - r-base test: commands: - '$R -e "library(''SummarizedExperiment'')"' diff --git a/recipes/bioconductor-sva/meta.yaml b/recipes/bioconductor-sva/meta.yaml index ef3da3c9c5..2f8e294747 100644 --- a/recipes/bioconductor-sva/meta.yaml +++ b/recipes/bioconductor-sva/meta.yaml @@ -15,11 +15,11 @@ requirements: - gcc # [linux] - llvm # [osx] - bioconductor-genefilter - - r + - r-base run: - libgcc # [linux] - bioconductor-genefilter - - r + - r-base test: commands: - '$R -e "library(''sva'')"' diff --git a/recipes/bioconductor-systempiper/meta.yaml b/recipes/bioconductor-systempiper/meta.yaml index 42bd5196fd..3a393c6675 100644 --- a/recipes/bioconductor-systempiper/meta.yaml +++ b/recipes/bioconductor-systempiper/meta.yaml @@ -34,7 +34,7 @@ requirements: - bioconductor-shortread - bioconductor-summarizedexperiment - bioconductor-variantannotation - - r + - r-base - r-batchjobs - r-ggplot2 - r-pheatmap @@ -54,7 +54,7 @@ requirements: - bioconductor-shortread - bioconductor-summarizedexperiment - bioconductor-variantannotation - - r + - r-base - r-batchjobs - r-ggplot2 - r-pheatmap diff --git a/recipes/bioconductor-topgo/meta.yaml b/recipes/bioconductor-topgo/meta.yaml index 9d87d0215d..9d4f6d6ee9 100644 --- a/recipes/bioconductor-topgo/meta.yaml +++ b/recipes/bioconductor-topgo/meta.yaml @@ -17,7 +17,7 @@ requirements: - 'bioconductor-biocgenerics >=0.13.6' - 'bioconductor-go.db >=2.3.0' - 'bioconductor-graph >=1.14.0' - - r + - r-base - r-dbi - r-matrixstats - 'r-sparsem >=0.73' @@ -27,7 +27,7 @@ requirements: - 'bioconductor-biocgenerics >=0.13.6' - 'bioconductor-go.db >=2.3.0' - 'bioconductor-graph >=1.14.0' - - r + - r-base - r-dbi - r-matrixstats - 'r-sparsem >=0.73' diff --git a/recipes/bioconductor-txdb.dmelanogaster.ucsc.dm3.ensgene/meta.yaml b/recipes/bioconductor-txdb.dmelanogaster.ucsc.dm3.ensgene/meta.yaml index aa2ce82a10..0f3c981dee 100644 --- a/recipes/bioconductor-txdb.dmelanogaster.ucsc.dm3.ensgene/meta.yaml +++ b/recipes/bioconductor-txdb.dmelanogaster.ucsc.dm3.ensgene/meta.yaml @@ -15,11 +15,11 @@ requirements: build: - bioconductor-annotationdbi - 'bioconductor-genomicfeatures >=1.21.30' - - r + - r-base run: - bioconductor-annotationdbi - 'bioconductor-genomicfeatures >=1.21.30' - - r + - r-base test: commands: - '$R -e "library(''TxDb.Dmelanogaster.UCSC.dm3.ensGene'')"' diff --git a/recipes/bioconductor-txdb.hsapiens.ucsc.hg19.knowngene/meta.yaml b/recipes/bioconductor-txdb.hsapiens.ucsc.hg19.knowngene/meta.yaml index 66208dd574..c0fd0bd76e 100644 --- a/recipes/bioconductor-txdb.hsapiens.ucsc.hg19.knowngene/meta.yaml +++ b/recipes/bioconductor-txdb.hsapiens.ucsc.hg19.knowngene/meta.yaml @@ -14,11 +14,11 @@ requirements: build: - bioconductor-annotationdbi - 'bioconductor-genomicfeatures >=1.21.30' - - r + - r-base run: - bioconductor-annotationdbi - 'bioconductor-genomicfeatures >=1.21.30' - - r + - r-base test: commands: - '$R -e "library(''TxDb.Hsapiens.UCSC.hg19.knownGene'')"' diff --git a/recipes/bioconductor-txdb.mmusculus.ucsc.mm10.ensgene/meta.yaml b/recipes/bioconductor-txdb.mmusculus.ucsc.mm10.ensgene/meta.yaml index 47fd245fb6..d96cc258c5 100644 --- a/recipes/bioconductor-txdb.mmusculus.ucsc.mm10.ensgene/meta.yaml +++ b/recipes/bioconductor-txdb.mmusculus.ucsc.mm10.ensgene/meta.yaml @@ -15,11 +15,11 @@ requirements: build: - bioconductor-annotationdbi - 'bioconductor-genomicfeatures >=1.21.30' - - r + - r-base run: - bioconductor-annotationdbi - 'bioconductor-genomicfeatures >=1.21.30' - - r + - r-base test: commands: - '$R -e "library(''TxDb.Mmusculus.UCSC.mm10.ensGene'')"' diff --git a/recipes/bioconductor-tximport/meta.yaml b/recipes/bioconductor-tximport/meta.yaml index 58166f91ff..134b1c244e 100644 --- a/recipes/bioconductor-tximport/meta.yaml +++ b/recipes/bioconductor-tximport/meta.yaml @@ -12,9 +12,9 @@ build: - lib/ requirements: build: - - r + - r-base run: - - r + - r-base test: commands: - '$R -e "library(''tximport'')"' diff --git a/recipes/bioconductor-variantannotation/meta.yaml b/recipes/bioconductor-variantannotation/meta.yaml index 97a65383a5..8aeb5feee3 100644 --- a/recipes/bioconductor-variantannotation/meta.yaml +++ b/recipes/bioconductor-variantannotation/meta.yaml @@ -27,7 +27,7 @@ requirements: - 'bioconductor-summarizedexperiment >=0.3.1' - 'bioconductor-xvector >=0.5.6' - bioconductor-zlibbioc - - r + - r-base - r-dbi run: - 'bioconductor-annotationdbi >=1.27.9' @@ -45,7 +45,7 @@ requirements: - 'bioconductor-summarizedexperiment >=0.3.1' - 'bioconductor-xvector >=0.5.6' - bioconductor-zlibbioc - - r + - r-base - r-dbi test: commands: diff --git a/recipes/bioconductor-vsn/meta.yaml b/recipes/bioconductor-vsn/meta.yaml index 4e5a20027d..8faf838ad2 100644 --- a/recipes/bioconductor-vsn/meta.yaml +++ b/recipes/bioconductor-vsn/meta.yaml @@ -15,7 +15,7 @@ build: requirements: build: - - r + - r-base - bioconductor-biobase - bioconductor-limma - bioconductor-affy @@ -24,7 +24,7 @@ requirements: run: - - r + - r-base - bioconductor-biobase - bioconductor-limma - bioconductor-affy diff --git a/recipes/bioconductor-xcms/1.44.0/meta.yaml b/recipes/bioconductor-xcms/1.44.0/meta.yaml index 53103f3a9d..21e9667ee0 100644 --- a/recipes/bioconductor-xcms/1.44.0/meta.yaml +++ b/recipes/bioconductor-xcms/1.44.0/meta.yaml @@ -17,14 +17,14 @@ requirements: - bioconductor-biocgenerics - 'bioconductor-mzr >=1.1.6' - bioconductor-protgenerics - - r + - r-base - r-rcolorbrewer run: - bioconductor-biobase - bioconductor-biocgenerics - 'bioconductor-mzr >=1.1.6' - bioconductor-protgenerics - - r + - r-base - r-rcolorbrewer test: commands: diff --git a/recipes/bioconductor-xcms/1.46.0/meta.yaml b/recipes/bioconductor-xcms/1.46.0/meta.yaml index 3080a48f44..eb276ab3c3 100644 --- a/recipes/bioconductor-xcms/1.46.0/meta.yaml +++ b/recipes/bioconductor-xcms/1.46.0/meta.yaml @@ -17,14 +17,14 @@ requirements: - bioconductor-biocgenerics - 'bioconductor-mzr >=1.1.6' - bioconductor-protgenerics - - r + - r-base - r-rcolorbrewer run: - bioconductor-biobase - bioconductor-biocgenerics - 'bioconductor-mzr >=1.1.6' - bioconductor-protgenerics - - r + - r-base - r-rcolorbrewer test: commands: diff --git a/recipes/bioconductor-xcms/1.48.0/meta.yaml b/recipes/bioconductor-xcms/1.48.0/meta.yaml index 40aee104da..d77045b390 100644 --- a/recipes/bioconductor-xcms/1.48.0/meta.yaml +++ b/recipes/bioconductor-xcms/1.48.0/meta.yaml @@ -17,14 +17,14 @@ requirements: - bioconductor-biocgenerics - 'bioconductor-mzr >=1.1.6' - bioconductor-protgenerics - - r + - r-base - r-rcolorbrewer run: - bioconductor-biobase - bioconductor-biocgenerics - 'bioconductor-mzr >=1.1.6' - bioconductor-protgenerics - - r + - r-base - r-rcolorbrewer test: commands: diff --git a/recipes/bioconductor-xcms/meta.yaml b/recipes/bioconductor-xcms/meta.yaml index 9e192260bc..9df332de5a 100644 --- a/recipes/bioconductor-xcms/meta.yaml +++ b/recipes/bioconductor-xcms/meta.yaml @@ -17,7 +17,7 @@ requirements: - bioconductor-biocgenerics - 'bioconductor-mzr >=1.1.6' - bioconductor-protgenerics - - r + - r-base - r-rcolorbrewer - r-plyr - r-rann @@ -30,7 +30,7 @@ requirements: - bioconductor-biocgenerics - 'bioconductor-mzr >=1.1.6' - bioconductor-protgenerics - - r + - r-base - r-rcolorbrewer - r-plyr - r-rann diff --git a/recipes/bioconductor-zlibbioc/meta.yaml b/recipes/bioconductor-zlibbioc/meta.yaml index 511be7fdc0..5c79d099b0 100644 --- a/recipes/bioconductor-zlibbioc/meta.yaml +++ b/recipes/bioconductor-zlibbioc/meta.yaml @@ -12,9 +12,9 @@ build: - lib/ requirements: build: - - r + - r-base run: - - r + - r-base test: commands: - '$R -e "library(''zlibbioc'')"' From 68c91576a396789e9bc2ce95d28c2e7ae5641d07 Mon Sep 17 00:00:00 2001 From: Bjoern Gruening Date: Sat, 3 Jun 2017 21:06:02 +0200 Subject: [PATCH 016/116] change r to r-base --- recipes/bcbio-rnaseq/meta.yaml | 2 +- recipes/breseq/meta.yaml | 2 +- recipes/cgat-scripts-devel/meta.yaml | 2 +- recipes/cgat-scripts/meta.yaml | 4 ++-- recipes/control-freec/meta.yaml | 2 +- recipes/eqtlbma/meta.yaml | 2 +- recipes/ericscript/meta.yaml | 2 +- recipes/hicup/meta.yaml | 2 +- recipes/jamm/1.0.7.2/meta.yaml | 2 +- recipes/kobas/meta.yaml | 2 +- recipes/lefse/meta.yaml | 2 +- recipes/maaslin/meta.yaml | 4 ++-- recipes/maxbin2/meta.yaml | 2 +- recipes/metilene/meta.yaml | 2 +- recipes/mgkit/meta.yaml | 4 ++-- recipes/multigps/0.72/meta.yaml | 2 +- recipes/multigps/0.73/meta.yaml | 2 +- recipes/multigps/0.74/meta.yaml | 2 +- recipes/nanosim-h/meta.yaml | 4 ++-- recipes/nanosim/meta.yaml | 4 ++-- recipes/nonpareil/meta.yaml | 4 ++-- recipes/peakranger/meta.yaml | 2 +- recipes/quake/meta.yaml | 2 +- recipes/rpy2/meta.yaml | 4 ++-- recipes/rseqc/meta.yaml | 2 +- recipes/triform2/meta.yaml | 4 ++-- recipes/tssar/meta.yaml | 4 ++-- 27 files changed, 36 insertions(+), 36 deletions(-) diff --git a/recipes/bcbio-rnaseq/meta.yaml b/recipes/bcbio-rnaseq/meta.yaml index 0bf0114215..207c74f5e4 100644 --- a/recipes/bcbio-rnaseq/meta.yaml +++ b/recipes/bcbio-rnaseq/meta.yaml @@ -13,7 +13,7 @@ build: requirements: run: - java-jdk - - r + - r-base - r-ggplot2 - r-stringr - r-dplyr diff --git a/recipes/breseq/meta.yaml b/recipes/breseq/meta.yaml index 3cf71ca392..a4637cfa14 100644 --- a/recipes/breseq/meta.yaml +++ b/recipes/breseq/meta.yaml @@ -22,7 +22,7 @@ requirements: run: - libgcc # [not osx] - zlib - - r + - r-base - bowtie2 test: diff --git a/recipes/cgat-scripts-devel/meta.yaml b/recipes/cgat-scripts-devel/meta.yaml index bb1b249517..e28fe9c363 100644 --- a/recipes/cgat-scripts-devel/meta.yaml +++ b/recipes/cgat-scripts-devel/meta.yaml @@ -52,7 +52,7 @@ requirements: - python-weblogo - pyyaml # R deps - - r + - r-base - r-coloc - r-flashclust - r-ggplot2 diff --git a/recipes/cgat-scripts/meta.yaml b/recipes/cgat-scripts/meta.yaml index 312b90e7b5..f9ee6a37ec 100644 --- a/recipes/cgat-scripts/meta.yaml +++ b/recipes/cgat-scripts/meta.yaml @@ -58,7 +58,7 @@ requirements: - six ==1.10.0 - scikit-learn ==0.18.1 # R deps - - r + - r-base - r-coloc - r-flashclust - r-ggplot2 ==2.2.1 @@ -138,7 +138,7 @@ requirements: - six ==1.10.0 - scikit-learn ==0.18.1 # R deps - - r + - r-base - r-coloc - r-flashclust - r-ggplot2 ==2.2.1 diff --git a/recipes/control-freec/meta.yaml b/recipes/control-freec/meta.yaml index f07a6f97af..d76d19e7e1 100644 --- a/recipes/control-freec/meta.yaml +++ b/recipes/control-freec/meta.yaml @@ -22,7 +22,7 @@ requirements: run: - libgcc - perl - - r + - r-base - bioconductor-rtracklayer test: diff --git a/recipes/eqtlbma/meta.yaml b/recipes/eqtlbma/meta.yaml index 76d373e8cd..af0cbd3ecd 100644 --- a/recipes/eqtlbma/meta.yaml +++ b/recipes/eqtlbma/meta.yaml @@ -26,7 +26,7 @@ requirements: - libgcc - gsl >=1.15,<2.0 - zlib - - r + - r-base - r-mass - bioconductor-genomicranges diff --git a/recipes/ericscript/meta.yaml b/recipes/ericscript/meta.yaml index 82ae607baf..888623f439 100644 --- a/recipes/ericscript/meta.yaml +++ b/recipes/ericscript/meta.yaml @@ -14,7 +14,7 @@ build: requirements: run: - - r + - r-base - perl - bedtools - blat diff --git a/recipes/hicup/meta.yaml b/recipes/hicup/meta.yaml index 6845675aed..58792b42df 100644 --- a/recipes/hicup/meta.yaml +++ b/recipes/hicup/meta.yaml @@ -12,7 +12,7 @@ requirements: - perl - bowtie2 - bowtie - - r + - r-base - samtools source: diff --git a/recipes/jamm/1.0.7.2/meta.yaml b/recipes/jamm/1.0.7.2/meta.yaml index 7530f0876a..af4cca9aed 100644 --- a/recipes/jamm/1.0.7.2/meta.yaml +++ b/recipes/jamm/1.0.7.2/meta.yaml @@ -16,7 +16,7 @@ build: requirements: run: - - r + - r-base - perl-threaded - r-signal - r-mclust >=4 diff --git a/recipes/kobas/meta.yaml b/recipes/kobas/meta.yaml index 7077751752..e431726b84 100644 --- a/recipes/kobas/meta.yaml +++ b/recipes/kobas/meta.yaml @@ -25,7 +25,7 @@ requirements: - pandas - biopython - sqlite - - r + - r-base - rpy2 test: diff --git a/recipes/lefse/meta.yaml b/recipes/lefse/meta.yaml index da047ce66d..1b8e2ce282 100644 --- a/recipes/lefse/meta.yaml +++ b/recipes/lefse/meta.yaml @@ -15,7 +15,7 @@ requirements: - python run: - python - - r + - r-base - r-survival - r-mvtnorm - r-modeltools diff --git a/recipes/maaslin/meta.yaml b/recipes/maaslin/meta.yaml index 43cfc62e05..b9b04fa3cf 100644 --- a/recipes/maaslin/meta.yaml +++ b/recipes/maaslin/meta.yaml @@ -19,7 +19,7 @@ build: requirements: build: - - r + - r-base - r-agricolae - r-gam - r-gamlss @@ -34,7 +34,7 @@ requirements: - r-robustbase run: - - r + - r-base - r-agricolae - r-gam - r-gamlss diff --git a/recipes/maxbin2/meta.yaml b/recipes/maxbin2/meta.yaml index ec27a35c6f..57be7f6bce 100644 --- a/recipes/maxbin2/meta.yaml +++ b/recipes/maxbin2/meta.yaml @@ -24,7 +24,7 @@ requirements: - hmmer - idba - perl-lwp-simple - - r + - r-base - r-gplots test: commands: diff --git a/recipes/metilene/meta.yaml b/recipes/metilene/meta.yaml index 0ca413d052..ff2915988d 100644 --- a/recipes/metilene/meta.yaml +++ b/recipes/metilene/meta.yaml @@ -26,7 +26,7 @@ requirements: run: - perl-threaded - bedtools >=2.24 - - r + - r-base - r-ggplot2 >=2.0.0 - libgcc # [linux] diff --git a/recipes/mgkit/meta.yaml b/recipes/mgkit/meta.yaml index 9776c105fe..6719760be9 100644 --- a/recipes/mgkit/meta.yaml +++ b/recipes/mgkit/meta.yaml @@ -40,7 +40,7 @@ requirements: - scipy >=0.15.1 - semidbm >=0.5.1 - pymongo >=3.1.1 - - r + - r-base - htseq >=0.6.0 - rpy2 >=2.3.8 - enum34 @@ -55,7 +55,7 @@ requirements: - scipy >=0.15.1 - semidbm >=0.5.1 - pymongo >=3.1.1 - - r + - r-base - htseq >=0.6.0 - rpy2 >=2.3.8 - enum34 diff --git a/recipes/multigps/0.72/meta.yaml b/recipes/multigps/0.72/meta.yaml index ee36d3a74b..4a62b62438 100644 --- a/recipes/multigps/0.72/meta.yaml +++ b/recipes/multigps/0.72/meta.yaml @@ -14,7 +14,7 @@ source: requirements: run: - - r + - r-base - bioconductor-edger - java-jdk >=8 - meme diff --git a/recipes/multigps/0.73/meta.yaml b/recipes/multigps/0.73/meta.yaml index aa7a285db6..938a3349b0 100644 --- a/recipes/multigps/0.73/meta.yaml +++ b/recipes/multigps/0.73/meta.yaml @@ -14,7 +14,7 @@ source: requirements: run: - - r + - r-base - bioconductor-edger - java-jdk >=8 - meme >=4.11.2 diff --git a/recipes/multigps/0.74/meta.yaml b/recipes/multigps/0.74/meta.yaml index 9ef0292333..4462e07561 100644 --- a/recipes/multigps/0.74/meta.yaml +++ b/recipes/multigps/0.74/meta.yaml @@ -16,7 +16,7 @@ source: requirements: run: - - r + - r-base - bioconductor-edger - java-jdk >=8 - meme >=4.11.2 diff --git a/recipes/nanosim-h/meta.yaml b/recipes/nanosim-h/meta.yaml index 6477844234..0cd4e2f6f3 100644 --- a/recipes/nanosim-h/meta.yaml +++ b/recipes/nanosim-h/meta.yaml @@ -19,13 +19,13 @@ requirements: - python - numpy - last - - r + - r-base - progressbar2 run: - python - numpy - last - - r + - r-base - progressbar2 test: diff --git a/recipes/nanosim/meta.yaml b/recipes/nanosim/meta.yaml index d53d262ecb..949f5897e3 100644 --- a/recipes/nanosim/meta.yaml +++ b/recipes/nanosim/meta.yaml @@ -19,12 +19,12 @@ requirements: - python - numpy - last - - r + - r-base run: - python - numpy - last - - r + - r-base test: commands: diff --git a/recipes/nonpareil/meta.yaml b/recipes/nonpareil/meta.yaml index 498d70f634..a2be967785 100644 --- a/recipes/nonpareil/meta.yaml +++ b/recipes/nonpareil/meta.yaml @@ -10,9 +10,9 @@ requirements: - autoconf - m4 - gcc - - r + - r-base run: - - r + - r-base build: skip: False test: diff --git a/recipes/peakranger/meta.yaml b/recipes/peakranger/meta.yaml index 842c37f224..a5d5431399 100644 --- a/recipes/peakranger/meta.yaml +++ b/recipes/peakranger/meta.yaml @@ -22,7 +22,7 @@ requirements: run: - boost {{CONDA_BOOST}}* - zlib - - r + - r-base test: commands: diff --git a/recipes/quake/meta.yaml b/recipes/quake/meta.yaml index 8bfc28defc..ea1a2778bc 100644 --- a/recipes/quake/meta.yaml +++ b/recipes/quake/meta.yaml @@ -27,7 +27,7 @@ requirements: - libgcc - boost {{CONDA_BOOST}}* - jellyfish - - r + - r-base - r-vgam - python diff --git a/recipes/rpy2/meta.yaml b/recipes/rpy2/meta.yaml index 5aeca78e77..8d2cd57a49 100644 --- a/recipes/rpy2/meta.yaml +++ b/recipes/rpy2/meta.yaml @@ -20,7 +20,7 @@ build: requirements: build: - python - - r + - r-base - setuptools - argparse # [py26] - singledispatch # [not (py34 or py35)] @@ -29,7 +29,7 @@ requirements: run: - python - - r + - r-base - argparse # [py26] - singledispatch # [not (py34 or py35)] - six diff --git a/recipes/rseqc/meta.yaml b/recipes/rseqc/meta.yaml index bd5efd49b4..dd224f7c38 100644 --- a/recipes/rseqc/meta.yaml +++ b/recipes/rseqc/meta.yaml @@ -27,7 +27,7 @@ requirements: - pysam - bx-python - numpy - - r + - r-base test: imports: diff --git a/recipes/triform2/meta.yaml b/recipes/triform2/meta.yaml index 0a922bd4ed..69ae990505 100644 --- a/recipes/triform2/meta.yaml +++ b/recipes/triform2/meta.yaml @@ -24,7 +24,7 @@ requirements: - bioconductor-iranges - bioconductor-biocgenerics - bioconductor-genomicranges - - r + - r-base - bx-python run: @@ -39,7 +39,7 @@ requirements: - bioconductor-iranges - bioconductor-biocgenerics - bioconductor-genomicranges - - r + - r-base - bx-python test: diff --git a/recipes/tssar/meta.yaml b/recipes/tssar/meta.yaml index efd3415e3e..a3dad71728 100644 --- a/recipes/tssar/meta.yaml +++ b/recipes/tssar/meta.yaml @@ -16,11 +16,11 @@ build: requirements: build: - - r + - r-base - gcc # [not win] run: - - r + - r-base - r-vgam - r-skellam - perl From 90bac3be6913838bc02d7a74205c57f281058f20 Mon Sep 17 00:00:00 2001 From: Bjoern Gruening Date: Sat, 3 Jun 2017 21:07:47 +0200 Subject: [PATCH 017/116] url fix --- recipes/r-bio3d/meta.yaml | 49 ++--------------------------------------------- 1 file changed, 2 insertions(+), 47 deletions(-) diff --git a/recipes/r-bio3d/meta.yaml b/recipes/r-bio3d/meta.yaml index d145d07b5d..e16afa2cd8 100644 --- a/recipes/r-bio3d/meta.yaml +++ b/recipes/r-bio3d/meta.yaml @@ -1,39 +1,24 @@ package: name: r-bio3d - # Note that conda versions cannot contain -, so any -'s in the version have - # been replaced with _'s. version: "2.2_3" source: fn: bio3d_2.2-3.tar.gz url: - - http://cran.r-project.org/src/contrib/bio3d_2.2-3.tar.gz - http://cran.r-project.org/src/contrib/Archive/bio3d/bio3d_2.2-3.tar.gz + sha256: 58afd7f9682c2355b62831793bef93159f91ab804a01bc05a16b208994815181 - # You can add a hash for the file here, like md5 or sha1 - # md5: 49448ba4863157652311cc5ea4fea3ea - # sha1: 3bcfbee008276084cbb37a2b453963c61176a322 - # patches: - # List any patch files here - # - fix.patch - build: - # If this is a new build for the same version, increment the build - # number. If you do not include this key, it defaults to 0. - # number: 1 + number: 0 skip: False - - # This is required to make R link correctly on Linux. rpaths: - lib/R/lib/ - lib/ -# Suggests: XML, RCurl, lattice, ncdf, igraph, bigmemory, knitr, testthat (>= 0.9.1) requirements: build: - r-base - run: - r-base @@ -43,12 +28,6 @@ test: - $R -e "library('bio3d')" # [not win] - "\"%R%\" -e \"library('bio3d')\"" # [win] - # You can also put a file called run_test.py, run_test.sh, or run_test.bat - # in the recipe that will be run at test time. - - # requires: - # Put any additional test requirements here. - about: home: http://thegrantlab.org/bio3d/, http://bitbucket.org/Grantlab/bio3d license: GPL (>= 2) @@ -62,27 +41,3 @@ about: addition, various utility functions are provided to enable the statistical and graphical power of the R environment to work with biological sequence and structural data. Please refer to the URLs below for more information. - -# The original CRAN metadata for this package was: - -# Package: bio3d -# Title: Biological Structure Analysis -# Version: 2.2-3 -# Author: Barry Grant, Xin-Qiu Yao, Lars Skjaerven, Julien Ide -# VignetteBuilder: knitr -# Imports: parallel, grid, graphics, grDevices, stats, utils -# Suggests: XML, RCurl, lattice, ncdf, igraph, bigmemory, knitr, testthat (>= 0.9.1) -# Depends: R (>= 3.1.0) -# LazyData: yes -# Description: Utilities to process, organize and explore protein structure, sequence and dynamics data. Features include the ability to read and write structure, sequence and dynamic trajectory data, perform sequence and structure database searches, data summaries, atom selection, alignment, superposition, rigid core identification, clustering, torsion analysis, distance matrix analysis, structure and sequence conservation analysis, normal mode analysis, principal component analysis of heterogeneous structure data, and correlation network analysis from normal mode and molecular dynamics data. In addition, various utility functions are provided to enable the statistical and graphical power of the R environment to work with biological sequence and structural data. Please refer to the URLs below for more information. -# Maintainer: Barry Grant -# License: GPL (>= 2) -# URL: http://thegrantlab.org/bio3d/, http://bitbucket.org/Grantlab/bio3d -# NeedsCompilation: no -# Packaged: 2015-09-04 17:42:13 UTC; xinqyao -# Repository: CRAN -# Date/Publication: 2015-09-04 21:49:41 - -# See -# http://docs.continuum.io/conda/build.html for -# more information about meta.yaml From 490a3fb544f6d71fabb43cfbb9e0fa889151f3e5 Mon Sep 17 00:00:00 2001 From: Bjoern Gruening Date: Sat, 3 Jun 2017 22:41:52 +0200 Subject: [PATCH 018/116] r fixes --- recipes/r-ade4/meta.yaml | 8 -------- recipes/r-bbmle/meta.yaml | 1 - recipes/r-deoptimr/meta.yaml | 29 ++++------------------------- recipes/r-logging/meta.yaml | 2 -- recipes/r-ptw/meta.yaml | 1 - recipes/r-scrm/meta.yaml | 34 +--------------------------------- recipes/r-speedglm/meta.yaml | 21 +-------------------- 7 files changed, 6 insertions(+), 90 deletions(-) diff --git a/recipes/r-ade4/meta.yaml b/recipes/r-ade4/meta.yaml index 25dfdf7112..8bb17c73d7 100644 --- a/recipes/r-ade4/meta.yaml +++ b/recipes/r-ade4/meta.yaml @@ -7,17 +7,9 @@ package: source: fn: ade4_1.7-2.tar.gz url: - - http://cran.r-project.org/src/contrib/ade4_1.7-2.tar.gz - http://cran.r-project.org/src/contrib/Archive/ade4/ade4_1.7-2.tar.gz - # You can add a hash for the file here, like md5 or sha1 - # md5: 49448ba4863157652311cc5ea4fea3ea - # sha1: 3bcfbee008276084cbb37a2b453963c61176a322 - # patches: - # List any patch files here - # - fix.patch - build: # If this is a new build for the same version, increment the build # number. If you do not include this key, it defaults to 0. diff --git a/recipes/r-bbmle/meta.yaml b/recipes/r-bbmle/meta.yaml index 911daac1ae..62a50c762f 100644 --- a/recipes/r-bbmle/meta.yaml +++ b/recipes/r-bbmle/meta.yaml @@ -10,7 +10,6 @@ package: source: fn: bbmle_1.0.18.tar.gz url: - - http://cran.r-project.org/src/contrib/bbmle_1.0.18.tar.gz - http://cran.r-project.org/src/contrib/Archive/bbmle/bbmle_1.0.18.tar.gz md5: e14e672c3d14a6d36133c54292fc57f9 diff --git a/recipes/r-deoptimr/meta.yaml b/recipes/r-deoptimr/meta.yaml index 5fb3f4b82b..92c71c7c31 100644 --- a/recipes/r-deoptimr/meta.yaml +++ b/recipes/r-deoptimr/meta.yaml @@ -7,22 +7,25 @@ package: source: fn: DEoptimR_1.0-6.tar.gz url: - - http://cran.r-project.org/src/contrib/DEoptimR_1.0-6.tar.gz - http://cran.r-project.org/src/contrib/Archive/DEoptimR/DEoptimR_1.0-6.tar.gz md5: 882cac87c736fc4c66c51065e81287ff + build: rpaths: - lib/R/lib/ - lib/ + requirements: build: - r-base run: - r-base + test: commands: - $R -e "library('DEoptimR')" # [not win] - "\"%R%\" -e \"library('DEoptimR')\"" # [win] + about: #home: license: GPL (>= 2) @@ -30,27 +33,3 @@ about: algorithm for global optimization of nonlinear programming problems. license_family: GPL3 -# The original CRAN metadata for this package was: - -# Package: DEoptimR -# Version: 1.0-6 -# Date: 2016-07-05 -# Title: Differential Evolution Optimization in Pure R -# Author: Eduardo L. T. Conceicao [aut, cre] and Martin Maechler [ctb] -# Maintainer: Eduardo L. T. Conceicao -# Description: An implementation of a bespoke jDE variant of the Differential Evolution stochastic algorithm for global optimization of nonlinear programming problems. -# Imports: stats -# Enhances: robustbase -# License: GPL (>= 2) -# ByteCompile: yes -# Repository: CRAN -# Repository/R-Forge/Project: robustbase -# Repository/R-Forge/Revision: 728 -# Repository/R-Forge/DateTimeStamp: 2016-07-05 14:38:06 -# Date/Publication: 2016-07-06 01:09:27 -# NeedsCompilation: no -# Packaged: 2016-07-05 15:25:22 UTC; rforge - -# See -# http://docs.continuum.io/conda/build.html for -# more information about meta.yaml diff --git a/recipes/r-logging/meta.yaml b/recipes/r-logging/meta.yaml index 94907352f7..637395d704 100644 --- a/recipes/r-logging/meta.yaml +++ b/recipes/r-logging/meta.yaml @@ -18,10 +18,8 @@ build: requirements: build: - r-base - - icu 58.* run: - r-base - - icu 58.* test: commands: diff --git a/recipes/r-ptw/meta.yaml b/recipes/r-ptw/meta.yaml index 1d52ccd0e3..ffb5dac06a 100644 --- a/recipes/r-ptw/meta.yaml +++ b/recipes/r-ptw/meta.yaml @@ -8,7 +8,6 @@ package: source: fn: {{ name }}_{{ version }}.tar.gz url: - - https://cran.r-project.org/src/contrib/{{ name }}_{{ version }}.tar.gz - https://cran.r-project.org/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz md5: 5d8a55494552f62c8c9d6826db9087ad diff --git a/recipes/r-scrm/meta.yaml b/recipes/r-scrm/meta.yaml index b2bb1f1659..4c54e76a43 100644 --- a/recipes/r-scrm/meta.yaml +++ b/recipes/r-scrm/meta.yaml @@ -3,24 +3,20 @@ package: name: r-scrm - # Note that conda versions cannot contain -, so any -'s in the version have - # been replaced with _'s. version: "1.6.0_2" source: fn: scrm_1.6.0-2.tar.gz url: - - http://cran.r-project.org/src/contrib/scrm_1.6.0-2.tar.gz - http://cran.r-project.org/src/contrib/Archive/scrm/scrm_1.6.0-2.tar.gz + sha256: 36b0090d8bbed01482b27705decc184aae328f49001e066535a22846a42975a8 build: - # This is required to make R link correctly on Linux. rpaths: - lib/R/lib/ - lib/ skip: True # [osx] -# Suggests: testthat (>= 0.9.0), knitr, ape requirements: build: - r-base @@ -34,7 +30,6 @@ requirements: test: commands: - # You can put additional test commands to be run here. - $R -e "library('scrm')" # [not win] - "\"%R%\" -e \"library('scrm')\"" # [win] @@ -49,30 +44,3 @@ about: thousand sequences. license_family: GPL3 -# The original CRAN metadata for this package was: - -# Package: scrm -# Type: Package -# Title: Simulating the Evolution of Biological Sequences -# Version: 1.6.0-2 -# Date: 2015-06-06 -# Authors@R: c( person('Paul', 'Staab', , 'develop@paulstaab.de', role=c('aut', 'cre', 'cph')), person('Zhu', 'Sha', role=c('aut', 'cph')), person('Dirk', 'Metzler', role=c('aut', 'cph', 'ths')), person('Gerton', 'Lunter', role=c('aut', 'cph', 'ths')) ) -# Description: A coalescent simulator that allows the rapid simulation of biological sequences under neutral models of evolution. Different to other coalescent based simulations, it has an optional approximation parameter that allows for high accuracy while maintaining a linear run time cost for long sequences. It is optimized for simulating massive data sets as produced by Next-Generation Sequencing technologies for up to several thousand sequences. -# URL: https://github.com/scrm/scrm-r -# License: GPL (>= 3) -# Depends: R (>= 3.1.0) -# Imports: Rcpp (>= 0.11.2) -# Suggests: testthat (>= 0.9.0), knitr, ape -# SystemRequirements: C++11 -# VignetteBuilder: knitr -# LinkingTo: Rcpp -# NeedsCompilation: yes -# Packaged: 2015-06-06 14:03:32 UTC; paul -# Author: Paul Staab [aut, cre, cph], Zhu Sha [aut, cph], Dirk Metzler [aut, cph, ths], Gerton Lunter [aut, cph, ths] -# Maintainer: Paul Staab -# Repository: CRAN -# Date/Publication: 2015-06-07 08:24:01 - -# See -# http://docs.continuum.io/conda/build.html for -# more information about meta.yaml diff --git a/recipes/r-speedglm/meta.yaml b/recipes/r-speedglm/meta.yaml index e49f638fca..18a38c1b09 100644 --- a/recipes/r-speedglm/meta.yaml +++ b/recipes/r-speedglm/meta.yaml @@ -3,30 +3,18 @@ package: name: r-speedglm - # Note that conda versions cannot contain -, so any -'s in the version have - # been replaced with _'s. version: "0.3_1" source: fn: speedglm_0.3-1.tar.gz url: - - http://cran.r-project.org/src/contrib/speedglm_0.3-1.tar.gz - http://cran.r-project.org/src/contrib/Archive/speedglm/speedglm_0.3-1.tar.gz - - # You can add a hash for the file here, like md5 or sha1 - # md5: 49448ba4863157652311cc5ea4fea3ea - # sha1: 3bcfbee008276084cbb37a2b453963c61176a322 - # patches: - # List any patch files here - # - fix.patch - build: # If this is a new build for the same version, increment the build # number. If you do not include this key, it defaults to 0. # number: 1 - # This is required to make R link correctly on Linux. rpaths: - lib/R/lib/ - lib/ @@ -49,14 +37,7 @@ test: - $R -e "library('speedglm')" # [not win] - "\"%R%\" -e \"library('speedglm')\"" # [win] - # You can also put a file called run_test.py, run_test.sh, or run_test.bat - # in the recipe that will be run at test time. - - # requires: - # Put any additional test requirements here. - about: #home: license: GPL - summary: Fitting linear models and generalized linear models to large data sets by updating - algorithms. + summary: Fitting linear models and generalized linear models to large data sets by updating algorithms. From 4994c6b0e25aa078bc614f9bd4ecbacd248453ad Mon Sep 17 00:00:00 2001 From: Bjoern Gruening Date: Sat, 3 Jun 2017 23:03:26 +0200 Subject: [PATCH 019/116] r fixes --- recipes/r-ade4/meta.yaml | 40 ----------------------------------- recipes/r-argparse/meta.yaml | 1 - recipes/r-r.methodss3/1.7.0/meta.yaml | 33 +++-------------------------- recipes/r-r.methodss3/meta.yaml | 7 +++--- 4 files changed, 6 insertions(+), 75 deletions(-) diff --git a/recipes/r-ade4/meta.yaml b/recipes/r-ade4/meta.yaml index 8bb17c73d7..59de764fc2 100644 --- a/recipes/r-ade4/meta.yaml +++ b/recipes/r-ade4/meta.yaml @@ -1,7 +1,5 @@ package: name: r-ade4 - # Note that conda versions cannot contain -, so any -'s in the version have - # been replaced with _'s. version: "1.7_2" source: @@ -9,22 +7,18 @@ source: url: - http://cran.r-project.org/src/contrib/Archive/ade4/ade4_1.7-2.tar.gz - build: # If this is a new build for the same version, increment the build # number. If you do not include this key, it defaults to 0. # number: 1 skip: False - # This is required to make R link correctly on Linux. rpaths: - lib/R/lib/ - lib/ -# Suggests: waveslim, splancs, MASS, maptools, spdep, pixmap, ape, deldir, ade4TkGUI, adegraphics, sp, lattice requirements: build: - r-base - run: - r-base @@ -34,41 +28,7 @@ test: - $R -e "library('ade4')" # [not win] - "\"%R%\" -e \"library('ade4')\"" # [win] - # You can also put a file called run_test.py, run_test.sh, or run_test.bat - # in the recipe that will be run at test time. - - # requires: - # Put any additional test requirements here. - about: home: 'http://pbil.univ-lyon1.fr/ADE-4, Mailing list: http://listes.univ-lyon1.fr/wws/info/adelist' - license: GPL (>= 2) summary: Multivariate data analysis and graphical display. - -# The original CRAN metadata for this package was: - -# Package: ade4 -# Version: 1.7-2 -# Date: 2015-04-14 -# Title: Analysis of Ecological Data : Exploratory and Euclidean Methods in Environmental Sciences -# Author: Stephane Dray , Anne-Beatrice Dufour , and Jean Thioulouse , with contributions from Thibaut Jombart, Sandrine Pavoine, Jean R. Lobry, Sebastien Ollier, and Aurelie Siberchicot. Based on earlier work by Daniel Chessel. -# Maintainer: Aurelie Siberchicot -# Imports: methods -# Suggests: waveslim, splancs, MASS, maptools, spdep, pixmap, ape, deldir, ade4TkGUI, adegraphics, sp, lattice -# Depends: R (>= 2.10) -# Description: Multivariate data analysis and graphical display. -# License: GPL (>= 2) -# URL: http://pbil.univ-lyon1.fr/ADE-4, Mailing list: http://listes.univ-lyon1.fr/wws/info/adelist -# Encoding: UTF-8 -# Repository: CRAN -# Repository/R-Forge/Project: ade4 -# Repository/R-Forge/Revision: 799 -# Repository/R-Forge/DateTimeStamp: 2015-04-14 07:38:21 -# Date/Publication: 2015-04-14 13:47:39 -# Packaged: 2015-04-14 07:45:42 UTC; rforge -# NeedsCompilation: yes - -# See -# http://docs.continuum.io/conda/build.html for -# more information about meta.yaml diff --git a/recipes/r-argparse/meta.yaml b/recipes/r-argparse/meta.yaml index eb54325157..869d98f7f6 100644 --- a/recipes/r-argparse/meta.yaml +++ b/recipes/r-argparse/meta.yaml @@ -7,7 +7,6 @@ package: source: fn: argparse_1.0.1.tar.gz url: - - http://cran.r-project.org/src/contrib/argparse_1.0.1.tar.gz - http://cran.r-project.org/src/contrib/Archive/argparse/argparse_1.0.1.tar.gz md5: f5b703459cf324c5bb8dbe3520defe58 diff --git a/recipes/r-r.methodss3/1.7.0/meta.yaml b/recipes/r-r.methodss3/1.7.0/meta.yaml index 67f2ab350c..95b08c4f0f 100644 --- a/recipes/r-r.methodss3/1.7.0/meta.yaml +++ b/recipes/r-r.methodss3/1.7.0/meta.yaml @@ -5,12 +5,10 @@ package: source: fn: R.methodsS3_1.7.0.tar.gz url: - - http://cran.r-project.org/src/contrib/R.methodsS3_1.7.0.tar.gz - http://cran.r-project.org/src/contrib/Archive/R.methodsS3/R.methodsS3_1.7.0.tar.gz md5: 3198eccdb5b163bf1c4c94410dad71a3 build: - rpaths: - lib/R/lib/ - lib/ @@ -19,7 +17,6 @@ build: requirements: build: - r-base - run: - r-base @@ -28,38 +25,14 @@ test: - $R -e "library('R.methodsS3')" # [not win] - "\"%R%\" -e \"library('R.methodsS3')\"" # [win] - about: #home: license: LGPL (>= 2.1) - summary: !!python/unicode 'Methods that simplify the setup of S3 generic functions and S3 methods. Major + summary: | + Methods that simplify the setup of S3 generic functions and S3 methods. Major effort has been made in making definition of methods as simple as possible with a minimum of maintenance for package developers. For example, generic functions are created automatically, if missing, and naming conflict are automatically solved, if possible. The method setMethodS3() is a good start for those who in the future may want to migrate to S4. This is a cross-platform package implemented in pure - R that generates standard S3 methods.' - - -# The original CRAN metadata for this package was: - -# Package: R.methodsS3 -# Version: 1.7.0 -# Depends: R (>= 2.2.0) -# Imports: utils -# Date: 2015-02-19 -# Title: S3 Methods Simplified -# Authors@R: c(person("Henrik", "Bengtsson", role=c("aut", "cre", "cph"), email = "henrikb@braju.com")) -# Author: Henrik Bengtsson [aut, cre, cph] -# Maintainer: Henrik Bengtsson -# Description: Methods that simplify the setup of S3 generic functions and S3 methods. Major effort has been made in making definition of methods as simple as possible with a minimum of maintenance for package developers. For example, generic functions are created automatically, if missing, and naming conflict are automatically solved, if possible. The method setMethodS3() is a good start for those who in the future may want to migrate to S4. This is a cross-platform package implemented in pure R that generates standard S3 methods. -# License: LGPL (>= 2.1) -# LazyLoad: TRUE -# NeedsCompilation: no -# Packaged: 2015-02-20 03:15:35 UTC; hb -# Repository: CRAN -# Date/Publication: 2015-02-20 09:16:51 - -# See -# http://docs.continuum.io/conda/build.html for -# more information about meta.yaml + R that generates standard S3 methods. diff --git a/recipes/r-r.methodss3/meta.yaml b/recipes/r-r.methodss3/meta.yaml index da85cc8c28..2b2ad6e7f6 100644 --- a/recipes/r-r.methodss3/meta.yaml +++ b/recipes/r-r.methodss3/meta.yaml @@ -8,6 +8,7 @@ package: source: fn: R.methodsS3_1.7.1.tar.gz url: + - https://cran.r-project.org/src/contrib/R.methodsS3_1.7.1.tar.gz - http://cran.r-project.org/src/contrib/Archive/R.methodsS3/R.methodsS3_1.7.1.tar.gz md5: c88e815837f268affd4f2a39c737d969 @@ -16,11 +17,9 @@ build: - lib/R/lib/ - lib/ - requirements: build: - r-base - run: - r-base @@ -28,11 +27,11 @@ test: commands: - $R -e "library('R.methodsS3')" - about: #home: license: LGPL (>= 2.1) - summary: Methods that simplify the setup of S3 generic functions and S3 methods. Major effort + summary: | + Methods that simplify the setup of S3 generic functions and S3 methods. Major effort has been made in making definition of methods as simple as possible with a minimum of maintenance for package developers. For example, generic functions are created automatically, if missing, and naming conflict are automatically solved, if possible. The From f1f1ea1a9fcd90f7455d594ff27c5b84e9fc09d8 Mon Sep 17 00:00:00 2001 From: Bjoern Gruening Date: Sun, 4 Jun 2017 00:20:30 +0200 Subject: [PATCH 020/116] remove irganes 2.4.7 --- recipes/bioconductor-iranges/2.4.7/build.sh | 17 -------------- recipes/bioconductor-iranges/2.4.7/meta.yaml | 34 ---------------------------- 2 files changed, 51 deletions(-) delete mode 100644 recipes/bioconductor-iranges/2.4.7/build.sh delete mode 100644 recipes/bioconductor-iranges/2.4.7/meta.yaml diff --git a/recipes/bioconductor-iranges/2.4.7/build.sh b/recipes/bioconductor-iranges/2.4.7/build.sh deleted file mode 100644 index 6c7a1726e3..0000000000 --- a/recipes/bioconductor-iranges/2.4.7/build.sh +++ /dev/null @@ -1,17 +0,0 @@ - -#!/bin/bash - -# R refuses to build packages that mark themselves as -# "Priority: Recommended" -mv DESCRIPTION DESCRIPTION.old -grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION -# -$R CMD INSTALL --build . -# -# # Add more build steps here, if they are necessary. -# -# See -# http://docs.continuum.io/conda/build.html -# for a list of environment variables that are set during the build -# process. -# \ No newline at end of file diff --git a/recipes/bioconductor-iranges/2.4.7/meta.yaml b/recipes/bioconductor-iranges/2.4.7/meta.yaml deleted file mode 100644 index 518bef3941..0000000000 --- a/recipes/bioconductor-iranges/2.4.7/meta.yaml +++ /dev/null @@ -1,34 +0,0 @@ -package: - name: bioconductor-iranges - version: 2.4.7 -source: - fn: IRanges_2.4.7.tar.gz - url: http://archive.ubuntu.com/ubuntu/pool/universe/r/r-bioc-iranges/r-bioc-iranges_2.4.7.orig.tar.gz - md5: 838be15d5f7837ee7258e0af2e2f8d9d -build: - number: 0 - rpaths: - - lib/R/lib/ - - lib/ -requirements: - build: - - bioconductor-biocgenerics >=0.15.10 - - bioconductor-s4vectors >=0.8.4 - - r-base - run: - - bioconductor-biocgenerics >=0.15.10 - - bioconductor-s4vectors >=0.8.4 - - r-base -test: - commands: - - $R -e "library('IRanges')" -about: - home: http://bioconductor.org/packages/release/bioc/html/IRanges.html - license: Artistic-2.0 - summary: 'The package provides efficient low-level and highly reusable S4 classes - for storing ranges of integers, RLE vectors (Run-Length Encoding), and, more generally, - data that can be organized sequentially (formally defined as Vector objects), - as well as views on these Vector objects. Efficient list-like classes are also - provided for storing big collections of instances of the basic classes. All classes - in the package use consistent naming and share the same rich and consistent "Vector - API" as much as possible.' From b2a42d636e8cac051685347b0272ca67b14e503b Mon Sep 17 00:00:00 2001 From: Bjoern Gruening Date: Sun, 4 Jun 2017 00:22:28 +0200 Subject: [PATCH 021/116] r fixes --- recipes/bioconductor-biobase/meta.yaml | 9 +++++++-- recipes/r-fields/meta.yaml | 1 - recipes/r-fitdistrplus/meta.yaml | 36 --------------------------------- recipes/r-getoptlong/meta.yaml | 37 ---------------------------------- recipes/r-leaps/meta.yaml | 11 ---------- recipes/r-matrixeqtl/meta.yaml | 25 ----------------------- recipes/r-mclust/meta.yaml | 29 -------------------------- recipes/r-r.oo/meta.yaml | 1 - 8 files changed, 7 insertions(+), 142 deletions(-) diff --git a/recipes/bioconductor-biobase/meta.yaml b/recipes/bioconductor-biobase/meta.yaml index a8891e7092..449166f3d9 100644 --- a/recipes/bioconductor-biobase/meta.yaml +++ b/recipes/bioconductor-biobase/meta.yaml @@ -1,14 +1,17 @@ package: name: bioconductor-biobase version: 2.34.0 + source: - url: https://bioconductor.org/packages/release/bioc/src/contrib/Biobase_2.34.0.tar.gz - md5: b761d9241462a4c6403731203c9fbb94 + url: https://depot.galaxyproject.org/software/bioconductor-biobase/bioconductor-biobase_2.34.0_src_all.tar.gz + sha256: f4ab46c3a02e2c9e9f70b99d751c8749a5b528a53e5117c3290e698a7992494b + build: number: 0 rpaths: - lib/R/lib/ - lib/ + requirements: build: - 'bioconductor-biocgenerics >=0.3.2' @@ -16,9 +19,11 @@ requirements: run: - 'bioconductor-biocgenerics >=0.3.2' - r-base + test: commands: - '$R -e "library(''Biobase'')"' + about: home: https://bioconductor.org/packages/release/bioc/html/Biobase.html license: Artistic-2.0 diff --git a/recipes/r-fields/meta.yaml b/recipes/r-fields/meta.yaml index 1c68eeb76c..453e477444 100644 --- a/recipes/r-fields/meta.yaml +++ b/recipes/r-fields/meta.yaml @@ -11,7 +11,6 @@ package: source: fn: {{ name }}_{{ version }}.tar.gz url: - - https://cran.r-project.org/src/contrib/{{ name }}_{{ version }}.tar.gz - https://cran.r-project.org/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz md5: 9be135ef91812627c7830e39fffd19c5 diff --git a/recipes/r-fitdistrplus/meta.yaml b/recipes/r-fitdistrplus/meta.yaml index 6a7084d026..78f4b5a009 100644 --- a/recipes/r-fitdistrplus/meta.yaml +++ b/recipes/r-fitdistrplus/meta.yaml @@ -7,17 +7,8 @@ package: source: fn: fitdistrplus_1.0-6.tar.gz url: - - http://cran.r-project.org/src/contrib/fitdistrplus_1.0-6.tar.gz - http://cran.r-project.org/src/contrib/Archive/fitdistrplus/fitdistrplus_1.0-6.tar.gz - - # You can add a hash for the file here, like md5 or sha1 - # md5: 49448ba4863157652311cc5ea4fea3ea - # sha1: 3bcfbee008276084cbb37a2b453963c61176a322 - # patches: - # List any patch files here - # - fix.patch - build: # If this is a new build for the same version, increment the build # number. If you do not include this key, it defaults to 0. @@ -62,30 +53,3 @@ about: the package provides moment matching (MME), quantile matching (QME) and maximum goodness-of-fit estimation (MGE) methods (available only for non-censored data). Weighted versions of MLE, MME and QME are available. - -# The original CRAN metadata for this package was: - -# Package: fitdistrplus -# Title: Help to Fit of a Parametric Distribution to Non-Censored or Censored Data -# Version: 1.0-6 -# Date: 2015-11-20 -# Authors@R: c(person("Marie Laure", "Delignette-Muller", role = c("aut", "cre"), email= "marielaure.delignettemuller@vetagro-sup.fr"),person("Christophe", "Dutang", role = "aut", email = "christophe.dutang@univ-lemans.fr"),person("Regis", "Pouillot", role = "ctb", email = "rpouillot@yahoo.fr"),person("Jean-Baptiste", "Denis", role = "ctb", email = "jbdenis@jouy.inra.fr")) -# Description: Extends the fitdistr function (of the MASS package) with several functions to help the fit of a parametric distribution to non-censored or censored data. Censored data may contain left censored, right censored and interval censored values, with several lower and upper bounds. In addition to maximum likelihood estimation (MLE), the package provides moment matching (MME), quantile matching (QME) and maximum goodness-of-fit estimation (MGE) methods (available only for non-censored data). Weighted versions of MLE, MME and QME are available. -# Depends: R (>= 3.2.0), MASS, grDevices -# Imports: stats, survival -# Suggests: actuar, rgenoud, mc2d, gamlss.dist -# License: GPL (>= 2) -# URL: http://riskassessment.r-forge.r-project.org -# Author: Marie Laure Delignette-Muller [aut, cre], Christophe Dutang [aut], Regis Pouillot [ctb], Jean-Baptiste Denis [ctb] -# Maintainer: Marie Laure Delignette-Muller -# Repository: CRAN -# Repository/R-Forge/Project: riskassessment -# Repository/R-Forge/Revision: 365 -# Repository/R-Forge/DateTimeStamp: 2015-11-24 15:15:04 -# Date/Publication: 2015-11-30 13:13:41 -# NeedsCompilation: no -# Packaged: 2015-11-24 15:25:58 UTC; rforge - -# See -# http://docs.continuum.io/conda/build.html for -# more information about meta.yaml diff --git a/recipes/r-getoptlong/meta.yaml b/recipes/r-getoptlong/meta.yaml index 3151001776..a520c368e5 100644 --- a/recipes/r-getoptlong/meta.yaml +++ b/recipes/r-getoptlong/meta.yaml @@ -1,23 +1,12 @@ package: name: r-getoptlong - # Note that conda versions cannot contain -, so any -'s in the version have - # been replaced with _'s. version: "0.1.0" source: fn: GetoptLong_0.1.0.tar.gz url: - - http://cran.r-project.org/src/contrib/GetoptLong_0.1.0.tar.gz - http://cran.r-project.org/src/contrib/Archive/GetoptLong/GetoptLong_0.1.0.tar.gz - - # You can add a hash for the file here, like md5 or sha1 - # md5: 49448ba4863157652311cc5ea4fea3ea - # sha1: 3bcfbee008276084cbb37a2b453963c61176a322 - # patches: - # List any patch files here - # - fix.patch - build: # If this is a new build for the same version, increment the build # number. If you do not include this key, it defaults to 0. @@ -58,29 +47,3 @@ about: summary: This is yet another command-line argument parser which wraps the powerful Perl module Getopt::Long and with some adaptation for easier use in R. It also provides a simple way for variable interpolation in R. - -# The original CRAN metadata for this package was: - -# Package: GetoptLong -# Type: Package -# Title: Parsing Command-Line Arguments and Variable Interpolation -# Version: 0.1.0 -# Date: 2015-3-8 -# Author: Zuguang Gu -# Maintainer: Zuguang Gu -# Depends: R (>= 2.10.0) -# Suggests: testthat (>= 0.3), knitr -# VignetteBuilder: knitr -# Imports: rjson, methods, GlobalOptions (>= 0.0.6) -# Description: This is yet another command-line argument parser which wraps the powerful Perl module Getopt::Long and with some adaptation for easier use in R. It also provides a simple way for variable interpolation in R. -# URL: https://github.com/jokergoo/GetoptLong -# SystemRequirements: Perl, Getopt::Long -# License: GPL (>= 2) -# Packaged: 2015-03-09 09:55:20 UTC; IBM -# Repository: CRAN -# Date/Publication: 2015-03-09 12:47:36 -# NeedsCompilation: no - -# See -# http://docs.continuum.io/conda/build.html for -# more information about meta.yaml diff --git a/recipes/r-leaps/meta.yaml b/recipes/r-leaps/meta.yaml index 06a444c5ef..1df2a3ae07 100644 --- a/recipes/r-leaps/meta.yaml +++ b/recipes/r-leaps/meta.yaml @@ -3,24 +3,13 @@ package: name: r-leaps - # Note that conda versions cannot contain -, so any -'s in the version have - # been replaced with _'s. version: "2.9" source: fn: leaps_2.9.tar.gz url: - - http://cran.r-project.org/src/contrib/leaps_2.9.tar.gz - http://cran.r-project.org/src/contrib/Archive/leaps/leaps_2.9.tar.gz - - # You can add a hash for the file here, like md5 or sha1 - # md5: 49448ba4863157652311cc5ea4fea3ea - # sha1: 3bcfbee008276084cbb37a2b453963c61176a322 - # patches: - # List any patch files here - # - fix.patch - build: # If this is a new build for the same version, increment the build # number. If you do not include this key, it defaults to 0. diff --git a/recipes/r-matrixeqtl/meta.yaml b/recipes/r-matrixeqtl/meta.yaml index 039d9eb536..31c5531e55 100644 --- a/recipes/r-matrixeqtl/meta.yaml +++ b/recipes/r-matrixeqtl/meta.yaml @@ -22,10 +22,8 @@ build: requirements: build: - r-base - - icu 58.* run: - r-base - - icu 58.* test: commands: @@ -42,26 +40,3 @@ about: also supports models with heteroscedastic and/or correlated errors, false discovery rate estimation and separate treatment of local (cis) and distant (trans) eQTLs. license_family: LGPL - -# The original CRAN metadata for this package was: - -# Package: MatrixEQTL -# Type: Package -# Title: Matrix eQTL: Ultra fast eQTL analysis via large matrix operations -# Version: 2.1.1 -# Date: 2014-02-24 -# Author: Andrey Shabalin -# Maintainer: Andrey Shabalin -# Description: Matrix eQTL is designed for fast eQTL analysis on large datasets. Matrix eQTL can test for association between genotype and gene expression using linear regression with either additive or ANOVA genotype effects. The models can include covariates to account for factors as population stratification, gender, and clinical variables. It also supports models with heteroscedastic and/or correlated errors, false discovery rate estimation and separate treatment of local (cis) and distant (trans) eQTLs. -# License: LGPL-3 -# LazyLoad: yes -# URL: http://www.bios.unc.edu/research/genomic_software/Matrix_eQTL/ -# Depends: R (>= 2.12.0), methods -# NeedsCompilation: no -# Packaged: 2015-02-03 05:30:21 UTC; Andrey -# Repository: CRAN -# Date/Publication: 2015-02-03 06:53:36 - -# See -# http://docs.continuum.io/conda/build.html for -# more information about meta.yaml diff --git a/recipes/r-mclust/meta.yaml b/recipes/r-mclust/meta.yaml index 8663c467c5..7ebcedd93e 100644 --- a/recipes/r-mclust/meta.yaml +++ b/recipes/r-mclust/meta.yaml @@ -5,7 +5,6 @@ package: source: fn: mclust_5.1.tar.gz url: - - http://cran.r-project.org/src/contrib/mclust_5.1.tar.gz - http://cran.r-project.org/src/contrib/Archive/mclust/mclust_5.1.tar.gz md5: f43b4bb255d8413fa932465a511f0c64 @@ -15,7 +14,6 @@ build: - lib/R/lib/ - lib/ -# Suggests: knitr (>= 1.8), rmarkdown (>= 0.6), mix requirements: build: - r-base @@ -34,30 +32,3 @@ about: license: GPL (>= 2) summary: Normal Mixture Modelling fitted via EM algorithm for Model-Based Clustering, Classification, and Density Estimation, including Bayesian regularization. - -# The original CRAN metadata for this package was: - -# Package: mclust -# Version: 5.1 -# Date: 2015-10-24 -# Authors@R: c(person("Chris", "Fraley", role = "aut"), person("Adrian E.", "Raftery", role = "aut"), person("Luca", "Scrucca", role = c("aut", "cre"), email = "luca@stat.unipg.it"), person("Thomas Brendan", "Murphy", role = "ctb"), person("Michael", "Fop", role = "ctb")) -# Title: Normal Mixture Modelling for Model-Based Clustering, Classification, and Density Estimation -# Description: Normal Mixture Modelling fitted via EM algorithm for Model-Based Clustering, Classification, and Density Estimation, including Bayesian regularization. -# Depends: R (>= 3.0) -# Imports: stats, utils, graphics, grDevices -# Suggests: knitr (>= 1.8), rmarkdown (>= 0.6), mix -# License: GPL (>= 2) -# URL: http://www.stat.washington.edu/mclust/ -# VignetteBuilder: knitr -# Repository: CRAN -# ByteCompile: true -# LazyLoad: yes -# NeedsCompilation: yes -# Packaged: 2015-10-26 17:30:30 UTC; luca -# Author: Chris Fraley [aut], Adrian E. Raftery [aut], Luca Scrucca [aut, cre], Thomas Brendan Murphy [ctb], Michael Fop [ctb] -# Maintainer: Luca Scrucca -# Date/Publication: 2015-10-27 08:10:04 - -# See -# http://docs.continuum.io/conda/build.html for -# more information about meta.yaml diff --git a/recipes/r-r.oo/meta.yaml b/recipes/r-r.oo/meta.yaml index b6888f6ede..25d5df6365 100644 --- a/recipes/r-r.oo/meta.yaml +++ b/recipes/r-r.oo/meta.yaml @@ -8,7 +8,6 @@ package: source: fn: R.oo_1.21.0.tar.gz url: - - http://cran.r-project.org/src/contrib/R.oo_1.21.0.tar.gz - http://cran.r-project.org/src/contrib/Archive/R.oo/R.oo_1.21.0.tar.gz md5: f0062095c763faaeba30558303f68bc3 From 14e163eac5a8ef1238042d96be37427e887a0ddd Mon Sep 17 00:00:00 2001 From: Bjoern Gruening Date: Sun, 4 Jun 2017 00:33:42 +0200 Subject: [PATCH 022/116] r fixes --- recipes/r-bit64/meta.yaml | 49 +++----------------------------------------- recipes/r-progress/meta.yaml | 32 ----------------------------- recipes/r-tibble/meta.yaml | 38 ---------------------------------- 3 files changed, 3 insertions(+), 116 deletions(-) diff --git a/recipes/r-bit64/meta.yaml b/recipes/r-bit64/meta.yaml index 67191ed8b0..b65ab601a9 100644 --- a/recipes/r-bit64/meta.yaml +++ b/recipes/r-bit64/meta.yaml @@ -1,26 +1,13 @@ package: name: r-bit64 - # Note that conda versions cannot contain -, so any -'s in the version have - # been replaced with _'s. version: "0.9_5" source: fn: bit64_0.9-5.tar.gz url: - - http://cran.r-project.org/src/contrib/bit64_0.9-5.tar.gz - http://cran.r-project.org/src/contrib/Archive/bit64/bit64_0.9-5.tar.gz - - # You can add a hash for the file here, like md5 or sha1 - # md5: 49448ba4863157652311cc5ea4fea3ea - # sha1: 3bcfbee008276084cbb37a2b453963c61176a322 - # patches: - # List any patch files here - # - fix.patch - build: - # If this is a new build for the same version, increment the build - # number. If you do not include this key, it defaults to 0. # number: 1 # This is required to make R link correctly on Linux. @@ -47,44 +34,14 @@ test: - $R -e "library('bit64')" # [not win] - "\"%R%\" -e \"library('bit64')\"" # [win] - # You can also put a file called run_test.py, run_test.sh, or run_test.bat - # in the recipe that will be run at test time. - - # requires: - # Put any additional test requirements here. - about: home: http://ff.r-forge.r-project.org/ license: GPL-2 - summary: ' Package ''bit64'' provides serializable S3 atomic 64bit (signed) integers that + summary: | + Package ''bit64'' provides serializable S3 atomic 64bit (signed) integers that can be used in vectors, matrices, arrays and data.frames. Methods are available for coercion from and to logicals, integers, doubles, characters and factors as well as many elementwise and summary functions. Many fast algorithmic operations such as ''match'' and ''order'' support interactive data exploration and manipulation - and optionally leverage caching.' - - -# The original CRAN metadata for this package was: - -# Package: bit64 -# Type: Package -# Title: A S3 Class for Vectors of 64bit Integers -# Version: 0.9-5 -# Date: 2015-06-24 -# Author: Jens Oehlschlägel -# Maintainer: Jens Oehlschlägel -# Depends: R (>= 3.0.1), bit (>= 1.1-12), utils, methods, stats -# Description: Package 'bit64' provides serializable S3 atomic 64bit (signed) integers that can be used in vectors, matrices, arrays and data.frames. Methods are available for coercion from and to logicals, integers, doubles, characters and factors as well as many elementwise and summary functions. Many fast algorithmic operations such as 'match' and 'order' support interactive data exploration and manipulation and optionally leverage caching. -# License: GPL-2 -# LazyLoad: yes -# ByteCompile: yes -# URL: http://ff.r-forge.r-project.org/ -# Encoding: latin1 -# Packaged: 2015-07-04 09:58:24 UTC; jo -# NeedsCompilation: yes -# Repository: CRAN -# Date/Publication: 2015-07-05 09:24:32 + and optionally leverage caching. -# See -# http://docs.continuum.io/conda/build.html for -# more information about meta.yaml diff --git a/recipes/r-progress/meta.yaml b/recipes/r-progress/meta.yaml index ae2bed4965..f9d4b21f83 100644 --- a/recipes/r-progress/meta.yaml +++ b/recipes/r-progress/meta.yaml @@ -3,14 +3,11 @@ package: name: r-progress - # Note that conda versions cannot contain -, so any -'s in the version have - # been replaced with _'s. version: "1.0.2" source: fn: progress_1.0.2.tar.gz url: - - http://cran.r-project.org/src/contrib/progress_1.0.2.tar.gz - http://cran.r-project.org/src/contrib/Archive/progress/progress_1.0.2.tar.gz @@ -49,12 +46,6 @@ test: - $R -e "library('progress')" # [not win] - "\"%R%\" -e \"library('progress')\"" # [win] - # You can also put a file called run_test.py, run_test.sh, or run_test.bat - # in the recipe that will be run at test time. - - # requires: - # Put any additional test requirements here. - about: home: https://github.com/gaborcsardi/progress license: MIT + file LICENSE @@ -63,26 +54,3 @@ about: Studio, Windows Rgui and Mac OSX R.app. The package also provides a C++ API, that works with or without Rcpp. license_family: MIT - -# The original CRAN metadata for this package was: - -# Package: progress -# Title: Terminal Progress Bars -# Version: 1.0.2 -# Author: Gabor Csardi [aut, cre] -# Maintainer: Gabor Csardi -# Description: Terminal progress bars. They are configurable, may include percentage, elapsed time, and/or the estimated completion time. They work in the command line, in Emacs, R Studio, Windows Rgui and Mac OSX R.app. The package also provides a C++ API, that works with or without Rcpp. -# License: MIT + file LICENSE -# LazyData: true -# URL: https://github.com/gaborcsardi/progress -# BugReports: https://github.com/gaborcsardi/progress/issues -# Imports: prettyunits, R6 -# Suggests: testthat -# NeedsCompilation: no -# Packaged: 2015-06-04 22:26:34 UTC; gaborcsardi -# Repository: CRAN -# Date/Publication: 2015-06-05 01:14:18 - -# See -# http://docs.continuum.io/conda/build.html for -# more information about meta.yaml diff --git a/recipes/r-tibble/meta.yaml b/recipes/r-tibble/meta.yaml index 5e9bbcb280..6b5c7a27b3 100644 --- a/recipes/r-tibble/meta.yaml +++ b/recipes/r-tibble/meta.yaml @@ -3,14 +3,11 @@ package: name: r-tibble - # Note that conda versions cannot contain -, so any -'s in the version have - # been replaced with _'s. version: "1.2" source: fn: tibble_1.2.tar.gz url: - - http://cran.r-project.org/src/contrib/tibble_1.2.tar.gz - http://cran.r-project.org/src/contrib/Archive/tibble/tibble_1.2.tar.gz md5sum: bdbc3d67aa16860741add6d6ec20ea13 @@ -56,44 +53,9 @@ test: - $R -e "library('tibble')" # [not win] - "\"%R%\" -e \"library('tibble')\"" # [win] - # You can also put a file called run_test.py, run_test.sh, or run_test.bat - # in the recipe that will be run at test time. - - # requires: - # Put any additional test requirements here. - about: home: https://github.com/hadley/tibble license: MIT + file LICENSE summary: Provides a 'tbl_df' class that offers better checking and printing capabilities than traditional data frames. license_family: MIT - -# The original CRAN metadata for this package was: - -# Package: tibble -# Encoding: UTF-8 -# Version: 1.2 -# Title: Simple Data Frames -# Description: Provides a 'tbl_df' class that offers better checking and printing capabilities than traditional data frames. -# Authors@R: c( person("Hadley", "Wickham", , "hadley@rstudio.com", "aut"), person("Romain", "Francois", , "romain@r-enthusiasts.com", "aut"), person("Kirill", "Muller", , "krlmlr+r@mailbox.org", c("aut", "cre")), person("RStudio", role = "cph") ) -# URL: https://github.com/hadley/tibble -# BugReports: https://github.com/hadley/tibble/issues -# Depends: R (>= 3.1.2) -# Imports: methods, assertthat, utils, lazyeval (>= 0.1.10), Rcpp -# Suggests: testthat, withr, knitr (>= 1.5.32), rmarkdown, nycflights13, microbenchmark -# LinkingTo: Rcpp -# LazyData: yes -# License: MIT + file LICENSE -# RoxygenNote: 5.0.1 -# VignetteBuilder: knitr -# NeedsCompilation: yes -# Packaged: 2016-08-26 11:42:44 UTC; muelleki -# Author: Hadley Wickham [aut], Romain Francois [aut], Kirill Muller [aut, cre], RStudio [cph] -# Maintainer: Kirill Muller -# Repository: CRAN -# Date/Publication: 2016-08-26 21:50:28 - -# See -# http://docs.continuum.io/conda/build.html for -# more information about meta.yaml From 326996ea881cf95b817dca8ee638804708f02508 Mon Sep 17 00:00:00 2001 From: Bjoern Gruening Date: Sun, 4 Jun 2017 10:01:58 +0200 Subject: [PATCH 023/116] r fixes --- recipes/bioconductor-biocinstaller/meta.yaml | 4 ++-- recipes/bioconductor-cardinal/meta.yaml | 4 ++-- recipes/bioconductor-ropls/meta.yaml | 4 ++-- recipes/r-bh/meta.yaml | 1 - recipes/r-circlize/meta.yaml | 1 - recipes/r-delaporte/meta.yaml | 1 - recipes/r-dendextend/meta.yaml | 1 - recipes/r-dorng/meta.yaml | 1 - recipes/r-fastcluster/meta.yaml | 1 - recipes/r-gamlss/meta.yaml | 1 - recipes/r-ggally/meta.yaml | 1 - recipes/r-globals/meta.yaml | 1 - recipes/r-googlevis/meta.yaml | 1 - recipes/r-lambda.r/meta.yaml | 1 - recipes/r-listenv/meta.yaml | 1 - recipes/r-penalized/meta.yaml | 2 +- recipes/r-pracma/meta.yaml | 1 - recipes/r-preseqr/meta.yaml | 1 - recipes/r-proxy/meta.yaml | 1 - recipes/r-prroc/meta.yaml | 1 - recipes/r-qqman/meta.yaml | 1 - recipes/r-r.oo/1.19.0/meta.yaml | 1 - recipes/r-r.oo/meta.yaml | 1 + recipes/r-rsm/meta.yaml | 1 - recipes/r-rwave/meta.yaml | 1 - recipes/r-seqinr/meta.yaml | 1 - recipes/r-sets/meta.yaml | 1 - recipes/r-snow/meta.yaml | 1 - recipes/r-upsetr/meta.yaml | 1 - recipes/r-vegan/2.3_3/meta.yaml | 1 - recipes/r-vegan/2.3_4/meta.yaml | 1 - 31 files changed, 8 insertions(+), 33 deletions(-) diff --git a/recipes/bioconductor-biocinstaller/meta.yaml b/recipes/bioconductor-biocinstaller/meta.yaml index 9f4b18756a..7e541846c0 100644 --- a/recipes/bioconductor-biocinstaller/meta.yaml +++ b/recipes/bioconductor-biocinstaller/meta.yaml @@ -3,8 +3,8 @@ package: version: 1.22.3 source: fn: BiocInstaller_1.22.3.tar.gz - url: http://bioconductor.org/packages/release/bioc/src/contrib/BiocInstaller_1.22.3.tar.gz - md5: b4547d5fd23d431f2e9ce78a1f619bac + url: https://depot.galaxyproject.org/software/bioconductor-biocinstaller/bioconductor-biocinstaller_1.22.3_src_all.tar.gz + sha256: d16c2c911a4c567d3ae996610be1882b1c9b6fc2643079e42173511ebeb87269 build: number: 0 rpaths: diff --git a/recipes/bioconductor-cardinal/meta.yaml b/recipes/bioconductor-cardinal/meta.yaml index 115c312cf3..bd2b4af1b6 100644 --- a/recipes/bioconductor-cardinal/meta.yaml +++ b/recipes/bioconductor-cardinal/meta.yaml @@ -4,8 +4,8 @@ package: source: fn: Cardinal_1.7.0.tar.gz - url: http://bioconductor.org/packages/devel/bioc/src/contrib/Cardinal_1.7.0.tar.gz - md5: 7f9aa8a3d5845b64ad574e28fe03840b + url: https://depot.galaxyproject.org/software/bioconductor-cardinal/bioconductor-cardinal_1.7.0_src_all.tar.gz + sha256: eece5d6dcabf347303af12dbf53354315f0511b71e752ba954fa51cf02cd2d9f build: number: 0 diff --git a/recipes/bioconductor-ropls/meta.yaml b/recipes/bioconductor-ropls/meta.yaml index c7508c5c38..7173c9c7b9 100644 --- a/recipes/bioconductor-ropls/meta.yaml +++ b/recipes/bioconductor-ropls/meta.yaml @@ -3,8 +3,8 @@ package: version: 1.4.4 source: fn: ropls_1.4.4.tar.gz - url: http://bioconductor.org/packages/release/bioc/src/contrib/ropls_1.4.4.tar.gz - md5: 6c05ca67d2ea28f8e49a22e01a38f699 + url: https://depot.galaxyproject.org/software/bioconductor-ropls/bioconductor-ropls_1.4.4_src_all.tar.gz + md5: b0d4cfb9b094e21fc6582eed126d0ca6 build: number: 1 rpaths: diff --git a/recipes/r-bh/meta.yaml b/recipes/r-bh/meta.yaml index 4fbb2adf9e..332ebb9539 100644 --- a/recipes/r-bh/meta.yaml +++ b/recipes/r-bh/meta.yaml @@ -7,7 +7,6 @@ package: source: fn: BH_1.60.0-2.tar.gz url: - - http://cran.r-project.org/src/contrib/BH_1.60.0-2.tar.gz - http://cran.r-project.org/src/contrib/Archive/BH/BH_1.60.0-2.tar.gz md5: b50fdc85285da05add4e9da664a2d551 build: diff --git a/recipes/r-circlize/meta.yaml b/recipes/r-circlize/meta.yaml index e247b5dbb8..0f36889b0e 100644 --- a/recipes/r-circlize/meta.yaml +++ b/recipes/r-circlize/meta.yaml @@ -7,7 +7,6 @@ package: source: fn: circlize_0.3.3.tar.gz url: - - http://cran.r-project.org/src/contrib/circlize_0.3.3.tar.gz - http://cran.r-project.org/src/contrib/Archive/circlize/circlize_0.3.3.tar.gz diff --git a/recipes/r-delaporte/meta.yaml b/recipes/r-delaporte/meta.yaml index 4e723fcb06..df16b3c163 100644 --- a/recipes/r-delaporte/meta.yaml +++ b/recipes/r-delaporte/meta.yaml @@ -5,7 +5,6 @@ package: source: fn: Delaporte_3.0.0.tar.gz url: - - http://cran.r-project.org/src/contrib/Delaporte_3.0.0.tar.gz - http://cran.r-project.org/src/contrib/Archive/Delaporte/Delaporte_3.0.0.tar.gz build: diff --git a/recipes/r-dendextend/meta.yaml b/recipes/r-dendextend/meta.yaml index d6d50ae6f9..14d184dccf 100644 --- a/recipes/r-dendextend/meta.yaml +++ b/recipes/r-dendextend/meta.yaml @@ -7,7 +7,6 @@ package: source: fn: dendextend_1.1.2.tar.gz url: - - http://cran.r-project.org/src/contrib/dendextend_1.1.2.tar.gz - http://cran.r-project.org/src/contrib/Archive/dendextend/dendextend_1.1.2.tar.gz diff --git a/recipes/r-dorng/meta.yaml b/recipes/r-dorng/meta.yaml index a616b383cc..396b87d853 100644 --- a/recipes/r-dorng/meta.yaml +++ b/recipes/r-dorng/meta.yaml @@ -7,7 +7,6 @@ package: source: fn: doRNG_1.6.tar.gz url: - - http://cran.r-project.org/src/contrib/doRNG_1.6.tar.gz - http://cran.r-project.org/src/contrib/Archive/doRNG/doRNG_1.6.tar.gz diff --git a/recipes/r-fastcluster/meta.yaml b/recipes/r-fastcluster/meta.yaml index e441982282..c9d7e7fe60 100644 --- a/recipes/r-fastcluster/meta.yaml +++ b/recipes/r-fastcluster/meta.yaml @@ -7,7 +7,6 @@ package: source: fn: fastcluster_1.1.20.tar.gz url: - - http://cran.r-project.org/src/contrib/fastcluster_1.1.20.tar.gz - http://cran.r-project.org/src/contrib/Archive/fastcluster/fastcluster_1.1.20.tar.gz sha256: 2d72589860dd36c6e27e17abc265c26fc5fb5bdaf375d04170f6938420ec8b66 diff --git a/recipes/r-gamlss/meta.yaml b/recipes/r-gamlss/meta.yaml index db58f48dc7..24fb311710 100644 --- a/recipes/r-gamlss/meta.yaml +++ b/recipes/r-gamlss/meta.yaml @@ -5,7 +5,6 @@ package: source: fn: gamlss_5.0-0.tar.gz url: - - http://cran.r-project.org/src/contrib/gamlss_5.0-0.tar.gz - http://cran.r-project.org/src/contrib/Archive/gamlss/gamlss_5.0-0.tar.gz md5: a22bb1a899139c84d54699abd12b4c68 diff --git a/recipes/r-ggally/meta.yaml b/recipes/r-ggally/meta.yaml index 26afabf1e7..dd8e6e01a6 100644 --- a/recipes/r-ggally/meta.yaml +++ b/recipes/r-ggally/meta.yaml @@ -7,7 +7,6 @@ package: source: fn: GGally_1.3.0.tar.gz url: - - http://cran.r-project.org/src/contrib/GGally_1.3.0.tar.gz - http://cran.r-project.org/src/contrib/Archive/GGally/GGally_1.3.0.tar.gz sha256: 6bdccc90a2cb6d363e5646ecae3b62db475a8560a333b3d661c98166c152ad89 diff --git a/recipes/r-globals/meta.yaml b/recipes/r-globals/meta.yaml index 9d6438c2da..1c20db1e36 100644 --- a/recipes/r-globals/meta.yaml +++ b/recipes/r-globals/meta.yaml @@ -8,7 +8,6 @@ package: source: fn: globals_0.7.1.tar.gz url: - - http://cran.r-project.org/src/contrib/globals_0.7.1.tar.gz - http://cran.r-project.org/src/contrib/Archive/globals/globals_0.7.1.tar.gz md5: fc1277025386e549bf79ff94735901d8 diff --git a/recipes/r-googlevis/meta.yaml b/recipes/r-googlevis/meta.yaml index abb65c9fe9..936e2b173d 100644 --- a/recipes/r-googlevis/meta.yaml +++ b/recipes/r-googlevis/meta.yaml @@ -7,7 +7,6 @@ package: source: fn: googleVis_0.5.10.tar.gz url: - - http://cran.r-project.org/src/contrib/googleVis_0.5.10.tar.gz - http://cran.r-project.org/src/contrib/Archive/googleVis/googleVis_0.5.10.tar.gz diff --git a/recipes/r-lambda.r/meta.yaml b/recipes/r-lambda.r/meta.yaml index d4a698fa2b..ce307f05ff 100644 --- a/recipes/r-lambda.r/meta.yaml +++ b/recipes/r-lambda.r/meta.yaml @@ -7,7 +7,6 @@ package: source: fn: lambda.r_1.1.7.tar.gz url: - - http://cran.r-project.org/src/contrib/lambda.r_1.1.7.tar.gz - http://cran.r-project.org/src/contrib/Archive/lambda.r/lambda.r_1.1.7.tar.gz diff --git a/recipes/r-listenv/meta.yaml b/recipes/r-listenv/meta.yaml index ecd380a498..6f936e9046 100644 --- a/recipes/r-listenv/meta.yaml +++ b/recipes/r-listenv/meta.yaml @@ -8,7 +8,6 @@ package: source: fn: listenv_0.6.0.tar.gz url: - - http://cran.r-project.org/src/contrib/listenv_0.6.0.tar.gz - http://cran.r-project.org/src/contrib/Archive/listenv/listenv_0.6.0.tar.gz md5: b6392412709154b0ee25be1a5da9d4b6 diff --git a/recipes/r-penalized/meta.yaml b/recipes/r-penalized/meta.yaml index 1cd0bf04d6..9216f2c830 100644 --- a/recipes/r-penalized/meta.yaml +++ b/recipes/r-penalized/meta.yaml @@ -5,7 +5,7 @@ package: source: fn: penalized_0.9-47.tar.gz url: - - https://cran.r-project.org/src/contrib/penalized_0.9-47.tar.gz + - https://cran.revolutionanalytics.com/src/contrib/Archive/penalized/penalized_0.9-47.tar.gz md5: '13cf7400f8840317b1bbfc980d3f0333' build: diff --git a/recipes/r-pracma/meta.yaml b/recipes/r-pracma/meta.yaml index 590b8c8879..3e6383937b 100644 --- a/recipes/r-pracma/meta.yaml +++ b/recipes/r-pracma/meta.yaml @@ -5,7 +5,6 @@ package: source: fn: pracma_1.8.8.tar.gz url: - - http://cran.r-project.org/src/contrib/pracma_1.8.8.tar.gz - http://cran.r-project.org/src/contrib/Archive/pracma/pracma_1.8.8.tar.gz md5: 83b8a02a086edf314979fd913c8d789e diff --git a/recipes/r-preseqr/meta.yaml b/recipes/r-preseqr/meta.yaml index 8fcd82543d..297631b44d 100644 --- a/recipes/r-preseqr/meta.yaml +++ b/recipes/r-preseqr/meta.yaml @@ -7,7 +7,6 @@ package: source: fn: preseqR_2.0.0.tar.gz url: - - http://cran.r-project.org/src/contrib/preseqR_2.0.0.tar.gz - http://cran.r-project.org/src/contrib/Archive/preseqR/preseqR_2.0.0.tar.gz diff --git a/recipes/r-proxy/meta.yaml b/recipes/r-proxy/meta.yaml index e24ea456ef..65e2707c12 100644 --- a/recipes/r-proxy/meta.yaml +++ b/recipes/r-proxy/meta.yaml @@ -10,7 +10,6 @@ package: source: fn: proxy_{{ version }}.tar.gz url: - - https://cran.r-project.org/src/contrib/proxy_{{ version }}.tar.gz - https://cran.r-project.org/src/contrib/Archive/proxy/proxy_{{ version }}.tar.gz sha256: 6fb7c416a590e03db6d99f46415fcc702c70cb6c8e32aba9c6d497dbc3e7c076 diff --git a/recipes/r-prroc/meta.yaml b/recipes/r-prroc/meta.yaml index 2681e77f32..c4c39e55c2 100644 --- a/recipes/r-prroc/meta.yaml +++ b/recipes/r-prroc/meta.yaml @@ -8,7 +8,6 @@ package: source: fn: PRROC_1.1.tar.gz url: - - http://cran.r-project.org/src/contrib/PRROC_1.1.tar.gz - http://cran.r-project.org/src/contrib/Archive/PRROC/PRROC_1.1.tar.gz md5: 464fefcd9af90590f9f08818cb1630ac diff --git a/recipes/r-qqman/meta.yaml b/recipes/r-qqman/meta.yaml index 494ea22a05..6a44525ebf 100644 --- a/recipes/r-qqman/meta.yaml +++ b/recipes/r-qqman/meta.yaml @@ -10,7 +10,6 @@ package: source: fn: qqman_0.1.2.tar.gz url: - - http://cran.r-project.org/src/contrib/qqman_0.1.2.tar.gz - http://cran.r-project.org/src/contrib/Archive/qqman/qqman_0.1.2.tar.gz diff --git a/recipes/r-r.oo/1.19.0/meta.yaml b/recipes/r-r.oo/1.19.0/meta.yaml index bc47db5c97..12e894612d 100644 --- a/recipes/r-r.oo/1.19.0/meta.yaml +++ b/recipes/r-r.oo/1.19.0/meta.yaml @@ -5,7 +5,6 @@ package: source: fn: R.oo_1.19.0.tar.gz url: - - http://cran.r-project.org/src/contrib/R.oo_1.19.0.tar.gz - http://cran.r-project.org/src/contrib/Archive/R.oo/R.oo_1.19.0.tar.gz md5: 5de25f313aa36903061db266ae74cc7c diff --git a/recipes/r-r.oo/meta.yaml b/recipes/r-r.oo/meta.yaml index 25d5df6365..02aae6ea6b 100644 --- a/recipes/r-r.oo/meta.yaml +++ b/recipes/r-r.oo/meta.yaml @@ -8,6 +8,7 @@ package: source: fn: R.oo_1.21.0.tar.gz url: + - https://cran.rstudio.com/src/contrib/R.oo_1.21.0.tar.gz - http://cran.r-project.org/src/contrib/Archive/R.oo/R.oo_1.21.0.tar.gz md5: f0062095c763faaeba30558303f68bc3 diff --git a/recipes/r-rsm/meta.yaml b/recipes/r-rsm/meta.yaml index 4ff61c493f..03ed0c4ab8 100644 --- a/recipes/r-rsm/meta.yaml +++ b/recipes/r-rsm/meta.yaml @@ -7,7 +7,6 @@ package: source: fn: rsm_2.7-4.tar.gz url: - - http://cran.r-project.org/src/contrib/rsm_2.7-4.tar.gz - http://cran.r-project.org/src/contrib/Archive/rsm/rsm_2.7-4.tar.gz diff --git a/recipes/r-rwave/meta.yaml b/recipes/r-rwave/meta.yaml index e226a7c02c..78ed01c11c 100644 --- a/recipes/r-rwave/meta.yaml +++ b/recipes/r-rwave/meta.yaml @@ -7,7 +7,6 @@ package: source: fn: Rwave_2.4.tar.gz url: - - http://cran.r-project.org/src/contrib/Rwave_2.4.tar.gz - http://cran.r-project.org/src/contrib/Archive/Rwave/Rwave_2.4.tar.gz md5: b67b324769db53297ab3c8309fece5a5 build: diff --git a/recipes/r-seqinr/meta.yaml b/recipes/r-seqinr/meta.yaml index 0eb3750db5..7ba96237a2 100644 --- a/recipes/r-seqinr/meta.yaml +++ b/recipes/r-seqinr/meta.yaml @@ -7,7 +7,6 @@ package: source: fn: seqinr_3.1-3.tar.gz url: - - http://cran.r-project.org/src/contrib/seqinr_3.1-3.tar.gz - http://cran.r-project.org/src/contrib/Archive/seqinr/seqinr_3.1-3.tar.gz diff --git a/recipes/r-sets/meta.yaml b/recipes/r-sets/meta.yaml index ca22fd7bb4..2f529e8aad 100644 --- a/recipes/r-sets/meta.yaml +++ b/recipes/r-sets/meta.yaml @@ -10,7 +10,6 @@ package: source: fn: sets_1.0-16.tar.gz url: - - http://cran.r-project.org/src/contrib/sets_1.0-16.tar.gz - http://cran.r-project.org/src/contrib/Archive/sets/sets_1.0-16.tar.gz diff --git a/recipes/r-snow/meta.yaml b/recipes/r-snow/meta.yaml index a970e773d2..84c7582f62 100644 --- a/recipes/r-snow/meta.yaml +++ b/recipes/r-snow/meta.yaml @@ -7,7 +7,6 @@ package: source: fn: snow_0.4-1.tar.gz url: - - http://cran.r-project.org/src/contrib/snow_0.4-1.tar.gz - http://cran.r-project.org/src/contrib/Archive/snow/snow_0.4-1.tar.gz diff --git a/recipes/r-upsetr/meta.yaml b/recipes/r-upsetr/meta.yaml index 396a298d2c..73766654a6 100644 --- a/recipes/r-upsetr/meta.yaml +++ b/recipes/r-upsetr/meta.yaml @@ -7,7 +7,6 @@ package: source: fn: UpSetR_1.0.3.tar.gz url: - - http://cran.r-project.org/src/contrib/UpSetR_1.0.3.tar.gz - http://cran.r-project.org/src/contrib/Archive/UpSetR/UpSetR_1.0.3.tar.gz build: diff --git a/recipes/r-vegan/2.3_3/meta.yaml b/recipes/r-vegan/2.3_3/meta.yaml index 99b3b8bce6..4f2bdc7ce0 100644 --- a/recipes/r-vegan/2.3_3/meta.yaml +++ b/recipes/r-vegan/2.3_3/meta.yaml @@ -7,7 +7,6 @@ package: source: fn: vegan_2.3-3.tar.gz url: - - http://cran.r-project.org/src/contrib/vegan_2.3-3.tar.gz - http://cran.r-project.org/src/contrib/Archive/vegan/vegan_2.3-3.tar.gz diff --git a/recipes/r-vegan/2.3_4/meta.yaml b/recipes/r-vegan/2.3_4/meta.yaml index b9a08c36d3..2dc8c62bfd 100644 --- a/recipes/r-vegan/2.3_4/meta.yaml +++ b/recipes/r-vegan/2.3_4/meta.yaml @@ -7,7 +7,6 @@ package: source: fn: vegan_2.3-4.tar.gz url: - - http://cran.r-project.org/src/contrib/vegan_2.3-4.tar.gz - http://cran.r-project.org/src/contrib/Archive/vegan/vegan_2.3-4.tar.gz sha256: b9efeb684421670ac0cc8d5f8fe7c2b7e2d2ac92be5122d9703bd56a91f4efd9 From 9d5969e852f62055a0c7fb0d8f6210cb93e01854 Mon Sep 17 00:00:00 2001 From: Bjoern Gruening Date: Sun, 4 Jun 2017 11:26:36 +0200 Subject: [PATCH 024/116] remove older version --- recipes/bioconductor-iranges/2.4.6/build.sh | 17 ------------- recipes/bioconductor-iranges/2.4.6/meta.yaml | 36 ---------------------------- 2 files changed, 53 deletions(-) delete mode 100644 recipes/bioconductor-iranges/2.4.6/build.sh delete mode 100644 recipes/bioconductor-iranges/2.4.6/meta.yaml diff --git a/recipes/bioconductor-iranges/2.4.6/build.sh b/recipes/bioconductor-iranges/2.4.6/build.sh deleted file mode 100644 index 0434cf01a2..0000000000 --- a/recipes/bioconductor-iranges/2.4.6/build.sh +++ /dev/null @@ -1,17 +0,0 @@ - -#!/bin/bash - -# R refuses to build packages that mark themselves as -# "Priority: Recommended" -mv DESCRIPTION DESCRIPTION.old -grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION -# -$R CMD INSTALL --build . -# -# # Add more build steps here, if they are necessary. -# -# See -# http://docs.continuum.io/conda/build.html -# for a list of environment variables that are set during the build -# process. -# diff --git a/recipes/bioconductor-iranges/2.4.6/meta.yaml b/recipes/bioconductor-iranges/2.4.6/meta.yaml deleted file mode 100644 index e6acec73dd..0000000000 --- a/recipes/bioconductor-iranges/2.4.6/meta.yaml +++ /dev/null @@ -1,36 +0,0 @@ -package: - name: bioconductor-iranges - version: 2.4.6 -source: - fn: IRanges_2.4.6.tar.gz - url: http://bioconductor.org/packages/release/bioc/src/contrib/IRanges_2.4.6.tar.gz - md5: 8a55ec82f777f61a76b6c467af92b4f6 - -build: - skip: False - number: 0 - rpaths: - - lib/R/lib/ - - lib/ -requirements: - build: - - 'bioconductor-biocgenerics >=0.15.10' - - 'bioconductor-s4vectors >=0.8.4' - - r-base - run: - - 'bioconductor-biocgenerics >=0.15.10' - - 'bioconductor-s4vectors >=0.8.4' - - r-base -test: - commands: - - '$R -e "library(''IRanges'')"' -about: - home: http://bioconductor.org/packages/release/bioc/html/IRanges.html - license: Artistic-2.0 - summary: 'The package provides efficient low-level and highly reusable S4 classes - for storing ranges of integers, RLE vectors (Run-Length Encoding), and, more generally, - data that can be organized sequentially (formally defined as Vector objects), - as well as views on these Vector objects. Efficient list-like classes are also - provided for storing big collections of instances of the basic classes. All classes - in the package use consistent naming and share the same rich and consistent "Vector - API" as much as possible.' From 769031866e91bc1a51ea26fa7917c4be0e69180c Mon Sep 17 00:00:00 2001 From: Bjoern Gruening Date: Sun, 4 Jun 2017 12:03:15 +0200 Subject: [PATCH 025/116] r fixes --- recipes/bioconductor-dupradar/meta.yaml | 4 ++-- recipes/bioconductor-qvalue/meta.yaml | 4 ++-- recipes/bioconductor-tximport/meta.yaml | 4 ++-- recipes/r-deldir/meta.yaml | 1 - recipes/r-ggally/0.5.0/meta.yaml | 2 +- recipes/r-listenv/0.5.0/meta.yaml | 1 - recipes/r-listenv/meta.yaml | 1 + recipes/r-mba/meta.yaml | 22 ---------------------- recipes/r-psych/meta.yaml | 1 - recipes/r-segmented/meta.yaml | 1 - 10 files changed, 8 insertions(+), 33 deletions(-) diff --git a/recipes/bioconductor-dupradar/meta.yaml b/recipes/bioconductor-dupradar/meta.yaml index 709c09186a..7410c94b50 100644 --- a/recipes/bioconductor-dupradar/meta.yaml +++ b/recipes/bioconductor-dupradar/meta.yaml @@ -3,8 +3,8 @@ package: version: 1.2.2 source: fn: dupRadar_1.2.2.tar.gz - url: http://bioconductor.org/packages/release/bioc/src/contrib/dupRadar_1.2.2.tar.gz - md5: 2c4527c61a83bdcaa9fb46c9865ae3a6 + url: https://depot.galaxyproject.org/software/bioconductor-dupradar/bioconductor-dupradar_1.2.2_src_all.tar.gz + sha256: d16c2c911a4c567d3ae996610be1882b1c9b6fc2643079e42173511ebeb87269 build: number: 0 rpaths: diff --git a/recipes/bioconductor-qvalue/meta.yaml b/recipes/bioconductor-qvalue/meta.yaml index a1b87fd4f0..e4c5232035 100644 --- a/recipes/bioconductor-qvalue/meta.yaml +++ b/recipes/bioconductor-qvalue/meta.yaml @@ -2,8 +2,8 @@ package: name: bioconductor-qvalue version: 2.6.0 source: - url: https://bioconductor.org/packages/release/bioc/src/contrib/qvalue_2.6.0.tar.gz - md5: be8b7972cb37667edd96948c9b56ce89 + url: https://depot.galaxyproject.org/software/bioconductor-qvalue/bioconductor-qvalue_2.6.0_src_all.tar.gz + sha256: d8690a917dd548425387ca00a2c2ad1c8fbadbbc09e019ed4b22cfb0438032b6 build: number: 0 rpaths: diff --git a/recipes/bioconductor-tximport/meta.yaml b/recipes/bioconductor-tximport/meta.yaml index 134b1c244e..8bc8705a2f 100644 --- a/recipes/bioconductor-tximport/meta.yaml +++ b/recipes/bioconductor-tximport/meta.yaml @@ -3,8 +3,8 @@ package: version: 1.0.3 source: fn: tximport_1.0.3.tar.gz - url: http://bioconductor.org/packages/release/bioc/src/contrib/tximport_1.0.3.tar.gz - md5: c6e0a617f255af19fae34fe8e8096204 + url: https://depot.galaxyproject.org/software/bioconductor-tximport/bioconductor-tximport_1.0.3_src_all.tar.gz + sha256: d16c2c911a4c567d3ae996610be1882b1c9b6fc2643079e42173511ebeb87269 build: number: 0 rpaths: diff --git a/recipes/r-deldir/meta.yaml b/recipes/r-deldir/meta.yaml index fffad3f2e1..b547ab87a0 100644 --- a/recipes/r-deldir/meta.yaml +++ b/recipes/r-deldir/meta.yaml @@ -10,7 +10,6 @@ package: source: fn: deldir_0.1-12.tar.gz url: - - http://cran.r-project.org/src/contrib/deldir_0.1-12.tar.gz - http://cran.r-project.org/src/contrib/Archive/deldir/deldir_0.1-12.tar.gz sha256: afa6ecbba82b05cea9faa3b3044c3f5b99116fcfdbb30e94e81e434ed566f2bb diff --git a/recipes/r-ggally/0.5.0/meta.yaml b/recipes/r-ggally/0.5.0/meta.yaml index b4f86e24a1..6ef9c9c5da 100644 --- a/recipes/r-ggally/0.5.0/meta.yaml +++ b/recipes/r-ggally/0.5.0/meta.yaml @@ -7,7 +7,7 @@ package: source: fn: GGally_0.5.0.tar.gz url: - - http://cran.r-project.org/src/contrib/GGally_0.5.0.tar.gz + - https://cran.r-project.org/src/contrib/GGally_1.3.0.tar.gz - http://cran.r-project.org/src/contrib/Archive/GGally/GGally_0.5.0.tar.gz diff --git a/recipes/r-listenv/0.5.0/meta.yaml b/recipes/r-listenv/0.5.0/meta.yaml index 954f77e6d9..148c06069b 100644 --- a/recipes/r-listenv/0.5.0/meta.yaml +++ b/recipes/r-listenv/0.5.0/meta.yaml @@ -5,7 +5,6 @@ package: source: fn: listenv_0.5.0.tar.gz url: - - http://cran.r-project.org/src/contrib/listenv_0.5.0.tar.gz - http://cran.r-project.org/src/contrib/Archive/listenv/listenv_0.5.0.tar.gz md5: d12ded1d6e4478cd5d644bcb182cb024 diff --git a/recipes/r-listenv/meta.yaml b/recipes/r-listenv/meta.yaml index 6f936e9046..375164b492 100644 --- a/recipes/r-listenv/meta.yaml +++ b/recipes/r-listenv/meta.yaml @@ -8,6 +8,7 @@ package: source: fn: listenv_0.6.0.tar.gz url: + - https://cran.r-project.org/src/contrib/listenv_0.6.0.tar.gz - http://cran.r-project.org/src/contrib/Archive/listenv/listenv_0.6.0.tar.gz md5: b6392412709154b0ee25be1a5da9d4b6 diff --git a/recipes/r-mba/meta.yaml b/recipes/r-mba/meta.yaml index 4867f7e90b..a990458654 100644 --- a/recipes/r-mba/meta.yaml +++ b/recipes/r-mba/meta.yaml @@ -7,7 +7,6 @@ package: source: fn: MBA_0.0-8.tar.gz url: - - http://cran.r-project.org/src/contrib/MBA_0.0-8.tar.gz - http://cran.r-project.org/src/contrib/Archive/MBA/MBA_0.0-8.tar.gz md5: 9341f832a7db89f212ec776633d58b4b build: @@ -34,24 +33,3 @@ about: license: GPL (>= 2) summary: Scattered data interpolation with Multilevel B-Splines license_family: GPL3 - -# The original CRAN metadata for this package was: - -# Package: MBA -# Version: 0.0-8 -# Date: 2014-4-28 -# Title: Multilevel B-spline Approximation -# Author: Andrew O. Finley , Sudipto Banerjee -# Maintainer: Andrew O. Finley -# Depends: R (>= 2.8.0), sp -# LinkingTo: BH -# Description: Scattered data interpolation with Multilevel B-Splines -# License: GPL (>= 2) -# Repository: CRAN -# Date/Publication: 2014-04-29 07:59:02 -# Packaged: 2014-04-29 01:42:39 UTC; andy -# NeedsCompilation: yes - -# See -# http://docs.continuum.io/conda/build.html for -# more information about meta.yaml diff --git a/recipes/r-psych/meta.yaml b/recipes/r-psych/meta.yaml index 9d2f5feb42..0993c8478d 100644 --- a/recipes/r-psych/meta.yaml +++ b/recipes/r-psych/meta.yaml @@ -7,7 +7,6 @@ package: source: fn: psych_1.5.8.tar.gz url: - - http://cran.r-project.org/src/contrib/psych_1.5.8.tar.gz - http://cran.r-project.org/src/contrib/Archive/psych/psych_1.5.8.tar.gz diff --git a/recipes/r-segmented/meta.yaml b/recipes/r-segmented/meta.yaml index 136b0676d4..08fdec40ff 100644 --- a/recipes/r-segmented/meta.yaml +++ b/recipes/r-segmented/meta.yaml @@ -5,7 +5,6 @@ package: source: fn: segmented_0.5-1.4.tar.gz url: - - http://cran.r-project.org/src/contrib/segmented_0.5-1.4.tar.gz - http://cran.r-project.org/src/contrib/Archive/segmented/segmented_0.5-1.4.tar.gz md5: f9d76ea9e22ef5f40aa126b697351cae From 0ee3573ccc6266e38f010d3e262cdf02260c3156 Mon Sep 17 00:00:00 2001 From: Bjoern Gruening Date: Sun, 4 Jun 2017 12:46:39 +0200 Subject: [PATCH 026/116] r fixes --- recipes/bioconductor-annotationdbi/meta.yaml | 4 ++-- recipes/bioconductor-biocstyle/meta.yaml | 4 ++-- recipes/r-futile.logger/meta.yaml | 29 ---------------------------- recipes/r-rrcov/meta.yaml | 24 ----------------------- 4 files changed, 4 insertions(+), 57 deletions(-) diff --git a/recipes/bioconductor-annotationdbi/meta.yaml b/recipes/bioconductor-annotationdbi/meta.yaml index 6a3b5e1fee..779dcbcb5b 100644 --- a/recipes/bioconductor-annotationdbi/meta.yaml +++ b/recipes/bioconductor-annotationdbi/meta.yaml @@ -3,8 +3,8 @@ package: version: "1.38.0" source: - url: https://bioconductor.org/packages/release/bioc/src/contrib/AnnotationDbi_1.38.0.tar.gz - md5: e855f96541bbaf4565807d712a74abf1 + url: https://depot.galaxyproject.org/software/bioconductor-annotationdbi/bioconductor-annotationdbi_1.38.0_src_all.tar.gz + sha256: 47bc40347c3383ffb992bfd31768a6f69860fc02d9b2231073f504a451aacef5 build: number: 0 diff --git a/recipes/bioconductor-biocstyle/meta.yaml b/recipes/bioconductor-biocstyle/meta.yaml index 74606ba6ba..070f4f2716 100644 --- a/recipes/bioconductor-biocstyle/meta.yaml +++ b/recipes/bioconductor-biocstyle/meta.yaml @@ -3,8 +3,8 @@ package: version: 2.0.3 source: fn: BiocStyle_2.0.3.tar.gz - url: http://bioconductor.org/packages/release/bioc/src/contrib/BiocStyle_2.0.3.tar.gz - md5: 426dcf23e33d0d29b10b6d40cae2054e + url: https://depot.galaxyproject.org/software/bioconductor-biocstyle/bioconductor-biocstyle_2.0.3_src_all.tar.gz + sha256: d16c2c911a4c567d3ae996610be1882b1c9b6fc2643079e42173511ebeb87269 build: number: 0 rpaths: diff --git a/recipes/r-futile.logger/meta.yaml b/recipes/r-futile.logger/meta.yaml index c5212dd479..3ec998a677 100644 --- a/recipes/r-futile.logger/meta.yaml +++ b/recipes/r-futile.logger/meta.yaml @@ -1,13 +1,10 @@ package: name: r-futile.logger - # Note that conda versions cannot contain -, so any -'s in the version have - # been replaced with _'s. version: "1.4.1" source: fn: futile.logger_1.4.1.tar.gz url: - - http://cran.r-project.org/src/contrib/futile.logger_1.4.1.tar.gz - http://cran.r-project.org/src/contrib/Archive/futile.logger/futile.logger_1.4.1.tar.gz @@ -58,29 +55,3 @@ about: summary: !!python/unicode 'Provides a simple yet powerful logging utility. Based loosely on log4j, futile.logger takes advantage of R idioms to make logging a convenient and easy to use replacement for cat and print statements.' - - -# The original CRAN metadata for this package was: - -# Package: futile.logger -# Type: Package -# Title: A Logging Utility for R -# Version: 1.4.1 -# Date: 2015-04-18 -# Author: Brian Lee Yung Rowe -# Maintainer: Brian Lee Yung Rowe -# Depends: R (>= 3.0.0) -# Imports: lambda.r (>= 1.1.0), futile.options -# Suggests: testthat, jsonlite -# Description: Provides a simple yet powerful logging utility. Based loosely on log4j, futile.logger takes advantage of R idioms to make logging a convenient and easy to use replacement for cat and print statements. -# License: LGPL-3 -# LazyLoad: yes -# Collate: 'options.R' 'appender.R' 'constants.R' 'layout.R' 'logger.R' 'scat.R' 'futile.logger-package.R' -# Packaged: 2015-04-19 18:43:51 UTC; brian -# NeedsCompilation: no -# Repository: CRAN -# Date/Publication: 2015-04-20 11:48:19 - -# See -# http://docs.continuum.io/conda/build.html for -# more information about meta.yaml diff --git a/recipes/r-rrcov/meta.yaml b/recipes/r-rrcov/meta.yaml index e21f1039c4..4c90a72ef4 100644 --- a/recipes/r-rrcov/meta.yaml +++ b/recipes/r-rrcov/meta.yaml @@ -7,7 +7,6 @@ package: source: fn: rrcov_1.3-11.tar.gz url: - - http://cran.r-project.org/src/contrib/rrcov_1.3-11.tar.gz - http://cran.r-project.org/src/contrib/Archive/rrcov/rrcov_1.3-11.tar.gz md5: 1b053df90912ed3b55ae867c6866c326 build: @@ -42,26 +41,3 @@ about: summary: Robust Location and Scatter Estimation and Robust Multivariate Analysis with High Breakdown Point. license_family: GPL3 - -# The original CRAN metadata for this package was: - -# Package: rrcov -# Version: 1.3-11 -# Date: 2016-02-14 -# Title: Scalable Robust Estimators with High Breakdown Point -# Author: Valentin Todorov -# Description: Robust Location and Scatter Estimation and Robust Multivariate Analysis with High Breakdown Point. -# Maintainer: Valentin Todorov -# Depends: R (>= 2.10), robustbase (>= 0.92-1), methods -# Imports: stats, stats4, mvtnorm, lattice, cluster, pcaPP -# Suggests: grid, mclust, MASS, ellipse -# LazyLoad: yes -# License: GPL (>= 2) -# Repository: CRAN -# Packaged: 2016-02-14 23:18:29 UTC; Share -# NeedsCompilation: yes -# Date/Publication: 2016-02-15 08:27:51 - -# See -# http://docs.continuum.io/conda/build.html for -# more information about meta.yaml From 7a4c142411a1a7493194ef497e4762437db701dc Mon Sep 17 00:00:00 2001 From: Bjoern Gruening Date: Sun, 4 Jun 2017 12:46:54 +0200 Subject: [PATCH 027/116] r fixes --- recipes/r-viridis/meta.yaml | 1 - 1 file changed, 1 deletion(-) diff --git a/recipes/r-viridis/meta.yaml b/recipes/r-viridis/meta.yaml index c9c91d9e45..e6c39f7658 100644 --- a/recipes/r-viridis/meta.yaml +++ b/recipes/r-viridis/meta.yaml @@ -5,7 +5,6 @@ package: source: fn: viridis_0.3.1.tar.gz url: - - http://cran.r-project.org/src/contrib/viridis_0.3.1.tar.gz - http://cran.r-project.org/src/contrib/Archive/viridis/viridis_0.3.1.tar.gz build: From 01bfa640475f23948b99a25cd2320bb41d7fe941 Mon Sep 17 00:00:00 2001 From: Bjoern Gruening Date: Sun, 4 Jun 2017 14:54:57 +0200 Subject: [PATCH 028/116] r fixes --- recipes/bioconductor-biocinstaller/meta.yaml | 16 +++++++++------ recipes/bioconductor-dupradar/meta.yaml | 4 ++-- recipes/bioconductor-ropls/meta.yaml | 20 +++++++++++------- recipes/r-abind/meta.yaml | 1 - recipes/r-boutroslabplottinggeneral/meta.yaml | 4 ++-- recipes/r-dunn.test/meta.yaml | 29 --------------------------- recipes/r-globals/0.6.0/meta.yaml | 28 -------------------------- recipes/r-gplots/meta.yaml | 24 ---------------------- recipes/r-knitr/meta.yaml | 2 +- recipes/r-plotly/meta.yaml | 2 +- recipes/r-rBLAST/meta.yaml | 6 +++--- recipes/r-readbrukerflexdata/meta.yaml | 25 ----------------------- 12 files changed, 32 insertions(+), 129 deletions(-) diff --git a/recipes/bioconductor-biocinstaller/meta.yaml b/recipes/bioconductor-biocinstaller/meta.yaml index 7e541846c0..e88d9fcb36 100644 --- a/recipes/bioconductor-biocinstaller/meta.yaml +++ b/recipes/bioconductor-biocinstaller/meta.yaml @@ -1,25 +1,29 @@ package: name: bioconductor-biocinstaller - version: 1.22.3 + version: 1.24.0 + source: - fn: BiocInstaller_1.22.3.tar.gz - url: https://depot.galaxyproject.org/software/bioconductor-biocinstaller/bioconductor-biocinstaller_1.22.3_src_all.tar.gz - sha256: d16c2c911a4c567d3ae996610be1882b1c9b6fc2643079e42173511ebeb87269 + fn: BiocInstaller_1.24.0.tar.gz + url: https://bioarchive.galaxyproject.org/BiocInstaller_1.24.0.tar.gz + sha256: 74d89e27db12d216cd22d99e12372f3e1ffbad5eb71ab6f446ab7190cbcb7943 + build: number: 0 rpaths: - lib/R/lib/ - lib/ + requirements: build: - r-base run: - r-base + test: commands: - '$R -e "library(''BiocInstaller'')"' + about: home: http://bioconductor.org/packages/release/bioc/html/BiocInstaller.html license: Artistic-2.0 - summary: 'This package is used to install and update Bioconductor, CRAN, and (some) - github packages.' + summary: 'This package is used to install and update Bioconductor, CRAN, and (some) github packages.' diff --git a/recipes/bioconductor-dupradar/meta.yaml b/recipes/bioconductor-dupradar/meta.yaml index 7410c94b50..363b5287ce 100644 --- a/recipes/bioconductor-dupradar/meta.yaml +++ b/recipes/bioconductor-dupradar/meta.yaml @@ -3,8 +3,8 @@ package: version: 1.2.2 source: fn: dupRadar_1.2.2.tar.gz - url: https://depot.galaxyproject.org/software/bioconductor-dupradar/bioconductor-dupradar_1.2.2_src_all.tar.gz - sha256: d16c2c911a4c567d3ae996610be1882b1c9b6fc2643079e42173511ebeb87269 + url: http://www.imsbio.co.jp/RGM-files/R_BC/download/dupRadar_1.2.2.tar.gz + sha256: 0c6a907efe9035dc6ba386160f9f7fb47b18b39e8a2dcfeecb2743f14ad607d8 build: number: 0 rpaths: diff --git a/recipes/bioconductor-ropls/meta.yaml b/recipes/bioconductor-ropls/meta.yaml index 7173c9c7b9..50ed3e7706 100644 --- a/recipes/bioconductor-ropls/meta.yaml +++ b/recipes/bioconductor-ropls/meta.yaml @@ -1,27 +1,33 @@ package: name: bioconductor-ropls - version: 1.4.4 + version: 1.6.0 + source: - fn: ropls_1.4.4.tar.gz - url: https://depot.galaxyproject.org/software/bioconductor-ropls/bioconductor-ropls_1.4.4_src_all.tar.gz - md5: b0d4cfb9b094e21fc6582eed126d0ca6 + fn: ropls_1.6.0.tar.gz + url: https://bioarchive.galaxyproject.org/ropls_1.6.0.tar.gz + sha256: 2fc67ac86ea1d61ca679346a94b8d2cb66def477c6e5cafa6a10801b69111a02 + build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ + requirements: build: - r-base run: - r-base + test: commands: - '$R -e "library(''ropls'')"' + about: home: http://bioconductor.org/packages/release/bioc/html/ropls.html license: CeCILL - summary: 'Latent variable modeling with Principal Component Analysis (PCA) and Partial + summary: | + Latent variable modeling with Principal Component Analysis (PCA) and Partial Least Squares (PLS) are powerful methods for visualization, regression, classification, and feature selection of omics data where the number of variables exceeds the number of samples and with multicollinearity among variables. Orthogonal Partial @@ -36,4 +42,4 @@ about: testing, detect outliers, and perform feature selection (e.g. with Variable Importance in Projection or regression coefficients). The package can be accessed via a user interface on the Workflow4Metabolomics.org online resource for computational metabolomics - (built upon the Galaxy environment).' + (built upon the Galaxy environment). diff --git a/recipes/r-abind/meta.yaml b/recipes/r-abind/meta.yaml index 3053a46cee..a4100cf663 100644 --- a/recipes/r-abind/meta.yaml +++ b/recipes/r-abind/meta.yaml @@ -5,7 +5,6 @@ package: source: fn: abind_1.4-3.tar.gz url: - - http://cran.r-project.org/src/contrib/abind_1.4-3.tar.gz - http://cran.r-project.org/src/contrib/Archive/abind/abind_1.4-3.tar.gz build: diff --git a/recipes/r-boutroslabplottinggeneral/meta.yaml b/recipes/r-boutroslabplottinggeneral/meta.yaml index 1be7f03fe9..4bbd940f12 100644 --- a/recipes/r-boutroslabplottinggeneral/meta.yaml +++ b/recipes/r-boutroslabplottinggeneral/meta.yaml @@ -4,8 +4,8 @@ package: source: fn: BoutrosLab.plotting.general_5.3.4.tar.gz - url: http://bpg.oicr.on.ca/src/contrib/BoutrosLab.plotting.general_5.3.4.tar.gz - md5: 1ab7abc62897399b6681dd61d9567cd5 + url: https://depot.galaxyproject.org/software/boutroslabplottinggeneral/boutroslabplottinggeneral_5.3.4_src_all.tar.gz + sha256: aa72e402e6cd7206ce34dd74a174fe135e7d5ab00e36164effec50279ad6ae52 requirements: build: - r-base diff --git a/recipes/r-dunn.test/meta.yaml b/recipes/r-dunn.test/meta.yaml index 5b49c2fcd3..fd17e1b6f7 100644 --- a/recipes/r-dunn.test/meta.yaml +++ b/recipes/r-dunn.test/meta.yaml @@ -7,7 +7,6 @@ package: source: fn: dunn.test_1.3.1.tar.gz url: - - http://cran.r-project.org/src/contrib/dunn.test_1.3.1.tar.gz - http://cran.r-project.org/src/contrib/Archive/dunn.test/dunn.test_1.3.1.tar.gz @@ -29,7 +28,6 @@ build: - lib/R/lib/ - lib/ - requirements: build: - r-base @@ -43,12 +41,6 @@ test: - $R -e "library('dunn.test')" # [not win] - "\"%R%\" -e \"library('dunn.test')\"" # [win] - # You can also put a file called run_test.py, run_test.sh, or run_test.bat - # in the recipe that will be run at test time. - - # requires: - # Put any additional test requirements here. - about: #home: license: GPL-2 @@ -65,24 +57,3 @@ about: and the distributions are assumed identical except for a difference in location, Dunn's test may be understood as a test for median difference. 'dunn.test' accounts for tied ranks. - -# The original CRAN metadata for this package was: - -# Package: dunn.test -# Version: 1.3.1 -# Date: 2015-10-08 -# Title: Dunn's Test of Multiple Comparisons Using Rank Sums -# Author: Alexis Dinno -# Maintainer: Alexis Dinno -# Description: Computes Dunn's test (1964) for stochastic dominance and reports the results among multiple pairwise comparisons after a Kruskal-Wallis test for stochastic dominance among k groups (Kruskal and Wallis, 1952). The interpretation of stochastic dominance requires an assumption that the CDF of one group does not cross the CDF of the other. 'dunn.test' makes k(k-1)/2 multiple pairwise comparisons based on Dunn's z-test-statistic approximations to the actual rank statistics. The null hypothesis for each pairwise comparison is that the probability of observing a randomly selected value from the first group that is larger than a randomly selected value from the second group equals one half; this null hypothesis corresponds to that of the Wilcoxon-Mann-Whitney rank-sum test. Like the rank-sum test, if the data can be assumed to be continuous, and the distributions are assumed identical except for a difference in location, Dunn's test may be understood as a test for median difference. 'dunn.test' accounts for tied ranks. -# License: GPL-2 -# LazyData: no -# Encoding: UTF-8 -# NeedsCompilation: no -# Packaged: 2015-10-08 15:16:34 UTC; Alexis -# Repository: CRAN -# Date/Publication: 2015-10-08 20:13:40 - -# See -# http://docs.continuum.io/conda/build.html for -# more information about meta.yaml diff --git a/recipes/r-globals/0.6.0/meta.yaml b/recipes/r-globals/0.6.0/meta.yaml index 95db478577..7776b5c412 100644 --- a/recipes/r-globals/0.6.0/meta.yaml +++ b/recipes/r-globals/0.6.0/meta.yaml @@ -5,7 +5,6 @@ package: source: fn: globals_0.6.0.tar.gz url: - - http://cran.r-project.org/src/contrib/globals_0.6.0.tar.gz - http://cran.r-project.org/src/contrib/Archive/globals/globals_0.6.0.tar.gz md5: 1c20d1d24ae83ad595ad3fec1e63d8a1 @@ -38,30 +37,3 @@ about: using various strategies, e.g. conservative or liberal. The objective of this package is to make it as simple as possible to identify global objects for the purpose of exporting them in distributed compute environments.' - - -# The original CRAN metadata for this package was: - -# Package: globals -# Version: 0.6.0 -# Depends: R (>= 3.1.2) -# Imports: codetools -# Title: Identify Global Objects in R Expressions -# Authors@R: c( person("Henrik", "Bengtsson", role=c("aut", "cre", "cph"), email="henrikb@braju.com")) -# Description: Identifies global ("unknown") objects in R expressions by code inspection using various strategies, e.g. conservative or liberal. The objective of this package is to make it as simple as possible to identify global objects for the purpose of exporting them in distributed compute environments. -# License: LGPL (>= 2.1) -# LazyLoad: TRUE -# ByteCompile: TRUE -# URL: https://github.com/HenrikBengtsson/globals -# BugReports: https://github.com/HenrikBengtsson/globals/issues -# RoxygenNote: 5.0.1 -# NeedsCompilation: no -# Packaged: 2015-12-12 15:03:09 UTC; hb -# Author: Henrik Bengtsson [aut, cre, cph] -# Maintainer: Henrik Bengtsson -# Repository: CRAN -# Date/Publication: 2015-12-12 18:49:07 - -# See -# http://docs.continuum.io/conda/build.html for -# more information about meta.yaml diff --git a/recipes/r-gplots/meta.yaml b/recipes/r-gplots/meta.yaml index 90ef59e4dd..1075d779ab 100644 --- a/recipes/r-gplots/meta.yaml +++ b/recipes/r-gplots/meta.yaml @@ -7,7 +7,6 @@ package: source: fn: gplots_2.17.0.tar.gz url: - - http://cran.r-project.org/src/contrib/gplots_2.17.0.tar.gz - http://cran.r-project.org/src/contrib/Archive/gplots/gplots_2.17.0.tar.gz @@ -73,26 +72,3 @@ about: style plots (''ooplot''), - plotting multiple data sets on same region, with separate axes (''overplot''), - plotting means and confidence intervals (''plotCI'', ''plotmeans''), - spacing points in an x-y plot so they don''t overlap (''space'').' - - -# The original CRAN metadata for this package was: - -# Package: gplots -# Title: Various R Programming Tools for Plotting Data -# Description: Various R programming tools for plotting data, including: - calculating and plotting locally smoothed summary functionals ('bandplot', 'wapply'), - enhanced versions of standard plots ('barplot2', 'boxplot2', 'heatmap.2', 'smartlegend'), - manipulating colors ('col2hex', 'colorpanel', 'redgreen', 'greenred', 'bluered', 'redblue', 'rich.colors'), - calculating and plotting two-dimensional data summaries ('ci2d', 'hist2d'), - enhanced regression diagnostic plots ('lmplot2', 'residplot'), - formula-enabled interface to stats::lowess function ('lowess'), - displaying textual data in plots ('textplot', 'sinkplot'), - plotting a matrix where each cell contains a dot whose size reflects the relative magnitude of the elements ('balloonplot'), - plotting Venn diagrams ('venn'), - displaying Open-Office style plots ('ooplot'), - plotting multiple data sets on same region, with separate axes ('overplot'), - plotting means and confidence intervals ('plotCI', 'plotmeans'), - spacing points in an x-y plot so they don't overlap ('space'). -# Depends: R (>= 3.0) -# Imports: gtools, gdata, stats, caTools, KernSmooth -# Suggests: grid, MASS -# Version: 2.17.0 -# Date: 2015-05-01 -# Author: Gregory R. Warnes, Ben Bolker, Lodewijk Bonebakker, Robert Gentleman, Wolfgang Huber Andy Liaw, Thomas Lumley, Martin Maechler, Arni Magnusson, Steffen Moeller, Marc Schwartz, Bill Venables -# Maintainer: Gregory R. Warnes -# License: GPL-2 -# NeedsCompilation: no -# Packaged: 2015-05-01 23:03:50 UTC; warnes -# Repository: CRAN -# Date/Publication: 2015-05-02 14:20:01 - -# See -# http://docs.continuum.io/conda/build.html for -# more information about meta.yaml diff --git a/recipes/r-knitr/meta.yaml b/recipes/r-knitr/meta.yaml index 3b4077823c..f543310764 100644 --- a/recipes/r-knitr/meta.yaml +++ b/recipes/r-knitr/meta.yaml @@ -5,7 +5,7 @@ package: source: fn: knitr_1.12.3.tar.gz url: http://stat.ethz.ch/CRAN/src/contrib/Archive/knitr/knitr_1.12.3.tar.gz - md5: 1c880968cf5f18c70bfd72862bd7064d + md5: da55c4e9a5be942301ff26c9f49c29b5 build: number: 0 diff --git a/recipes/r-plotly/meta.yaml b/recipes/r-plotly/meta.yaml index 8e9b0e0e92..76475feb62 100644 --- a/recipes/r-plotly/meta.yaml +++ b/recipes/r-plotly/meta.yaml @@ -5,7 +5,7 @@ package: source: fn: plotly_4.5.6.tar.gz url: - - https://cran.rstudio.com/src/contrib/plotly_4.5.6.tar.gz + - https://cran.r-project.org/src/contrib/Archive/plotly/plotly_4.5.6.tar.gz md5: e6e00177fa64dc6b1a199facfd73f585 build: diff --git a/recipes/r-rBLAST/meta.yaml b/recipes/r-rBLAST/meta.yaml index 28eacddb21..7618851450 100644 --- a/recipes/r-rBLAST/meta.yaml +++ b/recipes/r-rBLAST/meta.yaml @@ -2,10 +2,10 @@ package: name: r-rblast version: "0.99.1" source: - fn: master.zip + fn: 5cbc5039705e45c83d88c324c4f2a64dfc63e4e1.tar.gz url: - - https://github.com/mhahsler/rBLAST/archive/master.zip - md5: d28323d28c505784e73a16108a3b6e96 + - https://github.com/mhahsler/rBLAST/archive/5cbc5039705e45c83d88c324c4f2a64dfc63e4e1.tar.gz + md5: 5773ffb34b208af1d7999518c645728a build: rpaths: - lib/R/lib/ diff --git a/recipes/r-readbrukerflexdata/meta.yaml b/recipes/r-readbrukerflexdata/meta.yaml index ce7c524aa2..163c66053c 100644 --- a/recipes/r-readbrukerflexdata/meta.yaml +++ b/recipes/r-readbrukerflexdata/meta.yaml @@ -5,7 +5,6 @@ package: source: fn: readBrukerFlexData_1.8.2.tar.gz url: - - http://cran.r-project.org/src/contrib/readBrukerFlexData_1.8.2.tar.gz - http://cran.r-project.org/src/contrib/Archive/readBrukerFlexData/readBrukerFlexData_1.8.2.tar.gz sha256: 6c745e43e8a21a02660bef933785ce9d8b3d845a6f0976e04177c024a8d94fb1 @@ -43,27 +42,3 @@ about: license: GPL (>= 3) summary: Reads data files acquired by MALDI-TOF MS on Bruker Daltonics machines of the \*flex series. - -# The original CRAN metadata for this package was: - -# Package: readBrukerFlexData -# Version: 1.8.2 -# Date: 2014-12-15 -# Title: Reads Mass Spectrometry Data in Bruker *flex Format -# Authors@R: person("Sebastian", "Gibb", role=c("aut", "cre"), email="mail@sebastiangibb.de") -# Depends: R (>= 2.15.0) -# Description: Reads data files acquired by MALDI-TOF MS on Bruker Daltonics machines of the *flex series. -# License: GPL (>= 3) -# URL: http://strimmerlab.org/software/maldiquant/ https://github.com/sgibb/readBrukerFlexData/ -# BugReports: https://github.com/sgibb/readBrukerFlexData/issues/ -# LazyLoad: yes -# Packaged: 2014-12-15 21:40:58 UTC; sebastian -# Author: Sebastian Gibb [aut, cre] -# Maintainer: Sebastian Gibb -# NeedsCompilation: no -# Repository: CRAN -# Date/Publication: 2014-12-16 00:43:10 - -# See -# http://docs.continuum.io/conda/build.html for -# more information about meta.yaml From c7d25acae0df9de787df0d799a172d48b176a8e9 Mon Sep 17 00:00:00 2001 From: Bjoern Gruening Date: Sun, 4 Jun 2017 16:53:42 +0200 Subject: [PATCH 029/116] r fixes --- recipes/bioconductor-gagedata/meta.yaml | 2 +- recipes/bioconductor-noiseq/meta.yaml | 4 +-- recipes/bioconductor-org.mm.eg.db/meta.yaml | 6 ++-- recipes/bioconductor-seqpattern/meta.yaml | 2 +- recipes/r-fftwtools/meta.yaml | 1 - recipes/r-gam/meta.yaml | 1 - recipes/r-rcircos/1.1.3/meta.yaml | 1 - recipes/r-rcppgsl/meta.yaml | 53 ++++++++--------------------- recipes/r-rseis/meta.yaml | 1 - recipes/r-venndiagram/meta.yaml | 31 ----------------- 10 files changed, 22 insertions(+), 80 deletions(-) diff --git a/recipes/bioconductor-gagedata/meta.yaml b/recipes/bioconductor-gagedata/meta.yaml index 47decde094..5166739b80 100644 --- a/recipes/bioconductor-gagedata/meta.yaml +++ b/recipes/bioconductor-gagedata/meta.yaml @@ -3,7 +3,7 @@ package: version: 2.10.0 source: fn: gageData_2.10.0.tar.gz - url: http://bioconductor.org/packages/release/data/experiment/src/contrib/gageData_2.10.0.tar.gz + url: https://bioconductor.statistik.tu-dortmund.de/packages/2.12/bioc/src/contrib/gage_2.10.0.tar.gz md5: a143308c83d08d470695c8449f84490d build: number: 0 diff --git a/recipes/bioconductor-noiseq/meta.yaml b/recipes/bioconductor-noiseq/meta.yaml index 1972a81536..c3bf4676d2 100644 --- a/recipes/bioconductor-noiseq/meta.yaml +++ b/recipes/bioconductor-noiseq/meta.yaml @@ -3,8 +3,8 @@ package: version: 2.18.0 source: fn: NOISeq_2.18.0.tar.gz - url: http://bioconductor.org/packages/release/bioc/src/contrib/NOISeq_2.18.0.tar.gz - md5: d74de38f0369b58c3e203f29e8a64f3c + url: https://depot.galaxyproject.org/software/bioconductor-noiseq/bioconductor-noiseq_2.18.0_src_all.tar.gz + sha256: 050e6ab51f91e9a5574eefb708596f8128f8aa1c7c120c8c3593021580ff8447 build: number: 0 rpaths: diff --git a/recipes/bioconductor-org.mm.eg.db/meta.yaml b/recipes/bioconductor-org.mm.eg.db/meta.yaml index f78eac381d..f5c19b6598 100644 --- a/recipes/bioconductor-org.mm.eg.db/meta.yaml +++ b/recipes/bioconductor-org.mm.eg.db/meta.yaml @@ -3,7 +3,7 @@ package: version: 3.4.0 source: fn: org.Mm.eg.db_3.4.0.tar.gz - url: https://bioconductor.org/packages/release/data/annotation/src/contrib/org.Mm.eg.db_3.4.0.tar.gz + url: https://depot.galaxyproject.org/software/bioconductor-org.mm.eg.db/bioconductor-org.mm.eg.db_3.4.0_src_all.tar.gz md5: d8cb71bbaa7568107192a580d3c50415 build: number: 0 @@ -23,5 +23,5 @@ test: about: home: http://bioconductor.org/packages/release/data/annotation/html/org.Mm.eg.db.html license: Artistic-2.0 - summary: 'Genome wide annotation for Mouse, primarily based on mapping using Entrez - Gene identifiers.' + summary: | + Genome wide annotation for Mouse, primarily based on mapping using Entrez Gene identifiers. diff --git a/recipes/bioconductor-seqpattern/meta.yaml b/recipes/bioconductor-seqpattern/meta.yaml index 0b7cd93d4b..60d5acbd36 100644 --- a/recipes/bioconductor-seqpattern/meta.yaml +++ b/recipes/bioconductor-seqpattern/meta.yaml @@ -3,7 +3,7 @@ package: version: "1.6.0" source: fn: seqPattern_1.6.0.tar.gz - url: https://bioconductor.org/packages/release/bioc/src/contrib/seqPattern_1.6.0.tar.gz + url: https://depot.galaxyproject.org/software/bioconductor-seqpattern/bioconductor-seqpattern_1.6.0_src_all.tar.gz md5: b0f51e76f8e30b7bcd2969f97622d83c build: diff --git a/recipes/r-fftwtools/meta.yaml b/recipes/r-fftwtools/meta.yaml index f0efec064a..fbd719abbe 100644 --- a/recipes/r-fftwtools/meta.yaml +++ b/recipes/r-fftwtools/meta.yaml @@ -5,7 +5,6 @@ package: source: fn: fftwtools_0.9-7.tar.gz url: - - http://cran.r-project.org/src/contrib/fftwtools_0.9-7.tar.gz - http://cran.r-project.org/src/contrib/Archive/fftwtools/fftwtools_0.9-7.tar.gz build: diff --git a/recipes/r-gam/meta.yaml b/recipes/r-gam/meta.yaml index d64397998e..cfab2126c5 100644 --- a/recipes/r-gam/meta.yaml +++ b/recipes/r-gam/meta.yaml @@ -5,7 +5,6 @@ package: source: fn: gam_1.14.tar.gz url: - - http://cran.r-project.org/src/contrib/gam_1.14.tar.gz - http://cran.r-project.org/src/contrib/Archive/gam/gam_1.14.tar.gz md5: '6f34c6b3b6133d28c8715102b52b4e86' diff --git a/recipes/r-rcircos/1.1.3/meta.yaml b/recipes/r-rcircos/1.1.3/meta.yaml index 5f498f48d0..b4909d3a3c 100644 --- a/recipes/r-rcircos/1.1.3/meta.yaml +++ b/recipes/r-rcircos/1.1.3/meta.yaml @@ -7,7 +7,6 @@ package: source: fn: RCircos_1.1.3.tar.gz url: - - http://cran.r-project.org/src/contrib/RCircos_1.1.3.tar.gz - http://cran.r-project.org/src/contrib/Archive/RCircos/RCircos_1.1.3.tar.gz diff --git a/recipes/r-rcppgsl/meta.yaml b/recipes/r-rcppgsl/meta.yaml index 39d6e5fa71..1dd16a7720 100644 --- a/recipes/r-rcppgsl/meta.yaml +++ b/recipes/r-rcppgsl/meta.yaml @@ -1,55 +1,32 @@ -about: {license: GPL-3} +package: + - name: r-rcppgsl + - version: 0.3.1 + +source: + fn: RcppGSL_0.3.1.tar.gz + md5: 37ae012f54f04c33490ad5a9d0142cb83f836f30e14786ec0ffb62d063b05802 + url: + - https://cran.r-project.org/src/contrib/Archive/RcppGSL/RcppGSL_0.3.1.tar.gz + +about: + - license: GPL-3 + build: - entry_points: [] skip: True # [osx] - features: [] rpaths: - lib/R/lib/ - lib/ - string: '' - track_features: [] -package: {name: r-rcppgsl, version: 0.3.1} + requirements: build: - r-base - r-rcpp >=0.11 - gsl {{CONDA_GSL}}* - conflicts: [] run: - r-base - r-rcpp >=0.11 - gsl {{CONDA_GSL}}* -source: - fn: RcppGSL_0.3.1.tar.gz - git_rev: '' - md5: '' - patches: [] - path: '' - svn_rev: '' - url: - - http://cran.r-project.org/src/contrib/RcppGSL_0.3.1.tar.gz + test: commands: - $R -e "library('RcppGSL')" - files: [] - imports: [] - requires: [] - -# The original CRAN metadata for this package was: - -# Version: 0.3.1 -# Imports: Rcpp (≥ 0.11.0), stats -# LinkingTo: Rcpp -# Suggests: RUnit, inline, highlight -# Published: 2016-10-03 -# Author: Dirk Eddelbuettel and Romain Francois -# Maintainer: Dirk Eddelbuettel -# License: GPL-2 | GPL-3 [expanded from: GPL (≥ 2)] -# NeedsCompilation: yes -# SystemRequirements: GNU GSL -# Materials: README NEWS ChangeLog -# CRAN checks: RcppGSL results - -# See -# http://docs.continuum.io/conda/build.html for -# more information about meta.yaml diff --git a/recipes/r-rseis/meta.yaml b/recipes/r-rseis/meta.yaml index ae220b230f..78128fd2c1 100644 --- a/recipes/r-rseis/meta.yaml +++ b/recipes/r-rseis/meta.yaml @@ -7,7 +7,6 @@ package: source: fn: RSEIS_3.5-2.tar.gz url: - - http://cran.r-project.org/src/contrib/RSEIS_3.5-2.tar.gz - http://cran.r-project.org/src/contrib/Archive/RSEIS/RSEIS_3.5-2.tar.gz md5: 81613d4125c7c57f1690362cc2aae399 build: diff --git a/recipes/r-venndiagram/meta.yaml b/recipes/r-venndiagram/meta.yaml index 0232455a9c..3a230e48e9 100644 --- a/recipes/r-venndiagram/meta.yaml +++ b/recipes/r-venndiagram/meta.yaml @@ -7,17 +7,8 @@ package: source: fn: VennDiagram_1.6.16.tar.gz url: - - http://cran.r-project.org/src/contrib/VennDiagram_1.6.16.tar.gz - http://cran.r-project.org/src/contrib/Archive/VennDiagram/VennDiagram_1.6.16.tar.gz - - # You can add a hash for the file here, like md5 or sha1 - # md5: 49448ba4863157652311cc5ea4fea3ea - # sha1: 3bcfbee008276084cbb37a2b453963c61176a322 - # patches: - # List any patch files here - # - fix.patch - build: skip: False # number: 1 @@ -56,25 +47,3 @@ about: for several special cases, including two-case scaling, and extensive customization of plot shape and structure. -# The original CRAN metadata for this package was: - -# Package: VennDiagram -# Version: 1.6.16 -# Type: Package -# Title: Generate High-Resolution Venn and Euler Plots -# Date: 2015-08-28 -# Author: Hanbo Chen -# Maintainer: Paul Boutros -# Depends: R (>= 2.14.1), grid (>= 2.14.1), futile.logger -# Description: A set of functions to generate high-resolution Venn and Euler plots. Includes handling for several special cases, including two-case scaling, and extensive customization of plot shape and structure. -# License: GPL-2 -# LazyLoad: yes -# Suggests: testthat -# NeedsCompilation: no -# Packaged: 2015-09-10 20:59:45 UTC; clalansingh -# Repository: CRAN -# Date/Publication: 2015-09-17 07:51:02 - -# See -# http://docs.continuum.io/conda/build.html for -# more information about meta.yaml From 5c168b465dc7635e015395f4ea27a86ed2ca78fe Mon Sep 17 00:00:00 2001 From: Bjoern Gruening Date: Sun, 4 Jun 2017 17:09:46 +0200 Subject: [PATCH 030/116] r fixes --- recipes/r-rcppgsl/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/r-rcppgsl/meta.yaml b/recipes/r-rcppgsl/meta.yaml index 1dd16a7720..33d9c250ff 100644 --- a/recipes/r-rcppgsl/meta.yaml +++ b/recipes/r-rcppgsl/meta.yaml @@ -1,6 +1,6 @@ package: - - name: r-rcppgsl - - version: 0.3.1 + name: r-rcppgsl + version: 0.3.1 source: fn: RcppGSL_0.3.1.tar.gz @@ -9,7 +9,7 @@ source: - https://cran.r-project.org/src/contrib/Archive/RcppGSL/RcppGSL_0.3.1.tar.gz about: - - license: GPL-3 + license: GPL-3 build: skip: True # [osx] From 4f1c4db14451c30d01c176078416c81abdf4ad8c Mon Sep 17 00:00:00 2001 From: Bjoern Gruening Date: Sun, 4 Jun 2017 19:11:19 +0200 Subject: [PATCH 031/116] r fixes --- recipes/bioconductor-tximport/meta.yaml | 4 ++-- recipes/r-rcppgsl/meta.yaml | 2 +- recipes/r-vegan/2.3_4/meta.yaml | 32 ++++++++++++-------------------- 3 files changed, 15 insertions(+), 23 deletions(-) diff --git a/recipes/bioconductor-tximport/meta.yaml b/recipes/bioconductor-tximport/meta.yaml index 8bc8705a2f..0c80c3d5ab 100644 --- a/recipes/bioconductor-tximport/meta.yaml +++ b/recipes/bioconductor-tximport/meta.yaml @@ -3,8 +3,8 @@ package: version: 1.0.3 source: fn: tximport_1.0.3.tar.gz - url: https://depot.galaxyproject.org/software/bioconductor-tximport/bioconductor-tximport_1.0.3_src_all.tar.gz - sha256: d16c2c911a4c567d3ae996610be1882b1c9b6fc2643079e42173511ebeb87269 + url: https://bioconductor.statistik.tu-dortmund.de/packages/3.3/bioc/src/contrib/tximport_1.0.3.tar.gz + sha256: e03d1bbaca438eccbab42429098e172d02a99700f29e69a5525f4318b82a4892 build: number: 0 rpaths: diff --git a/recipes/r-rcppgsl/meta.yaml b/recipes/r-rcppgsl/meta.yaml index 33d9c250ff..0e9d49e95e 100644 --- a/recipes/r-rcppgsl/meta.yaml +++ b/recipes/r-rcppgsl/meta.yaml @@ -4,7 +4,7 @@ package: source: fn: RcppGSL_0.3.1.tar.gz - md5: 37ae012f54f04c33490ad5a9d0142cb83f836f30e14786ec0ffb62d063b05802 + sha256: 37ae012f54f04c33490ad5a9d0142cb83f836f30e14786ec0ffb62d063b05802 url: - https://cran.r-project.org/src/contrib/Archive/RcppGSL/RcppGSL_0.3.1.tar.gz diff --git a/recipes/r-vegan/2.3_4/meta.yaml b/recipes/r-vegan/2.3_4/meta.yaml index 2dc8c62bfd..592cddeafc 100644 --- a/recipes/r-vegan/2.3_4/meta.yaml +++ b/recipes/r-vegan/2.3_4/meta.yaml @@ -1,7 +1,5 @@ package: name: r-vegan - # Note that conda versions cannot contain -, so any -'s in the version have - # been replaced with _'s. version: "2.3_4" source: @@ -11,38 +9,32 @@ source: sha256: b9efeb684421670ac0cc8d5f8fe7c2b7e2d2ac92be5122d9703bd56a91f4efd9 build: - # If this is a new build for the same version, increment the build - # number. If you do not include this key, it defaults to 0. - number: 2 - - # This is required to make R link correctly on Linux. + number: 0 rpaths: - lib/R/lib/ - lib/ -# Suggests: parallel, tcltk requirements: build: - r-base - - r-mass # [not win] - - r-cluster # [not win] - - r-lattice # [not win] - - r-mgcv # [not win] + - r-mass + - r-cluster + - r-lattice + - r-mgcv - r-permute >=0.8_0 - - gcc # [not win] + - gcc run: - r-base - - r-mass # [not win] - - r-cluster # [not win] - - r-lattice # [not win] - - r-mgcv # [not win] + - r-mass + - r-cluster + - r-lattice + - r-mgcv - r-permute >=0.8_0 - - libgcc # [not win] + - libgcc test: commands: - # You can put additional test commands to be run here. - - $R -e "library('vegan')" # [not win] + - $R -e "library('vegan')" about: home: http://cran.r-project.org, https://github.com/vegandevs/vegan From c48873e9d204070659794f5ceeaca3b8608e11bb Mon Sep 17 00:00:00 2001 From: Bjoern Gruening Date: Sun, 4 Jun 2017 19:45:29 +0200 Subject: [PATCH 032/116] r fixes --- recipes/bioconductor-limma/3.28.2/meta.yaml | 11 ++++++++--- recipes/bioconductor-limma/3.28.6/meta.yaml | 17 +++++++++++------ 2 files changed, 19 insertions(+), 9 deletions(-) diff --git a/recipes/bioconductor-limma/3.28.2/meta.yaml b/recipes/bioconductor-limma/3.28.2/meta.yaml index 6bcc9a550e..7deced5505 100644 --- a/recipes/bioconductor-limma/3.28.2/meta.yaml +++ b/recipes/bioconductor-limma/3.28.2/meta.yaml @@ -1,25 +1,30 @@ package: name: bioconductor-limma version: 3.28.2 + source: fn: limma_3.28.2.tar.gz url: https://depot.galaxyproject.org/software/limma/limma_3.28.2_src_all.tar.gz - sha256: 96b3c01e2c6709ee8fb4c43583b22ea0a6f32624b73a9c05d74cac4c443ad342 + sha256: 70acdd49e77b8514afd8ca364c3c47b6fbeef46b7a40881d5312832e90cf9c75 + build: number: 0 rpaths: - lib/R/lib/ - lib/ + requirements: build: - r-base run: - r-base + test: commands: - '$R -e "library(''limma'')"' + about: home: http://bioconductor.org/packages/release/bioc/html/limma.html license: 'GPL (>=2)' - summary: 'Data analysis, linear models and differential expression for microarray - data.' + summary: | + Data analysis, linear models and differential expression for microarray data. diff --git a/recipes/bioconductor-limma/3.28.6/meta.yaml b/recipes/bioconductor-limma/3.28.6/meta.yaml index 06875fa695..9eab2136ba 100644 --- a/recipes/bioconductor-limma/3.28.6/meta.yaml +++ b/recipes/bioconductor-limma/3.28.6/meta.yaml @@ -1,25 +1,30 @@ package: name: bioconductor-limma - version: 3.28.6 + version: 3.28.10 + source: - fn: limma_3.28.6.tar.gz - url: http://bioconductor.org/packages/release/bioc/src/contrib/limma_3.28.6.tar.gz - sha256: 7895c7b81aa6fb8f34729916ba04c44f9bb4be48a85e8022b1106bb592b36936 + fn: limma_3.28.10_src_all.tar.gz + url: https://depot.galaxyproject.org/software/limma/limma_3.28.10_src_all.tar.gz + sha256: 62c9337a640d4ee31abbec77df37ea3b0d75826cbace3de9914561106e04dfdc + build: number: 0 rpaths: - lib/R/lib/ - lib/ + requirements: build: - r-base run: - r-base + test: commands: - '$R -e "library(''limma'')"' + about: home: http://bioconductor.org/packages/release/bioc/html/limma.html license: 'GPL (>=2)' - summary: 'Data analysis, linear models and differential expression for microarray - data.' + summary: | + Data analysis, linear models and differential expression for microarray data. From 787f73f9e1f309afa94425649404c81fcb5391e2 Mon Sep 17 00:00:00 2001 From: Bjoern Gruening Date: Sun, 4 Jun 2017 19:46:14 +0200 Subject: [PATCH 033/116] rename folder --- recipes/bioconductor-limma/{3.28.6 => 3.28.10}/build.sh | 0 recipes/bioconductor-limma/{3.28.6 => 3.28.10}/meta.yaml | 0 2 files changed, 0 insertions(+), 0 deletions(-) rename recipes/bioconductor-limma/{3.28.6 => 3.28.10}/build.sh (100%) rename recipes/bioconductor-limma/{3.28.6 => 3.28.10}/meta.yaml (100%) diff --git a/recipes/bioconductor-limma/3.28.6/build.sh b/recipes/bioconductor-limma/3.28.10/build.sh similarity index 100% rename from recipes/bioconductor-limma/3.28.6/build.sh rename to recipes/bioconductor-limma/3.28.10/build.sh diff --git a/recipes/bioconductor-limma/3.28.6/meta.yaml b/recipes/bioconductor-limma/3.28.10/meta.yaml similarity index 100% rename from recipes/bioconductor-limma/3.28.6/meta.yaml rename to recipes/bioconductor-limma/3.28.10/meta.yaml From 019c04e396dcf3895a80613fe003582e0c97caeb Mon Sep 17 00:00:00 2001 From: Bjoern Gruening Date: Sun, 4 Jun 2017 19:48:41 +0200 Subject: [PATCH 034/116] remove recipe --- recipes/bioconductor-limma/3.26.7/build.sh | 17 ----------------- recipes/bioconductor-limma/3.26.7/meta.yaml | 25 ------------------------- 2 files changed, 42 deletions(-) delete mode 100644 recipes/bioconductor-limma/3.26.7/build.sh delete mode 100644 recipes/bioconductor-limma/3.26.7/meta.yaml diff --git a/recipes/bioconductor-limma/3.26.7/build.sh b/recipes/bioconductor-limma/3.26.7/build.sh deleted file mode 100644 index 6c7a1726e3..0000000000 --- a/recipes/bioconductor-limma/3.26.7/build.sh +++ /dev/null @@ -1,17 +0,0 @@ - -#!/bin/bash - -# R refuses to build packages that mark themselves as -# "Priority: Recommended" -mv DESCRIPTION DESCRIPTION.old -grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION -# -$R CMD INSTALL --build . -# -# # Add more build steps here, if they are necessary. -# -# See -# http://docs.continuum.io/conda/build.html -# for a list of environment variables that are set during the build -# process. -# \ No newline at end of file diff --git a/recipes/bioconductor-limma/3.26.7/meta.yaml b/recipes/bioconductor-limma/3.26.7/meta.yaml deleted file mode 100644 index aad2b2bfe5..0000000000 --- a/recipes/bioconductor-limma/3.26.7/meta.yaml +++ /dev/null @@ -1,25 +0,0 @@ -package: - name: bioconductor-limma - version: 3.26.7 -source: - fn: limma_3.26.7.tar.gz - url: http://bioconductor.org/packages/release/bioc/src/contrib/limma_3.26.7.tar.gz - md5: 0d5047e78e188cf316fc3577cadeadb0 -build: - number: 1 - rpaths: - - lib/R/lib/ - - lib/ -requirements: - build: - - r-base - run: - - r-base -test: - commands: - - '$R -e "library(''limma'')"' -about: - home: http://bioconductor.org/packages/release/bioc/html/limma.html - license: 'GPL (>=2)' - summary: 'Data analysis, linear models and differential expression for microarray - data.' From ee1ca562ae2501bb76d7b4ab73b282ca7d19dc20 Mon Sep 17 00:00:00 2001 From: Ryan Dale Date: Sun, 4 Jun 2017 21:55:18 -0400 Subject: [PATCH 035/116] update bioc skeleton; fix tximport & biomformat --- recipes/bioconductor-biomformat/build.sh | 11 -- recipes/bioconductor-biomformat/meta.yaml | 11 +- recipes/bioconductor-tximport/build.sh | 11 -- recipes/bioconductor-tximport/meta.yaml | 10 +- scripts/bioconductor/bioconductor_skeleton.py | 258 +++++++++++++++++++------- 5 files changed, 207 insertions(+), 94 deletions(-) diff --git a/recipes/bioconductor-biomformat/build.sh b/recipes/bioconductor-biomformat/build.sh index 6c7a1726e3..8218eda948 100644 --- a/recipes/bioconductor-biomformat/build.sh +++ b/recipes/bioconductor-biomformat/build.sh @@ -1,17 +1,6 @@ #!/bin/bash - -# R refuses to build packages that mark themselves as -# "Priority: Recommended" mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION -# $R CMD INSTALL --build . -# -# # Add more build steps here, if they are necessary. -# -# See -# http://docs.continuum.io/conda/build.html -# for a list of environment variables that are set during the build -# process. # \ No newline at end of file diff --git a/recipes/bioconductor-biomformat/meta.yaml b/recipes/bioconductor-biomformat/meta.yaml index 004fa7ef44..a3824207e0 100644 --- a/recipes/bioconductor-biomformat/meta.yaml +++ b/recipes/bioconductor-biomformat/meta.yaml @@ -3,10 +3,13 @@ package: version: 1.2.0 source: fn: biomformat_1.2.0.tar.gz - url: https://bioarchive.galaxyproject.org/biomformat_1.2.0.tar.gz - md5: 2e9efdd64bf09eecdc3699018203c18e + url: + - http://bioconductor.org/packages/3.4/bioc/src/contrib/biomformat_1.2.0.tar.gz + - https://bioarchive.galaxyproject.org/biomformat_1.2.0.tar.gz + - https://depot.galaxyproject.org/software/biomformat/biomformat_1.2.0_src_all.tar.gz + md5: 0a418f48c731375953ff7389b9b6f7a0 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -25,7 +28,7 @@ test: commands: - '$R -e "library(''biomformat'')"' about: - home: http://bioconductor.org/packages/release/bioc/html/biomformat.html + home: http://bioconductor.org/packages/3.5/bioc/html/biomformat.html license: GPL-2 summary: 'This is an R package for interfacing with the BIOM format. This package includes basic tools for reading biom-format files, accessing and subsetting data diff --git a/recipes/bioconductor-tximport/build.sh b/recipes/bioconductor-tximport/build.sh index 6c7a1726e3..8218eda948 100644 --- a/recipes/bioconductor-tximport/build.sh +++ b/recipes/bioconductor-tximport/build.sh @@ -1,17 +1,6 @@ #!/bin/bash - -# R refuses to build packages that mark themselves as -# "Priority: Recommended" mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION -# $R CMD INSTALL --build . -# -# # Add more build steps here, if they are necessary. -# -# See -# http://docs.continuum.io/conda/build.html -# for a list of environment variables that are set during the build -# process. # \ No newline at end of file diff --git a/recipes/bioconductor-tximport/meta.yaml b/recipes/bioconductor-tximport/meta.yaml index 0c80c3d5ab..8584349e0d 100644 --- a/recipes/bioconductor-tximport/meta.yaml +++ b/recipes/bioconductor-tximport/meta.yaml @@ -3,10 +3,12 @@ package: version: 1.0.3 source: fn: tximport_1.0.3.tar.gz - url: https://bioconductor.statistik.tu-dortmund.de/packages/3.3/bioc/src/contrib/tximport_1.0.3.tar.gz - sha256: e03d1bbaca438eccbab42429098e172d02a99700f29e69a5525f4318b82a4892 + url: + - http://bioconductor.org/packages/3.3/bioc/src/contrib/tximport_1.0.3.tar.gz + - https://depot.galaxyproject.org/software/tximport/tximport_1.0.3_src_all.tar.gz + md5: c6e0a617f255af19fae34fe8e8096204 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -19,7 +21,7 @@ test: commands: - '$R -e "library(''tximport'')"' about: - home: http://bioconductor.org/packages/release/bioc/html/tximport.html + home: http://bioconductor.org/packages/3.5/bioc/html/tximport.html license: 'GPL (>=2)' summary: 'Imports transcript-level abundance, estimated counts and transcript lengths, and summarizes into matrices for use with downstream gene-level analysis packages. diff --git a/scripts/bioconductor/bioconductor_skeleton.py b/scripts/bioconductor/bioconductor_skeleton.py index c0a0e785f5..daee2fadba 100755 --- a/scripts/bioconductor/bioconductor_skeleton.py +++ b/scripts/bioconductor/bioconductor_skeleton.py @@ -17,11 +17,33 @@ from collections import OrderedDict import logging import requests +from colorlog import ColoredFormatter -logging.basicConfig(level=logging.INFO, format='[bioconductor_skeleton.py %(asctime)s]: %(message)s') -logger = logging.getLogger() logging.getLogger("requests").setLevel(logging.WARNING) +log_stream_handler = logging.StreamHandler() +log_stream_handler.setFormatter(ColoredFormatter( + "%(asctime)s %(log_color)sBIOCONDA %(levelname)s%(reset)s %(message)s", + datefmt="%H:%M:%S", + reset=True, + log_colors={ + 'DEBUG': 'cyan', + 'INFO': 'green', + 'WARNING': 'yellow', + 'ERROR': 'red', + 'CRITICAL': 'red', + })) +logger = logging.getLogger(__name__) + + + +def setup_logger(loglevel): + LEVEL = getattr(logging, loglevel.upper()) + l = logging.getLogger(__name__) + l.propagate = False + l.setLevel(getattr(logging, loglevel.upper())) + l.addHandler(log_stream_handler) + base_url = 'http://bioconductor.org/packages/' # Packages that might be specified in the DESCRIPTION of a package as @@ -44,10 +66,60 @@ HERE = os.path.abspath(os.path.dirname(__file__)) + +def bioconductor_versions(): + regex = re.compile('^/packages/(?P\d+\.\d+)/$') + url = 'https://www.bioconductor.org/about/release-announcements/#release-versions' + response = requests.get(url) + soup = bs4.BeautifulSoup(response.content, 'html.parser') + versions = [] + for a in soup.find_all('a', href=True): + ref = a.attrs['href'] + m = regex.search(ref) + if m: + versions.append(m.group('version')) + versions = sorted(versions, key=float, reverse=True) + return versions + + +def latest_bioconductor_version(): + return bioconductor_versions()[0] + + +def bioconductor_tarball_url(package, pkg_version, bioc_version): + return ( + 'http://bioconductor.org/packages/{bioc_version}' + '/bioc/src/contrib/{package}_{pkg_version}.tar.gz'.format(**locals()) + ) + + +def find_best_bioc_version(package, version): + """ + Given a package version number, identifies which BioC version[s] it is + in and returns the latest. + + Returns None if no valid package found. + """ + found_version = None + for bioc_version in bioconductor_versions(): + url = bioconductor_tarball_url(package, version, bioc_version) + if requests.head(url).status_code == 200: + logger.debug('success: %s', url) + logger.info( + 'A working URL for %s==%s was identified for Bioconductor version %s: %s', + package, version, bioc_version, url) + found_version = bioc_version + break + else: + logger.debug('missing: %s', url) + return found_version + + class PageNotFoundError(Exception): pass + class BioCProjectPage(object): - def __init__(self, package): + def __init__(self, package, bioc_version=None, pkg_version=None): """ Represents a single Bioconductor package page and provides access to scraped data. @@ -61,81 +133,130 @@ def __init__(self, package): self._cached_tarball = None self._dependencies = None self.build_number = 0 - self.request = requests.get(os.path.join(base_url, package)) + self.bioc_version = bioc_version + self.pkg_version = pkg_version + self._cargoport_url = None + self._bioarchive_url = None + self._tarball_url = None + self._bioconductor_tarball_url = None + + + # If no version specified, assume the latest + if not self.bioc_version: + self.bioc_version = latest_bioconductor_version() + self.request = requests.get( + os.path.join(base_url, self.bioc_version, 'bioc', 'html', package + '.html') + ) + if not self.request: - raise PageNotFoundError('Error {0.status_code} ({0.reason})'.format(self.request)) + raise PageNotFoundError('Error {0.status_code} ({0.reason}) for page {0.url}'.format(self.request)) # Since we provide the "short link" we will get redirected. Using # requests allows us to keep track of the final destination URL, which # we need for reconstructing the tarball URL. self.url = self.request.url - # The table at the bottom of the page has the info we want. An earlier # draft of this script parsed the dependencies from the details table. # That's still an option if we need a double-check on the DESCRIPTION # fields. - self.soup = bs4.BeautifulSoup( + soup = bs4.BeautifulSoup( self.request.content, 'html.parser') - self.details_table = self.soup.find_all(attrs={'class': 'details'})[0] + details_table = soup.find_all(attrs={'class': 'details'})[0] # However, it is helpful to get the version info from this table. That # way we can try getting the bioaRchive tarball and cache that. - for td in self.details_table.findAll('td'): + for td in details_table.findAll('td'): if td.getText() == 'Version': version = td.findNext().getText() break - self.version = version + + if self.pkg_version is not None and version != self.pkg_version: + logger.warn( + "Latest version of %s is %s, but using specified version %s", + self.package, version, self.pkg_version + ) + self.version = self.pkg_version + + else: + self.version = version self.depends_on_gcc = False + + # Used later to determine whether or not to auto-identify the best BioC + # version + self._auto = bioc_version is None + if self._auto: + self.bioc_version = find_best_bioc_version(self.package, self.version) + @property def bioaRchive_url(self): """ Returns the bioaRchive URL if one exists for this version of this package, otherwise returns None. + """ + if self._bioarchive_url is None: + url = 'https://bioarchive.galaxyproject.org/{0.package}_{0.version}.tar.gz'.format(self) + response = requests.head(url) + if response.status_code == 200: + return url - Note that to get the package version, we're still getting the - bioconductor tarball to extract the DESCRIPTION file. + @property + def cargoport_url(self): """ - url = 'https://bioarchive.galaxyproject.org/{0.package}_{0.version}.tar.gz'.format(self) - response = requests.get(url) - if response: - return url - elif response.status_code == 404: - return - else: - raise PageNotFoundError("Unexpected error: {0.status_code} ({0.reason})".format(response)) + Returns the Galaxy cargo-port URL for this version of this package, + whether it exists or not. If none exists, a warning is printed. + """ + if not self._cargoport_url: + url = ( + 'https://depot.galaxyproject.org/software/{0.package}/{0.package}_' + '{0.version}_src_all.tar.gz'.format(self) + ) + response = requests.get(url) + if response.status_code == 404: + logger.warn( + 'Cargo Port URL (%s) does not exist. This is expected if ' + 'this is a new package or an updated version. Cargo Port ' + 'will archive a working URL upon merging', url + ) + else: + raise PageNotFoundError("Unexpected error: {0.status_code} ({0.reason})".format(response)) + self._cargoport_url = url + return self._cargoport_url @property def bioconductor_tarball_url(self): """ Return the url to the tarball from the bioconductor site. """ - r = re.compile('{0}.*\.tar.gz'.format(self.package)) - - def f(href): - return href and r.search(href) + return bioconductor_tarball_url(self.package, self.version, self.bioc_version) - results = self.soup.find_all(href=f) - assert len(results) == 1, ( - "Found {0} tags with '.tar.gz' in href".format(len(results))) - s = list(results[0].stripped_strings) - assert len(s) == 1 - - # build the actual URL based on the identified package name and the - # relative URL from the source. Here we're just hard-coding - # '../src/contrib' based on the structure of the bioconductor site. - return os.path.join(parse.urljoin(self.url, '../src/contrib'), s[0]) @property def tarball_url(self): - url = self.bioaRchive_url - if url: - return url - return self.bioconductor_tarball_url + if not self._tarball_url: + urls = [self.bioconductor_tarball_url, self.bioaRchive_url, self.cargoport_url] + for url in urls: + response = requests.head(url) + if response.status_code == 200: + return url + + logger.error( + 'No working URL for %s==%s in Bioconductor %s. ' + 'Tried the following:\n\t' + '\n\t'.join(urls), + self.package, self.version, self.bioc_version + ) + + if self._auto: + find_best_bioc_version(self.package, self.version) + + if self._tarball_url is None: + raise ValueError("No working URLs found for this version in any bioconductor version") + return self._tarball_url + @property def tarball_basename(self): @@ -193,10 +314,6 @@ def description(self): return dict(e) - #@property - #def version(self): - # return self.description['version'] - @property def license(self): return self.description['license'] @@ -349,9 +466,11 @@ def meta_yaml(self): templating or the `$R` in the test commands, and replace the text once the yaml is written. """ - url = self.bioaRchive_url - if not url: - url = self.tarball_url + url = [ + u for u in + [self.bioconductor_tarball_url, self.bioaRchive_url, self.cargoport_url] + if u is not None + ] DEPENDENCIES = sorted(self.dependencies) d = OrderedDict(( @@ -409,17 +528,23 @@ def meta_yaml(self): return rendered -def write_recipe(package, recipe_dir, force=False): +def write_recipe(package, recipe_dir, force=False, bioc_version=None, + pkg_version=None, versioned=False): """ Write the meta.yaml and build.sh files. """ - proj = BioCProjectPage(package) - recipe_dir = os.path.join(recipe_dir, 'bioconductor-' + proj.package.lower()) + proj = BioCProjectPage(package, bioc_version, pkg_version) + logger.debug('%s==%s, BioC==%s', proj.package, proj.version, proj.bioc_version) + logger.info('Using tarball from %s', proj.tarball_url) + if versioned: + recipe_dir = os.path.join(recipe_dir, 'bioconductor-' + proj.package.lower(), proj.version) + else: + recipe_dir = os.path.join(recipe_dir, 'bioconductor-' + proj.package.lower()) if os.path.exists(recipe_dir) and not force: raise ValueError("{0} already exists, aborting".format(recipe_dir)) else: if not os.path.exists(recipe_dir): - print('creating %s' % recipe_dir) + logger.info('creating %s' % recipe_dir) os.makedirs(recipe_dir) # If the version number has not changed but something else in the recipe @@ -447,29 +572,17 @@ def write_recipe(package, recipe_dir, force=False): with open(os.path.join(recipe_dir, 'meta.yaml'), 'w') as fout: fout.write(proj.meta_yaml) - - with open(os.path.join(recipe_dir, 'build.sh'), 'w') as fout: fout.write(dedent( """ #!/bin/bash - - # R refuses to build packages that mark themselves as - # "Priority: Recommended" mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION - # $R CMD INSTALL --build . - # - # # Add more build steps here, if they are necessary. - # - # See - # http://docs.continuum.io/conda/build.html - # for a list of environment variables that are set during the build - # process. # """ ) ) + logger.info('Wrote recipe in %s', recipe_dir) if __name__ == "__main__": @@ -477,8 +590,25 @@ def write_recipe(package, recipe_dir, force=False): ap = argparse.ArgumentParser() ap.add_argument('package', help='Bioconductor package name') ap.add_argument('--recipes', default='recipes', - help='Recipe will be created in /') + help='Recipe will be created in RECIPES/') + ap.add_argument('--versioned', action='store_true', + help='''If specified, recipe will be created in + RECIPES//''') ap.add_argument('--force', action='store_true', help='Overwrite the contents of an existing recipe') + ap.add_argument('--pkg-version', + help='Package version to use instead of the current one') + ap.add_argument('--bioc-version', + help="""Version of Bioconductor to target. If not + specified, then automatically finds the latest version of + Bioconductor with the specified version in --pkg-version, + or if --pkg-version not specified, then finds the the + latest package version in the latest Bioconductor + version""") + ap.add_argument('--loglevel', default='debug', + help='Log level') args = ap.parse_args() - write_recipe(args.package, args.recipes, args.force) + setup_logger(args.loglevel) + write_recipe(args.package, args.recipes, args.force, + bioc_version=args.bioc_version, pkg_version=args.pkg_version, + versioned=args.versioned) From 4d13b016d20b9d8b1f3a0adff7b02879a6860d0f Mon Sep 17 00:00:00 2001 From: Bjoern Gruening Date: Mon, 5 Jun 2017 11:04:05 +0200 Subject: [PATCH 036/116] r fixes --- recipes/bioconductor-dupradar/meta.yaml | 4 ++-- recipes/bioconductor-geneplotter/meta.yaml | 2 ++ recipes/bioconductor-go.db/meta.yaml | 2 +- recipes/bioconductor-hilbertvis/meta.yaml | 2 ++ recipes/bioconductor-noiseq/meta.yaml | 2 ++ recipes/bioconductor-org.hs.eg.db/meta.yaml | 2 +- recipes/bioconductor-org.rn.eg.db/meta.yaml | 2 +- recipes/bioconductor-pcamethods/meta.yaml | 2 ++ recipes/r-boutroslabplottinggeneral/meta.yaml | 4 ++++ recipes/r-future/0.9.0/meta.yaml | 1 - recipes/r-future/meta.yaml | 1 - recipes/r-geomap/meta.yaml | 25 ------------------------- recipes/r-r.utils/2.2.0/meta.yaml | 1 - recipes/r-speaq/meta.yaml | 1 - 14 files changed, 17 insertions(+), 34 deletions(-) diff --git a/recipes/bioconductor-dupradar/meta.yaml b/recipes/bioconductor-dupradar/meta.yaml index 363b5287ce..b4c09b3d7f 100644 --- a/recipes/bioconductor-dupradar/meta.yaml +++ b/recipes/bioconductor-dupradar/meta.yaml @@ -13,10 +13,10 @@ build: requirements: build: - 'bioconductor-rsubread >=1.14.1' - - 'r' + - r-base run: - 'bioconductor-rsubread >=1.14.1' - - 'r' + - r-base test: commands: - '$R -e "library(''dupRadar'')"' diff --git a/recipes/bioconductor-geneplotter/meta.yaml b/recipes/bioconductor-geneplotter/meta.yaml index 6eba0e08ca..25954ca38f 100644 --- a/recipes/bioconductor-geneplotter/meta.yaml +++ b/recipes/bioconductor-geneplotter/meta.yaml @@ -18,6 +18,7 @@ requirements: - bioconductor-biocgenerics - r-base - r-rcolorbrewer + - r-lattice run: - bioconductor-annotate - bioconductor-annotationdbi @@ -25,6 +26,7 @@ requirements: - bioconductor-biocgenerics - r-base - r-rcolorbrewer + - r-lattice test: commands: - '$R -e "library(''geneplotter'')"' diff --git a/recipes/bioconductor-go.db/meta.yaml b/recipes/bioconductor-go.db/meta.yaml index d179998ab8..752fdabba6 100644 --- a/recipes/bioconductor-go.db/meta.yaml +++ b/recipes/bioconductor-go.db/meta.yaml @@ -2,7 +2,7 @@ package: name: bioconductor-go.db version: 3.4.0 source: - url: https://bioconductor.org/packages/release/data/annotation/src/contrib/GO.db_3.4.0.tar.gz + url: https://depot.galaxyproject.org/software/bioconductor-go.db/bioconductor-go.db_3.4.0_src_all.tar.gz md5: 06e4ea8bd692bda85ae546263f39912d build: number: 0 diff --git a/recipes/bioconductor-hilbertvis/meta.yaml b/recipes/bioconductor-hilbertvis/meta.yaml index 9ddc47aae2..d1fb9b5c5b 100644 --- a/recipes/bioconductor-hilbertvis/meta.yaml +++ b/recipes/bioconductor-hilbertvis/meta.yaml @@ -13,8 +13,10 @@ build: requirements: build: - r-base + - r-lattice run: - r-base + r-lattice test: commands: - '$R -e "library(''HilbertVis'')"' diff --git a/recipes/bioconductor-noiseq/meta.yaml b/recipes/bioconductor-noiseq/meta.yaml index c3bf4676d2..4fdacfb915 100644 --- a/recipes/bioconductor-noiseq/meta.yaml +++ b/recipes/bioconductor-noiseq/meta.yaml @@ -14,9 +14,11 @@ requirements: build: - 'bioconductor-biobase >=2.13.11' - r-base + - r-matrix run: - 'bioconductor-biobase >=2.13.11' - r-base + - r-matrix test: commands: - '$R -e "library(''NOISeq'')"' diff --git a/recipes/bioconductor-org.hs.eg.db/meta.yaml b/recipes/bioconductor-org.hs.eg.db/meta.yaml index be92d8bb92..edf8d86f54 100644 --- a/recipes/bioconductor-org.hs.eg.db/meta.yaml +++ b/recipes/bioconductor-org.hs.eg.db/meta.yaml @@ -3,7 +3,7 @@ package: version: 3.3.0 source: fn: org.Hs.eg.db_3.3.0.tar.gz - url: http://bioconductor.org/packages/release/data/annotation/src/contrib/org.Hs.eg.db_3.3.0.tar.gz + url: https://depot.galaxyproject.org/software/bioconductor-org.hs.eg.db/bioconductor-org.hs.eg.db_3.3.0_src_all.tar.gz md5: ef4a05f46e7cdb0ba23fcd898a4a1d57 build: number: 1 diff --git a/recipes/bioconductor-org.rn.eg.db/meta.yaml b/recipes/bioconductor-org.rn.eg.db/meta.yaml index 8bf231a488..f67fc61173 100644 --- a/recipes/bioconductor-org.rn.eg.db/meta.yaml +++ b/recipes/bioconductor-org.rn.eg.db/meta.yaml @@ -3,7 +3,7 @@ package: version: 3.4.1 source: fn: org.Rn.eg.db_3.4.1.tar.gz - url: http://bioconductor.org/packages/release/data/annotation/src/contrib/org.Rn.eg.db_3.4.1.tar.gz + url: https://depot.galaxyproject.org/software/bioconductor-org.rn.eg.db/bioconductor-org.rn.eg.db_3.4.1_src_all.tar.gz md5: b1eade0c815dc9a0d45cc5efb1e16c44 build: number: 0 diff --git a/recipes/bioconductor-pcamethods/meta.yaml b/recipes/bioconductor-pcamethods/meta.yaml index d814ff2cf2..211a09b946 100644 --- a/recipes/bioconductor-pcamethods/meta.yaml +++ b/recipes/bioconductor-pcamethods/meta.yaml @@ -16,6 +16,7 @@ requirements: - bioconductor-biocgenerics - r-base - 'r-rcpp >=0.11.3' + - r-mass - gcc # [linux] - llvm # [osx] run: @@ -23,6 +24,7 @@ requirements: - bioconductor-biocgenerics - r-base - 'r-rcpp >=0.11.3' + - r-mass test: commands: - '$R -e "library(''pcaMethods'')"' diff --git a/recipes/r-boutroslabplottinggeneral/meta.yaml b/recipes/r-boutroslabplottinggeneral/meta.yaml index 4bbd940f12..c26648e457 100644 --- a/recipes/r-boutroslabplottinggeneral/meta.yaml +++ b/recipes/r-boutroslabplottinggeneral/meta.yaml @@ -28,6 +28,8 @@ requirements: - r-dbi - r-bh - r-dplyr + - r-mass + - r-cluster run: - r-base @@ -50,6 +52,8 @@ requirements: - r-dbi - r-bh - r-dplyr + - r-mass + - r-cluster test: commands: diff --git a/recipes/r-future/0.9.0/meta.yaml b/recipes/r-future/0.9.0/meta.yaml index 5299f687b0..8a9c909b09 100644 --- a/recipes/r-future/0.9.0/meta.yaml +++ b/recipes/r-future/0.9.0/meta.yaml @@ -5,7 +5,6 @@ package: source: fn: future_0.9.0.tar.gz url: - - http://cran.r-project.org/src/contrib/future_0.9.0.tar.gz - http://cran.r-project.org/src/contrib/Archive/future/future_0.9.0.tar.gz md5: 12fa027bd65cc1bbc289d31d658d2940 diff --git a/recipes/r-future/meta.yaml b/recipes/r-future/meta.yaml index beffac847a..fcd247d00d 100644 --- a/recipes/r-future/meta.yaml +++ b/recipes/r-future/meta.yaml @@ -8,7 +8,6 @@ package: source: fn: future_1.2.0.tar.gz url: - - http://cran.r-project.org/src/contrib/future_1.2.0.tar.gz - http://cran.r-project.org/src/contrib/Archive/future/future_1.2.0.tar.gz md5: bb80c8061441a21cbf0dd539b051a23f diff --git a/recipes/r-geomap/meta.yaml b/recipes/r-geomap/meta.yaml index 4eae35f1f7..2c0417f687 100644 --- a/recipes/r-geomap/meta.yaml +++ b/recipes/r-geomap/meta.yaml @@ -7,7 +7,6 @@ package: source: fn: GEOmap_2.3-8.tar.gz url: - - http://cran.r-project.org/src/contrib/GEOmap_2.3-8.tar.gz - http://cran.r-project.org/src/contrib/Archive/GEOmap/GEOmap_2.3-8.tar.gz md5: 3207abd337906a9345fc6d2be6c2c212 build: @@ -41,27 +40,3 @@ about: Perspective plots, Geological Maps, geological map symbols, geological databases, interactive plotting and selection of focus regions. license_family: GPL3 - -# The original CRAN metadata for this package was: - -# Package: GEOmap -# Type: Package -# Title: Topographic and Geologic Mapping -# Version: 2.3-8 -# Date: 2015-11-08 -# Depends: R (>= 3.0) -# Imports: RPMG, splancs, fields, MBA -# Suggests: geomapdata, maps, RFOC -# LazyData: yes -# Author: Jonathan M. Lees -# Maintainer: Jonathan M. Lees -# Description: Set of routines for making Map Projections (forward and inverse), Topographic Maps, Perspective plots, Geological Maps, geological map symbols, geological databases, interactive plotting and selection of focus regions. -# License: GPL (>= 2) -# Packaged: 2015-11-08 21:14:53 UTC; lees -# NeedsCompilation: yes -# Repository: CRAN -# Date/Publication: 2015-11-09 14:55:43 - -# See -# http://docs.continuum.io/conda/build.html for -# more information about meta.yaml diff --git a/recipes/r-r.utils/2.2.0/meta.yaml b/recipes/r-r.utils/2.2.0/meta.yaml index 461fe8ca90..f9688d9d0e 100644 --- a/recipes/r-r.utils/2.2.0/meta.yaml +++ b/recipes/r-r.utils/2.2.0/meta.yaml @@ -5,7 +5,6 @@ package: source: fn: R.utils_2.2.0.tar.gz url: - - http://cran.r-project.org/src/contrib/R.utils_2.2.0.tar.gz - http://cran.r-project.org/src/contrib/Archive/R.utils/R.utils_2.2.0.tar.gz md5: 6490255d5e733dce11005551df2b0c07 diff --git a/recipes/r-speaq/meta.yaml b/recipes/r-speaq/meta.yaml index b9da3b0643..d95c72b610 100644 --- a/recipes/r-speaq/meta.yaml +++ b/recipes/r-speaq/meta.yaml @@ -6,7 +6,6 @@ package: source: fn: speaq_1.2.3.tar.gz url: - - http://cran.r-project.org/src/contrib/speaq_1.2.3.tar.gz - http://cran.r-project.org/src/contrib/Archive/speaq/speaq_1.2.3.tar.gz md5: 86aed46f82c4a58884cd30fed8fe50a3 From b01ced2314b42f007349020f787868701255e787 Mon Sep 17 00:00:00 2001 From: Bjoern Gruening Date: Mon, 5 Jun 2017 11:16:31 +0200 Subject: [PATCH 037/116] fix syntax --- recipes/bioconductor-hilbertvis/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/bioconductor-hilbertvis/meta.yaml b/recipes/bioconductor-hilbertvis/meta.yaml index d1fb9b5c5b..47ac951205 100644 --- a/recipes/bioconductor-hilbertvis/meta.yaml +++ b/recipes/bioconductor-hilbertvis/meta.yaml @@ -16,7 +16,7 @@ requirements: - r-lattice run: - r-base - r-lattice + - r-lattice test: commands: - '$R -e "library(''HilbertVis'')"' From dd80b6b9a5b2080b8b32e98700d005f9fa8831b4 Mon Sep 17 00:00:00 2001 From: Bjoern Gruening Date: Mon, 5 Jun 2017 13:26:57 +0200 Subject: [PATCH 038/116] r fixes --- recipes/bioconductor-edger/meta.yaml | 2 +- recipes/bioconductor-genefilter/meta.yaml | 2 +- recipes/bioconductor-org.hs.eg.db/meta.yaml | 2 +- recipes/bioconductor-ropls/meta.yaml | 2 ++ recipes/r-phonr/meta.yaml | 35 ----------------------------- recipes/r-spdep/meta.yaml | 1 - 6 files changed, 5 insertions(+), 39 deletions(-) diff --git a/recipes/bioconductor-edger/meta.yaml b/recipes/bioconductor-edger/meta.yaml index e8a5c6f1cc..7ba3992242 100644 --- a/recipes/bioconductor-edger/meta.yaml +++ b/recipes/bioconductor-edger/meta.yaml @@ -2,7 +2,7 @@ package: name: bioconductor-edger version: 3.16.5 source: - url: https://bioconductor.org/packages/release/bioc/src/contrib/edgeR_3.16.5.tar.gz + url: https://depot.galaxyproject.org/software/bioconductor-edger/bioconductor-edger_3.16.5_src_all.tar.gz md5: 7fa050082478fb13173ee758342a6861 build: number: 0 diff --git a/recipes/bioconductor-genefilter/meta.yaml b/recipes/bioconductor-genefilter/meta.yaml index 9c7eecfb5d..c62c9c6bff 100644 --- a/recipes/bioconductor-genefilter/meta.yaml +++ b/recipes/bioconductor-genefilter/meta.yaml @@ -3,7 +3,7 @@ package: version: 1.56.0 source: fn: genefilter_1.56.0.tar.gz - url: http://bioconductor.org/packages/release/bioc/src/contrib/genefilter_1.56.0.tar.gz + url: https://depot.galaxyproject.org/software/bioconductor-genefilter/bioconductor-genefilter_1.56.0_src_all.tar.gz md5: 919e4deb451ca4e9dbea1e125e15cf98 build: number: 0 diff --git a/recipes/bioconductor-org.hs.eg.db/meta.yaml b/recipes/bioconductor-org.hs.eg.db/meta.yaml index edf8d86f54..be92d8bb92 100644 --- a/recipes/bioconductor-org.hs.eg.db/meta.yaml +++ b/recipes/bioconductor-org.hs.eg.db/meta.yaml @@ -3,7 +3,7 @@ package: version: 3.3.0 source: fn: org.Hs.eg.db_3.3.0.tar.gz - url: https://depot.galaxyproject.org/software/bioconductor-org.hs.eg.db/bioconductor-org.hs.eg.db_3.3.0_src_all.tar.gz + url: http://bioconductor.org/packages/release/data/annotation/src/contrib/org.Hs.eg.db_3.3.0.tar.gz md5: ef4a05f46e7cdb0ba23fcd898a4a1d57 build: number: 1 diff --git a/recipes/bioconductor-ropls/meta.yaml b/recipes/bioconductor-ropls/meta.yaml index 50ed3e7706..6d40accb58 100644 --- a/recipes/bioconductor-ropls/meta.yaml +++ b/recipes/bioconductor-ropls/meta.yaml @@ -16,8 +16,10 @@ build: requirements: build: - r-base + - bioconductor-biobase run: - r-base + - bioconductor-biobase test: commands: diff --git a/recipes/r-phonr/meta.yaml b/recipes/r-phonr/meta.yaml index 6a92e5c162..31d6acdec9 100644 --- a/recipes/r-phonr/meta.yaml +++ b/recipes/r-phonr/meta.yaml @@ -10,17 +10,8 @@ package: source: fn: phonR_1.0-3.tar.gz url: - - http://cran.r-project.org/src/contrib/phonR_1.0-3.tar.gz - http://cran.r-project.org/src/contrib/Archive/phonR/phonR_1.0-3.tar.gz - - # You can add a hash for the file here, like md5 or sha1 - # md5: 49448ba4863157652311cc5ea4fea3ea - # sha1: 3bcfbee008276084cbb37a2b453963c61176a322 - # patches: - # List any patch files here - # - fix.patch - build: # If this is a new build for the same version, increment the build # number. If you do not include this key, it defaults to 0. @@ -63,29 +54,3 @@ about: summary: Tools for phoneticians and phonologists, including functions for normalization and plotting of vowels. license_family: GPL3 - -# The original CRAN metadata for this package was: - -# Package: phonR -# Type: Package -# Title: Tools for Phoneticians and Phonologists -# Version: 1.0-3 -# Date: 2015-04-18 -# Author: Daniel R. McCloy -# Maintainer: Daniel R. McCloy -# Depends: R (>= 2.10) -# Imports: splancs, deldir, plotrix -# Description: Tools for phoneticians and phonologists, including functions for normalization and plotting of vowels. -# License: GPL-3 -# URL: http://drammock.github.io/phonR/ -# BugReports: https://github.com/drammock/phonR/issues -# LazyLoad: yes -# LazyData: yes -# Packaged: 2015-04-19 01:42:07 UTC; dan -# NeedsCompilation: no -# Repository: CRAN -# Date/Publication: 2015-04-19 07:52:19 - -# See -# http://docs.continuum.io/conda/build.html for -# more information about meta.yaml diff --git a/recipes/r-spdep/meta.yaml b/recipes/r-spdep/meta.yaml index 8c60df5a88..3beed4a15f 100644 --- a/recipes/r-spdep/meta.yaml +++ b/recipes/r-spdep/meta.yaml @@ -5,7 +5,6 @@ package: source: fn: spdep_0.6-8.tar.gz url: - - http://cran.r-project.org/src/contrib/spdep_0.6-8.tar.gz - http://cran.r-project.org/src/contrib/Archive/spdep/spdep_0.6-8.tar.gz md5: 9849c8dd588590ff9040fb82ebcf9c6b From a9087c4a7208f052a42d2a8e39e8070c69f1828a Mon Sep 17 00:00:00 2001 From: Bjoern Gruening Date: Mon, 5 Jun 2017 15:19:24 +0200 Subject: [PATCH 039/116] r fixes --- recipes/r-bma/meta.yaml | 34 ------------------------- recipes/r-ggdendro/meta.yaml | 1 - recipes/r-pscbs/meta.yaml | 58 +++--------------------------------------- recipes/r-r.filesets/meta.yaml | 33 ------------------------ recipes/r-r.rsp/meta.yaml | 30 ---------------------- recipes/r-rniftyreg/meta.yaml | 4 +-- 6 files changed, 6 insertions(+), 154 deletions(-) diff --git a/recipes/r-bma/meta.yaml b/recipes/r-bma/meta.yaml index 6eecdbb92f..714abaa162 100644 --- a/recipes/r-bma/meta.yaml +++ b/recipes/r-bma/meta.yaml @@ -1,14 +1,10 @@ - package: name: r-bma - # Note that conda versions cannot contain -, so any -'s in the version have - # been replaced with _'s. version: "3.18.6" source: fn: BMA_3.18.6.tar.gz url: - - http://cran.r-project.org/src/contrib/BMA_3.18.6.tar.gz - http://cran.r-project.org/src/contrib/Archive/BMA/BMA_3.18.6.tar.gz build: @@ -16,7 +12,6 @@ build: - lib/R/lib/ - lib/ -# Suggests: MASS, forward requirements: build: - r-base @@ -42,38 +37,9 @@ test: - $R -e "library('BMA')" # [not win] - "\"%R%\" -e \"library('BMA')\"" # [win] - # You can also put a file called run_test.py, run_test.sh, or run_test.bat - # in the recipe that will be run at test time. - - # requires: - # Put any additional test requirements here. - about: home: http://www.r-project.org, http://www.research.att.com/~volinsky/bma.html license: GPL (>= 2) summary: Package for Bayesian model averaging and variable selection for linear models, generalized linear models and survival models (cox regression). license_family: GPL3 - -# The original CRAN metadata for this package was: - -# Package: BMA -# Version: 3.18.6 -# Date: 2015-11-05 -# Title: Bayesian Model Averaging -# Author: Adrian Raftery , Jennifer Hoeting, Chris Volinsky, Ian Painter, Ka Yee Yeung -# Maintainer: Hana Sevcikova -# Description: Package for Bayesian model averaging and variable selection for linear models, generalized linear models and survival models (cox regression). -# Depends: survival, leaps, robustbase, inline, rrcov -# Imports: methods -# Suggests: MASS, forward -# License: GPL (>= 2) -# URL: http://www.r-project.org, http://www.research.att.com/~volinsky/bma.html -# NeedsCompilation: yes -# Packaged: 2015-11-06 01:52:34 UTC; hana -# Repository: CRAN -# Date/Publication: 2015-11-06 05:49:45 - -# See -# http://docs.continuum.io/conda/build.html for -# more information about meta.yaml diff --git a/recipes/r-ggdendro/meta.yaml b/recipes/r-ggdendro/meta.yaml index 081604cf5c..6a08ea4fa9 100644 --- a/recipes/r-ggdendro/meta.yaml +++ b/recipes/r-ggdendro/meta.yaml @@ -7,7 +7,6 @@ package: source: fn: ggdendro_0.1-17.tar.gz url: - - http://cran.r-project.org/src/contrib/ggdendro_0.1-17.tar.gz - http://cran.r-project.org/src/contrib/Archive/ggdendro/ggdendro_0.1-17.tar.gz diff --git a/recipes/r-pscbs/meta.yaml b/recipes/r-pscbs/meta.yaml index c84b338841..b1d364803d 100644 --- a/recipes/r-pscbs/meta.yaml +++ b/recipes/r-pscbs/meta.yaml @@ -1,34 +1,19 @@ package: name: r-pscbs - # Note that conda versions cannot contain -, so any -'s in the version have - # been replaced with _'s. version: "0.60.0" source: fn: PSCBS_0.60.0.tar.gz url: - - http://cran.r-project.org/src/contrib/PSCBS_0.60.0.tar.gz - http://cran.r-project.org/src/contrib/Archive/PSCBS/PSCBS_0.60.0.tar.gz - - # You can add a hash for the file here, like md5 or sha1 - # md5: 49448ba4863157652311cc5ea4fea3ea - # sha1: 3bcfbee008276084cbb37a2b453963c61176a322 - # patches: - # List any patch files here - # - fix.patch - build: - # If this is a new build for the same version, increment the build - # number. If you do not include this key, it defaults to 0. # number: 1 - # This is required to make R link correctly on Linux. rpaths: - lib/R/lib/ - lib/ -# Suggests: Hmisc (>= 3.16-0), R.rsp (>= 0.20.0), R.devices (>= 2.13.1), ggplot2 (>= 1.0.1), aroma.light (>= 2.2.1) requirements: build: - r-base @@ -58,47 +43,12 @@ test: - $R -e "library('PSCBS')" # [not win] - "\"%R%\" -e \"library('PSCBS')\"" # [win] - # You can also put a file called run_test.py, run_test.sh, or run_test.bat - # in the recipe that will be run at test time. - - # requires: - # Put any additional test requirements here. - about: - home: !!python/unicode 'https://github.com/HenrikBengtsson/PSCBS' + home: 'https://github.com/HenrikBengtsson/PSCBS' license: GPL (>= 2) - summary: !!python/unicode 'Segmentation of allele-specific DNA copy number data and detection + summary: | + Segmentation of allele-specific DNA copy number data and detection of regions with abnormal copy number within each parental chromosome. Both tumor-normal - paired and tumor-only analyses are supported.' - - -# The original CRAN metadata for this package was: - -# Package: PSCBS -# Version: 0.60.0 -# Depends: R (>= 3.1.1), utils -# Imports: R.methodsS3 (>= 1.7.0), R.oo (>= 1.19.0), R.utils (>= 2.1.0), R.cache (>= 0.12.0), matrixStats (>= 0.15.0), DNAcopy (>= 1.40.0), listenv (>= 0.5.0), future (>= 0.8.2), parallel -# Suggests: Hmisc (>= 3.16-0), R.rsp (>= 0.20.0), R.devices (>= 2.13.1), ggplot2 (>= 1.0.1), aroma.light (>= 2.2.1) -# SuggestsNote: BioC (>= 3.0), Recommended: Hmisc, aroma.light -# VignetteBuilder: R.rsp -# Date: 2015-11-17 -# Title: Analysis of Parent-Specific DNA Copy Numbers -# Authors@R: c( person("Henrik", "Bengtsson", role=c("aut", "cre", "cph"), email="henrikb@braju.com"), person("Pierre", "Neuvial", role="aut"), person("Venkatraman E.", "Seshan", role="aut"), person("Adam B.", "Olshen", role="aut"), person("Paul T.", "Spellman", role="aut"), person("Richard A.", "Olshen", role="aut")) -# Description: Segmentation of allele-specific DNA copy number data and detection of regions with abnormal copy number within each parental chromosome. Both tumor-normal paired and tumor-only analyses are supported. -# License: GPL (>= 2) -# LazyLoad: TRUE -# ByteCompile: TRUE -# biocViews: aCGH, CopyNumberVariants, SNP, Microarray, OneChannel, TwoChannel, Genetics -# URL: https://github.com/HenrikBengtsson/PSCBS -# BugReports: https://github.com/HenrikBengtsson/PSCBS/issues -# NeedsCompilation: no -# Packaged: 2015-11-17 17:52:13 UTC; hb -# Author: Henrik Bengtsson [aut, cre, cph], Pierre Neuvial [aut], Venkatraman E. Seshan [aut], Adam B. Olshen [aut], Paul T. Spellman [aut], Richard A. Olshen [aut] -# Maintainer: Henrik Bengtsson -# Repository: CRAN -# Date/Publication: 2015-11-18 09:31:06 + paired and tumor-only analyses are supported. -# See -# http://docs.continuum.io/conda/build.html for -# more information about meta.yaml diff --git a/recipes/r-r.filesets/meta.yaml b/recipes/r-r.filesets/meta.yaml index c8e4ee1976..b512eb3703 100644 --- a/recipes/r-r.filesets/meta.yaml +++ b/recipes/r-r.filesets/meta.yaml @@ -8,17 +8,14 @@ package: source: fn: R.filesets_2.10.0.tar.gz url: - - http://cran.r-project.org/src/contrib/R.filesets_2.10.0.tar.gz - http://cran.r-project.org/src/contrib/Archive/R.filesets/R.filesets_2.10.0.tar.gz md5: 04a4f3b1ebbdd383709131b8584eb021 build: - rpaths: - lib/R/lib/ - lib/ -# Suggests: BatchJobs (>= 1.6), BiocParallel (>= 1.0.3), gtools (>= 3.5.0) requirements: build: - r-base @@ -45,8 +42,6 @@ test: - $R -e "library('R.filesets')" # [not win] - "\"%R%\" -e \"library('R.filesets')\"" # [win] - - about: home: https://github.com/HenrikBengtsson/R.filesets, http://www.aroma-project.org/ license: LGPL (>= 2.1) @@ -62,31 +57,3 @@ about: if you decide to build on top of this package, please contact the author first.' license_family: LGPL - -# The original CRAN metadata for this package was: - -# Package: R.filesets -# Version: 2.10.0 -# Depends: R (>= 3.1.2), R.oo (>= 1.19.0) -# Imports: digest (>= 0.6.8), future (>= 0.10.0), listenv (>= 0.6.0), R.methodsS3 (>= 1.7.0), R.utils (>= 2.2.0), R.cache (>= 0.12.0), stats -# Suggests: BatchJobs (>= 1.6), BiocParallel (>= 1.0.3), gtools (>= 3.5.0) -# SuggestsNote: BioC (>= 3.0), Recommended: gtools -# Date: 2016-01-04 -# Title: Easy Handling of and Access to Files Organized in Structured Directories -# Authors@R: c(person("Henrik", "Bengtsson", role=c("aut", "cre", "cph"), email = "henrikb@braju.com")) -# Author: Henrik Bengtsson [aut, cre, cph] -# Maintainer: Henrik Bengtsson -# Description: A file set refers to a set of files located in one or more directories on the file system. This package provides classes and methods to locate, setup, subset, navigate and iterate such sets. The API is designed such that these classes can be extended via inheritance to provide a richer API for special file formats. Moreover, a specific name format is defined such that filenames and directories can be considered to have full names which consists of a name followed by comma-separated tags. This adds additional flexibility to identify file sets and individual files. NOTE: This package's API should be considered to be in an beta stage. Its main purpose is currently to support the aroma.* packages, where it is one of the main core components; if you decide to build on top of this package, please contact the author first. -# License: LGPL (>= 2.1) -# URL: https://github.com/HenrikBengtsson/R.filesets, http://www.aroma-project.org/ -# BugReports: https://github.com/HenrikBengtsson/R.filesets/issues -# LazyLoad: TRUE -# biocViews: Infrastructure, DataImport, DataRepresentation -# NeedsCompilation: no -# Packaged: 2016-01-04 23:36:06 UTC; hb -# Repository: CRAN -# Date/Publication: 2016-01-05 07:03:05 - -# See -# http://docs.continuum.io/conda/build.html for -# more information about meta.yaml diff --git a/recipes/r-r.rsp/meta.yaml b/recipes/r-r.rsp/meta.yaml index cd56d211c2..a032c95bb8 100644 --- a/recipes/r-r.rsp/meta.yaml +++ b/recipes/r-r.rsp/meta.yaml @@ -8,7 +8,6 @@ package: source: fn: R.rsp_0.30.0.tar.gz url: - - http://cran.r-project.org/src/contrib/R.rsp_0.30.0.tar.gz - http://cran.r-project.org/src/contrib/Archive/R.rsp/R.rsp_0.30.0.tar.gz md5: 761a6c9422b67028400c79528d6e4287 @@ -18,7 +17,6 @@ build: - lib/R/lib/ - lib/ -# Suggests: tcltk, digest (>= 0.6.9), ascii (>= 2.1), markdown (>= 0.7.7), knitr (>= 1.9), R.devices (>= 2.14.0), base64enc (>= 0.1-3) requirements: build: - r-base @@ -57,31 +55,3 @@ about: vignettes. It's easy to use - if you know how to write an R script, you'll be up and running within minutes. license_family: LGPL - -# The original CRAN metadata for this package was: - -# Package: R.rsp -# Version: 0.30.0 -# Depends: R (>= 2.14.0) -# Imports: methods, stats, tools, utils, R.methodsS3 (>= 1.7.1), R.oo (>= 1.20.0), R.utils, R.cache (>= 0.12.0) -# Suggests: tcltk, digest (>= 0.6.9), ascii (>= 2.1), markdown (>= 0.7.7), knitr (>= 1.9), R.devices (>= 2.14.0), base64enc (>= 0.1-3) -# SuggestsNote: Recommended: digest, R.devices, base64enc, markdown -# VignetteBuilder: R.rsp -# Date: 2016-05-15 -# Title: Dynamic Generation of Scientific Reports -# Authors@R: c(person("Henrik", "Bengtsson", role=c("aut", "cre", "cph"), email = "henrikb@braju.com")) -# Author: Henrik Bengtsson [aut, cre, cph] -# Maintainer: Henrik Bengtsson -# Description: The RSP markup language makes any text-based document come alive. RSP provides a powerful markup for controlling the content and output of LaTeX, HTML, Markdown, AsciiDoc, Sweave and knitr documents (and more), e.g. 'Today's date is <%=Sys.Date()%>'. Contrary to many other literate programming languages, with RSP it is straightforward to loop over mixtures of code and text sections, e.g. in month-by-month summaries. RSP has also several preprocessing directives for incorporating static and dynamic contents of external files (local or online) among other things. Functions rstring() and rcat() make it easy to process RSP strings, rsource() sources an RSP file as it was an R script, while rfile() compiles it (even online) into its final output format, e.g. rfile('report.tex.rsp') generates 'report.pdf' and rfile('report.md.rsp') generates 'report.html'. RSP is ideal for self-contained scientific reports and R package vignettes. It's easy to use - if you know how to write an R script, you'll be up and running within minutes. -# License: LGPL (>= 2.1) -# URL: https://github.com/HenrikBengtsson/R.rsp -# BugReports: https://github.com/HenrikBengtsson/R.rsp/issues -# LazyLoad: TRUE -# NeedsCompilation: no -# Packaged: 2016-05-15 16:18:43 UTC; hb -# Repository: CRAN -# Date/Publication: 2016-05-15 22:09:23 - -# See -# http://docs.continuum.io/conda/build.html for -# more information about meta.yaml diff --git a/recipes/r-rniftyreg/meta.yaml b/recipes/r-rniftyreg/meta.yaml index ca95394de6..e8309dba43 100644 --- a/recipes/r-rniftyreg/meta.yaml +++ b/recipes/r-rniftyreg/meta.yaml @@ -5,7 +5,6 @@ package: source: fn: RNiftyReg_2.2.0.tar.gz url: - - http://cran.r-project.org/src/contrib/RNiftyReg_2.2.0.tar.gz - http://cran.r-project.org/src/contrib/Archive/RNiftyReg/RNiftyReg_2.2.0.tar.gz build: @@ -39,5 +38,6 @@ test: about: home: https://github.com/jonclayden/RNiftyReg license: GPL-2 - summary: Provides an R interface to the NiftyReg image registration tools . + summary: | + Provides an R interface to the NiftyReg image registration tools . Linear and nonlinear registration are supported, in two and three dimensions. From 4901b637e897701cb9a9f75b480d39eba05c514c Mon Sep 17 00:00:00 2001 From: Ryan Dale Date: Mon, 5 Jun 2017 11:03:22 -0400 Subject: [PATCH 040/116] update flowViz recipe --- recipes/bioconductor-flowviz/build.sh | 11 ----------- recipes/bioconductor-flowviz/meta.yaml | 11 +++++++---- 2 files changed, 7 insertions(+), 15 deletions(-) diff --git a/recipes/bioconductor-flowviz/build.sh b/recipes/bioconductor-flowviz/build.sh index 6c7a1726e3..8218eda948 100644 --- a/recipes/bioconductor-flowviz/build.sh +++ b/recipes/bioconductor-flowviz/build.sh @@ -1,17 +1,6 @@ #!/bin/bash - -# R refuses to build packages that mark themselves as -# "Priority: Recommended" mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION -# $R CMD INSTALL --build . -# -# # Add more build steps here, if they are necessary. -# -# See -# http://docs.continuum.io/conda/build.html -# for a list of environment variables that are set during the build -# process. # \ No newline at end of file diff --git a/recipes/bioconductor-flowviz/meta.yaml b/recipes/bioconductor-flowviz/meta.yaml index 1e84fa03fe..37cb67bcbc 100644 --- a/recipes/bioconductor-flowviz/meta.yaml +++ b/recipes/bioconductor-flowviz/meta.yaml @@ -3,10 +3,13 @@ package: version: 1.38.0 source: fn: flowViz_1.38.0.tar.gz - url: https://bioarchive.galaxyproject.org/flowViz_1.38.0.tar.gz - md5: f4305de6bad26e8b906c39cf14a01b2a + url: + - http://bioconductor.org/packages/3.4/bioc/src/contrib/flowViz_1.38.0.tar.gz + - https://bioarchive.galaxyproject.org/flowViz_1.38.0.tar.gz + - https://depot.galaxyproject.org/software/flowViz/flowViz_1.38.0_src_all.tar.gz + md5: ca001789da5bf4d21a63d222d69255c7 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -31,6 +34,6 @@ test: commands: - '$R -e "library(''flowViz'')"' about: - home: http://bioconductor.org/packages/release/bioc/html/flowViz.html + home: http://bioconductor.org/packages/3.5/bioc/html/flowViz.html license: Artistic-2.0 summary: 'Provides visualization tools for flow cytometry data.' From 46f31409f6fefc69dc837dd2ed3612e335f3497f Mon Sep 17 00:00:00 2001 From: Ryan Dale Date: Mon, 5 Jun 2017 11:04:33 -0400 Subject: [PATCH 041/116] fix BiocStyle recipe --- recipes/bioconductor-biocstyle/build.sh | 11 ----------- recipes/bioconductor-biocstyle/meta.yaml | 10 ++++++---- 2 files changed, 6 insertions(+), 15 deletions(-) diff --git a/recipes/bioconductor-biocstyle/build.sh b/recipes/bioconductor-biocstyle/build.sh index 6c7a1726e3..8218eda948 100644 --- a/recipes/bioconductor-biocstyle/build.sh +++ b/recipes/bioconductor-biocstyle/build.sh @@ -1,17 +1,6 @@ #!/bin/bash - -# R refuses to build packages that mark themselves as -# "Priority: Recommended" mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION -# $R CMD INSTALL --build . -# -# # Add more build steps here, if they are necessary. -# -# See -# http://docs.continuum.io/conda/build.html -# for a list of environment variables that are set during the build -# process. # \ No newline at end of file diff --git a/recipes/bioconductor-biocstyle/meta.yaml b/recipes/bioconductor-biocstyle/meta.yaml index 070f4f2716..ff555f2cc0 100644 --- a/recipes/bioconductor-biocstyle/meta.yaml +++ b/recipes/bioconductor-biocstyle/meta.yaml @@ -3,10 +3,12 @@ package: version: 2.0.3 source: fn: BiocStyle_2.0.3.tar.gz - url: https://depot.galaxyproject.org/software/bioconductor-biocstyle/bioconductor-biocstyle_2.0.3_src_all.tar.gz - sha256: d16c2c911a4c567d3ae996610be1882b1c9b6fc2643079e42173511ebeb87269 + url: + - http://bioconductor.org/packages/3.3/bioc/src/contrib/BiocStyle_2.0.3.tar.gz + - https://depot.galaxyproject.org/software/BiocStyle/BiocStyle_2.0.3_src_all.tar.gz + md5: 426dcf23e33d0d29b10b6d40cae2054e build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -19,7 +21,7 @@ test: commands: - '$R -e "library(''BiocStyle'')"' about: - home: http://bioconductor.org/packages/release/bioc/html/BiocStyle.html + home: http://bioconductor.org/packages/3.5/bioc/html/BiocStyle.html license: Artistic-2.0 summary: 'Provides standard formatting styles for Bioconductor PDF and HTML documents. Package vignettes illustrate use and functionality.' From 9119a1039d407d867a46e82bf1d9f85a98f39c6a Mon Sep 17 00:00:00 2001 From: Ryan Dale Date: Mon, 5 Jun 2017 12:22:27 -0400 Subject: [PATCH 042/116] fix org.Hs.eg.db --- recipes/bioconductor-org.hs.eg.db/build.sh | 11 ----------- recipes/bioconductor-org.hs.eg.db/meta.yaml | 8 +++++--- 2 files changed, 5 insertions(+), 14 deletions(-) diff --git a/recipes/bioconductor-org.hs.eg.db/build.sh b/recipes/bioconductor-org.hs.eg.db/build.sh index 6c7a1726e3..8218eda948 100644 --- a/recipes/bioconductor-org.hs.eg.db/build.sh +++ b/recipes/bioconductor-org.hs.eg.db/build.sh @@ -1,17 +1,6 @@ #!/bin/bash - -# R refuses to build packages that mark themselves as -# "Priority: Recommended" mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION -# $R CMD INSTALL --build . -# -# # Add more build steps here, if they are necessary. -# -# See -# http://docs.continuum.io/conda/build.html -# for a list of environment variables that are set during the build -# process. # \ No newline at end of file diff --git a/recipes/bioconductor-org.hs.eg.db/meta.yaml b/recipes/bioconductor-org.hs.eg.db/meta.yaml index be92d8bb92..142e737e93 100644 --- a/recipes/bioconductor-org.hs.eg.db/meta.yaml +++ b/recipes/bioconductor-org.hs.eg.db/meta.yaml @@ -3,10 +3,12 @@ package: version: 3.3.0 source: fn: org.Hs.eg.db_3.3.0.tar.gz - url: http://bioconductor.org/packages/release/data/annotation/src/contrib/org.Hs.eg.db_3.3.0.tar.gz + url: + - http://bioconductor.org/packages/3.3/bioc/src/contrib/org.Hs.eg.db_3.3.0.tar.gz + - https://depot.galaxyproject.org/software/org.Hs.eg.db/org.Hs.eg.db_3.3.0_src_all.tar.gz md5: ef4a05f46e7cdb0ba23fcd898a4a1d57 build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ @@ -21,7 +23,7 @@ test: commands: - '$R -e "library(''org.Hs.eg.db'')"' about: - home: http://bioconductor.org/packages/release/data/annotation/html/org.Hs.eg.db.html + home: http://bioconductor.org/packages/3.5/data/annotation/html/org.Hs.eg.db.html license: Artistic-2.0 summary: 'Genome wide annotation for Human, primarily based on mapping using Entrez Gene identifiers.' From d29079abe3ead9cf73c1dfe48712bd618a56bc9a Mon Sep 17 00:00:00 2001 From: Ryan Dale Date: Mon, 5 Jun 2017 12:22:47 -0400 Subject: [PATCH 043/116] fix bioconductor_skeleton to auto-find data packages --- scripts/bioconductor/bioconductor_skeleton.py | 46 ++++++++++++++++++++------- 1 file changed, 35 insertions(+), 11 deletions(-) diff --git a/scripts/bioconductor/bioconductor_skeleton.py b/scripts/bioconductor/bioconductor_skeleton.py index daee2fadba..0b23085e21 100755 --- a/scripts/bioconductor/bioconductor_skeleton.py +++ b/scripts/bioconductor/bioconductor_skeleton.py @@ -93,6 +93,12 @@ def bioconductor_tarball_url(package, pkg_version, bioc_version): ) +def bioconductor_data_url(package, pkg_version, bioc_version): + return ( + 'http://bioconductor.org/packages/{bioc_version}' + '/data/annotation/src/contrib/{package}_{pkg_version}.tar.gz'.format(**locals()) + ) + def find_best_bioc_version(package, version): """ Given a package version number, identifies which BioC version[s] it is @@ -101,17 +107,21 @@ def find_best_bioc_version(package, version): Returns None if no valid package found. """ found_version = None + for bioc_version in bioconductor_versions(): - url = bioconductor_tarball_url(package, version, bioc_version) - if requests.head(url).status_code == 200: - logger.debug('success: %s', url) - logger.info( - 'A working URL for %s==%s was identified for Bioconductor version %s: %s', - package, version, bioc_version, url) - found_version = bioc_version + for func in (bioconductor_tarball_url, bioconductor_data_url): + url = func(package, version, bioc_version) + if requests.head(url).status_code == 200: + logger.debug('success: %s', url) + logger.info( + 'A working URL for %s==%s was identified for Bioconductor version %s: %s', + package, version, bioc_version, url) + found_version = bioc_version + break + else: + logger.debug('missing: %s', url) + if found_version is not None: break - else: - logger.debug('missing: %s', url) return found_version @@ -144,11 +154,17 @@ def __init__(self, package, bioc_version=None, pkg_version=None): # If no version specified, assume the latest if not self.bioc_version: self.bioc_version = latest_bioconductor_version() + self.request = requests.get( os.path.join(base_url, self.bioc_version, 'bioc', 'html', package + '.html') ) if not self.request: + self.request = requests.get( + os.path.join(base_url, self.bioc_version, 'data', 'annotation', 'html', package + '.html') + ) + + if not self.request: raise PageNotFoundError('Error {0.status_code} ({0.reason}) for page {0.url}'.format(self.request)) # Since we provide the "short link" we will get redirected. Using @@ -236,12 +252,20 @@ def bioconductor_tarball_url(self): @property + def bioconductor_data_url(self): + """ + Return the url to the tarball from the bioconductor site. + """ + return bioconductor_data_url(self.package, self.version, self.bioc_version) + + + @property def tarball_url(self): if not self._tarball_url: - urls = [self.bioconductor_tarball_url, self.bioaRchive_url, self.cargoport_url] + urls = [self.bioconductor_tarball_url, self.bioconductor_data_url, self.bioaRchive_url, self.cargoport_url] for url in urls: response = requests.head(url) - if response.status_code == 200: + if response and response.status_code == 200: return url logger.error( From 4df9903ec563f7418a00b32c12f0f8c5af2c485f Mon Sep 17 00:00:00 2001 From: Ryan Dale Date: Mon, 5 Jun 2017 12:31:04 -0400 Subject: [PATCH 044/116] fix SummarizedExperiment --- recipes/bioconductor-summarizedexperiment/build.sh | 11 ------- .../bioconductor-summarizedexperiment/meta.yaml | 36 ++++++++++------------ 2 files changed, 16 insertions(+), 31 deletions(-) diff --git a/recipes/bioconductor-summarizedexperiment/build.sh b/recipes/bioconductor-summarizedexperiment/build.sh index 6c7a1726e3..8218eda948 100644 --- a/recipes/bioconductor-summarizedexperiment/build.sh +++ b/recipes/bioconductor-summarizedexperiment/build.sh @@ -1,17 +1,6 @@ #!/bin/bash - -# R refuses to build packages that mark themselves as -# "Priority: Recommended" mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION -# $R CMD INSTALL --build . -# -# # Add more build steps here, if they are necessary. -# -# See -# http://docs.continuum.io/conda/build.html -# for a list of environment variables that are set during the build -# process. # \ No newline at end of file diff --git a/recipes/bioconductor-summarizedexperiment/meta.yaml b/recipes/bioconductor-summarizedexperiment/meta.yaml index ac7c09d886..f069ec8016 100644 --- a/recipes/bioconductor-summarizedexperiment/meta.yaml +++ b/recipes/bioconductor-summarizedexperiment/meta.yaml @@ -1,44 +1,40 @@ package: name: bioconductor-summarizedexperiment - version: "1.4.0" - + version: 1.4.0 source: fn: SummarizedExperiment_1.4.0.tar.gz - url: https://bioconductor.org/packages/release/bioc/src/contrib/SummarizedExperiment_1.4.0.tar.gz + url: + - http://bioconductor.org/packages/3.4/bioc/src/contrib/SummarizedExperiment_1.4.0.tar.gz + - https://bioarchive.galaxyproject.org/SummarizedExperiment_1.4.0.tar.gz + - https://depot.galaxyproject.org/software/SummarizedExperiment/SummarizedExperiment_1.4.0_src_all.tar.gz md5: 35159a339981efa22e96db639dadc850 - build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ - requirements: build: - - bioconductor-biobase - - bioconductor-biocgenerics + - bioconductor-biobase + - 'bioconductor-biocgenerics >=0.15.3' - bioconductor-genomeinfodb - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-s4vectors + - 'bioconductor-genomicranges >=1.23.15' + - 'bioconductor-iranges >=2.7.2' + - 'bioconductor-s4vectors >=0.11.7' - r-base - - r-matrix 1.2_6 run: - bioconductor-biobase - - bioconductor-biocgenerics + - 'bioconductor-biocgenerics >=0.15.3' - bioconductor-genomeinfodb - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-s4vectors + - 'bioconductor-genomicranges >=1.23.15' + - 'bioconductor-iranges >=2.7.2' + - 'bioconductor-s4vectors >=0.11.7' - r-base - - r-matrix 1.2_6 - test: commands: - '$R -e "library(''SummarizedExperiment'')"' - about: - home: http://bioconductor.org/packages/release/bioc/html/SummarizedExperiment.html + home: http://bioconductor.org/packages/3.5/bioc/html/SummarizedExperiment.html license: Artistic-2.0 summary: 'The SummarizedExperiment container contains one or more assays, each represented by a matrix-like object of numeric or other mode. The rows typically represent From fb2a6c29efa61a6444f405405378d334f40db3d9 Mon Sep 17 00:00:00 2001 From: Ryan Dale Date: Mon, 5 Jun 2017 12:32:28 -0400 Subject: [PATCH 045/116] fix BiocParallel --- recipes/bioconductor-biocparallel/build.sh | 11 ----------- recipes/bioconductor-biocparallel/meta.yaml | 8 +++++--- 2 files changed, 5 insertions(+), 14 deletions(-) diff --git a/recipes/bioconductor-biocparallel/build.sh b/recipes/bioconductor-biocparallel/build.sh index 6c7a1726e3..8218eda948 100644 --- a/recipes/bioconductor-biocparallel/build.sh +++ b/recipes/bioconductor-biocparallel/build.sh @@ -1,17 +1,6 @@ #!/bin/bash - -# R refuses to build packages that mark themselves as -# "Priority: Recommended" mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION -# $R CMD INSTALL --build . -# -# # Add more build steps here, if they are necessary. -# -# See -# http://docs.continuum.io/conda/build.html -# for a list of environment variables that are set during the build -# process. # \ No newline at end of file diff --git a/recipes/bioconductor-biocparallel/meta.yaml b/recipes/bioconductor-biocparallel/meta.yaml index 2daa17a027..c9a2e405f0 100644 --- a/recipes/bioconductor-biocparallel/meta.yaml +++ b/recipes/bioconductor-biocparallel/meta.yaml @@ -3,10 +3,12 @@ package: version: 1.6.6 source: fn: BiocParallel_1.6.6.tar.gz - url: http://bioconductor.org/packages/release/bioc/src/contrib/BiocParallel_1.6.6.tar.gz + url: + - http://bioconductor.org/packages/3.3/bioc/src/contrib/BiocParallel_1.6.6.tar.gz + - https://depot.galaxyproject.org/software/BiocParallel/BiocParallel_1.6.6_src_all.tar.gz md5: 445ec78a20e348d678d2e7b8dc5b4354 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -23,7 +25,7 @@ test: commands: - '$R -e "library(''BiocParallel'')"' about: - home: http://bioconductor.org/packages/release/bioc/html/BiocParallel.html + home: http://bioconductor.org/packages/3.5/bioc/html/BiocParallel.html license: 'GPL-2 | GPL-3' summary: 'This package provides modified versions and novel implementation of functions for parallel evaluation, tailored to use with Bioconductor objects.' From ef810b7df8478992b61d1160edd114de894e46d1 Mon Sep 17 00:00:00 2001 From: Ryan Dale Date: Mon, 5 Jun 2017 12:33:19 -0400 Subject: [PATCH 046/116] fix fastseg --- recipes/bioconductor-fastseg/build.sh | 11 ----------- recipes/bioconductor-fastseg/meta.yaml | 9 ++++++--- 2 files changed, 6 insertions(+), 14 deletions(-) diff --git a/recipes/bioconductor-fastseg/build.sh b/recipes/bioconductor-fastseg/build.sh index 6c7a1726e3..8218eda948 100644 --- a/recipes/bioconductor-fastseg/build.sh +++ b/recipes/bioconductor-fastseg/build.sh @@ -1,17 +1,6 @@ #!/bin/bash - -# R refuses to build packages that mark themselves as -# "Priority: Recommended" mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION -# $R CMD INSTALL --build . -# -# # Add more build steps here, if they are necessary. -# -# See -# http://docs.continuum.io/conda/build.html -# for a list of environment variables that are set during the build -# process. # \ No newline at end of file diff --git a/recipes/bioconductor-fastseg/meta.yaml b/recipes/bioconductor-fastseg/meta.yaml index 9eca234a01..4df2fd72d8 100644 --- a/recipes/bioconductor-fastseg/meta.yaml +++ b/recipes/bioconductor-fastseg/meta.yaml @@ -3,10 +3,13 @@ package: version: 1.20.0 source: fn: fastseg_1.20.0.tar.gz - url: http://bioconductor.org/packages/release/bioc/src/contrib/fastseg_1.20.0.tar.gz + url: + - http://bioconductor.org/packages/3.4/bioc/src/contrib/fastseg_1.20.0.tar.gz + - https://bioarchive.galaxyproject.org/fastseg_1.20.0.tar.gz + - https://depot.galaxyproject.org/software/fastseg/fastseg_1.20.0_src_all.tar.gz md5: 1840f449546b1d89983e95a6280006c1 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -29,7 +32,7 @@ test: commands: - '$R -e "library(''fastseg'')"' about: - home: http://bioconductor.org/packages/release/bioc/html/fastseg.html + home: http://bioconductor.org/packages/3.5/bioc/html/fastseg.html license: 'LGPL (>= 2.0)' summary: 'fastseg implements a very fast and efficient segmentation algorithm. It has similar functionality as DNACopy (Olshen and Venkatraman 2004), but is considerably From 515f4f163cf7aba9790543041fa812871c3defdb Mon Sep 17 00:00:00 2001 From: Ryan Dale Date: Mon, 5 Jun 2017 12:34:35 -0400 Subject: [PATCH 047/116] fix org.Dm.eg.db --- recipes/bioconductor-org.dm.eg.db/build.sh | 11 ------ recipes/bioconductor-org.dm.eg.db/meta.yaml | 53 +++++++++++++---------------- 2 files changed, 23 insertions(+), 41 deletions(-) diff --git a/recipes/bioconductor-org.dm.eg.db/build.sh b/recipes/bioconductor-org.dm.eg.db/build.sh index 6c7a1726e3..8218eda948 100644 --- a/recipes/bioconductor-org.dm.eg.db/build.sh +++ b/recipes/bioconductor-org.dm.eg.db/build.sh @@ -1,17 +1,6 @@ #!/bin/bash - -# R refuses to build packages that mark themselves as -# "Priority: Recommended" mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION -# $R CMD INSTALL --build . -# -# # Add more build steps here, if they are necessary. -# -# See -# http://docs.continuum.io/conda/build.html -# for a list of environment variables that are set during the build -# process. # \ No newline at end of file diff --git a/recipes/bioconductor-org.dm.eg.db/meta.yaml b/recipes/bioconductor-org.dm.eg.db/meta.yaml index a386b440f2..ec4cd55395 100644 --- a/recipes/bioconductor-org.dm.eg.db/meta.yaml +++ b/recipes/bioconductor-org.dm.eg.db/meta.yaml @@ -1,36 +1,29 @@ -# This file created by conda-build 2.0.7 -# meta.yaml template originally from: -# /home/ydilimu/bioconda-recipes/recipes/bioconductor-org.dm.eg.db, last modified Mon Jan 2 09:33:40 2017 -# ------------------------------------------------ - package: - name: bioconductor-org.dm.eg.db - version: 3.4.0 - + name: bioconductor-org.dm.eg.db + version: 3.4.0 source: - fn: org.Dm.eg.db_3.4.0.tar.gz - url: http://bioconductor.org/packages/release/data/annotation/src/contrib/org.Dm.eg.db_3.4.0.tar.gz - md5: c5ad88582d5c12355d3fb4b98cf559a0 - + fn: org.Dm.eg.db_3.4.0.tar.gz + url: + - http://bioconductor.org/packages/3.4/bioc/src/contrib/org.Dm.eg.db_3.4.0.tar.gz + - https://depot.galaxyproject.org/software/org.Dm.eg.db/org.Dm.eg.db_3.4.0_src_all.tar.gz + md5: c5ad88582d5c12355d3fb4b98cf559a0 build: - number: 0 - rpaths: - - lib/R/lib/ - - lib/ + number: 1 + rpaths: + - lib/R/lib/ + - lib/ requirements: - build: - - bioconductor-annotationdbi - - r-base - run: - - bioconductor-annotationdbi - - r-base - + build: + - 'bioconductor-annotationdbi >=1.35.4' + - r-base + run: + - 'bioconductor-annotationdbi >=1.35.4' + - r-base test: - commands: - - $R -e "library('org.Dm.eg.db')" - + commands: + - '$R -e "library(''org.Dm.eg.db'')"' about: - home: http://bioconductor.org/packages/release/data/annotation/html/org.Dm.eg.db.html - license: Artistic-2.0 - summary: 'Genome wide annotation for Fly, primarily based on mapping using Entrez - Gene identifiers.' + home: http://bioconductor.org/packages/3.5/data/annotation/html/org.Dm.eg.db.html + license: Artistic-2.0 + summary: 'Genome wide annotation for Fly, primarily based on mapping using Entrez + Gene identifiers.' From ecfc84bad91efc41024938204cc7703d250f7579 Mon Sep 17 00:00:00 2001 From: Ryan Dale Date: Mon, 5 Jun 2017 14:12:17 -0400 Subject: [PATCH 048/116] R 3.3.2 has a different set of default packages --- scripts/bioconductor/bioconductor_skeleton.py | 10 ++++------ 1 file changed, 4 insertions(+), 6 deletions(-) diff --git a/scripts/bioconductor/bioconductor_skeleton.py b/scripts/bioconductor/bioconductor_skeleton.py index 0b23085e21..b6c5fd1b31 100755 --- a/scripts/bioconductor/bioconductor_skeleton.py +++ b/scripts/bioconductor/bioconductor_skeleton.py @@ -54,12 +54,10 @@ def setup_logger(loglevel): # # conda create -n rtest -c r r # R -e "rownames(installed.packages())" -BASE_R_PACKAGES = ["base", "boot", "class", "cluster", "codetools", "compiler", - "datasets", "foreign", "graphics", "grDevices", "grid", - "KernSmooth", "lattice", "MASS", "Matrix", "methods", - "mgcv", "nlme", "nnet", "parallel", "rpart", "spatial", - "splines", "stats", "stats4", "survival", "tcltk", "tools", - "utils"] +BASE_R_PACKAGES = ["base", "compiler", "datasets", "graphics", "grDevices", + "grid", "methods", "parallel", "splines", "stats", "stats4", + "tcltk", "tools", "utils"] + # A list of packages, in recipe name format GCC_PACKAGES = ['r-rcpp'] From 1236dd709d2c45f2751095f5412da8e20a8d551f Mon Sep 17 00:00:00 2001 From: Ryan Dale Date: Mon, 5 Jun 2017 14:12:30 -0400 Subject: [PATCH 049/116] fix bioconductor-biomformat --- recipes/bioconductor-biomformat/meta.yaml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/recipes/bioconductor-biomformat/meta.yaml b/recipes/bioconductor-biomformat/meta.yaml index a3824207e0..dc5ae9f7ae 100644 --- a/recipes/bioconductor-biomformat/meta.yaml +++ b/recipes/bioconductor-biomformat/meta.yaml @@ -18,11 +18,13 @@ requirements: - bioconductor-rhdf5 - r-base - 'r-jsonlite >=0.9.16' + - 'r-matrix >=1.2' - 'r-plyr >=1.8' run: - bioconductor-rhdf5 - r-base - 'r-jsonlite >=0.9.16' + - 'r-matrix >=1.2' - 'r-plyr >=1.8' test: commands: From d52b572551b7272b307edf5958ab632090e25dc9 Mon Sep 17 00:00:00 2001 From: Bjoern Gruening Date: Mon, 5 Jun 2017 20:17:35 +0200 Subject: [PATCH 050/116] r fixes --- recipes/bioconductor-masigpro/meta.yaml | 2 ++ recipes/bioconductor-topgo/meta.yaml | 2 ++ recipes/r-ggally/0.5.0/meta.yaml | 38 ++------------------------------- recipes/r-rfoc/meta.yaml | 23 -------------------- recipes/r-sleuth/meta.yaml | 2 ++ 5 files changed, 8 insertions(+), 59 deletions(-) diff --git a/recipes/bioconductor-masigpro/meta.yaml b/recipes/bioconductor-masigpro/meta.yaml index 016b5a5a08..0f0afdb450 100644 --- a/recipes/bioconductor-masigpro/meta.yaml +++ b/recipes/bioconductor-masigpro/meta.yaml @@ -16,11 +16,13 @@ requirements: - r-base - r-mclust - r-venn + - r-mass run: - bioconductor-biobase - r-base - r-mclust - r-venn + - r-mass test: commands: - '$R -e "library(''maSigPro'')"' diff --git a/recipes/bioconductor-topgo/meta.yaml b/recipes/bioconductor-topgo/meta.yaml index 9d4f6d6ee9..aa3977e543 100644 --- a/recipes/bioconductor-topgo/meta.yaml +++ b/recipes/bioconductor-topgo/meta.yaml @@ -21,6 +21,7 @@ requirements: - r-dbi - r-matrixstats - 'r-sparsem >=0.73' + - r-lattice run: - 'bioconductor-annotationdbi >=1.7.19' - 'bioconductor-biobase >=2.0.0' @@ -31,6 +32,7 @@ requirements: - r-dbi - r-matrixstats - 'r-sparsem >=0.73' + - r-lattice test: commands: - '$R -e "library(''topGO'')"' diff --git a/recipes/r-ggally/0.5.0/meta.yaml b/recipes/r-ggally/0.5.0/meta.yaml index 6ef9c9c5da..beb7eb8bc6 100644 --- a/recipes/r-ggally/0.5.0/meta.yaml +++ b/recipes/r-ggally/0.5.0/meta.yaml @@ -1,7 +1,5 @@ package: name: r-ggally - # Note that conda versions cannot contain -, so any -'s in the version have - # been replaced with _'s. version: "0.5.0" source: @@ -10,14 +8,6 @@ source: - https://cran.r-project.org/src/contrib/GGally_1.3.0.tar.gz - http://cran.r-project.org/src/contrib/Archive/GGally/GGally_0.5.0.tar.gz - - # You can add a hash for the file here, like md5 or sha1 - # md5: 49448ba4863157652311cc5ea4fea3ea - # sha1: 3bcfbee008276084cbb37a2b453963c61176a322 - # patches: - # List any patch files here - # - fix.patch - build: # If this is a new build for the same version, increment the build # number. If you do not include this key, it defaults to 0. @@ -37,6 +27,7 @@ requirements: - r-plyr >=1.8 - r-reshape >=0.8.4 - r-stringr >=0.6.2 + - r-progress run: - r-base @@ -45,6 +36,7 @@ requirements: - r-plyr >=1.8 - r-reshape >=0.8.4 - r-stringr >=0.6.2 + - r-progress test: commands: @@ -64,29 +56,3 @@ about: summary: !!python/unicode 'GGally is designed to be a helper to ggplot2. It contains templates for different plots to be combined into a plot matrix, a parallel coordinate plot function, as well as a function for making a network plot.' - - -# The original CRAN metadata for this package was: - -# Package: GGally -# Version: 0.5.0 -# Date: 2014-12-01 -# Maintainer: Barret Schloerke -# License: GPL (>= 2.0) -# Title: Extension to ggplot2. -# Type: Package -# LazyLoad: yes -# LazyData: true -# Author: Barret Schloerke , Jason Crowley , Di Cook , Heike Hofmann , Hadley Wickham , and Francois Briatte , Moritz Marbach , and Edwin Thoen -# Description: GGally is designed to be a helper to ggplot2. It contains templates for different plots to be combined into a plot matrix, a parallel coordinate plot function, as well as a function for making a network plot. -# Depends: R (>= 2.14) -# Imports: ggplot2 (>= 1.0.0), grid (>= 3.0.0), gtable (>= 0.1.2), plyr (>= 1.8), reshape (>= 0.8.4), stringr (>= 0.6.2) -# Suggests: arm (>= 1.7), intergraph (>= 2.0-0), network (>= 1.7.2), RColorBrewer (>= 1.0-5), scales (>= 0.2.3), scagnostics (>= 0.2-4), sna (>= 2.3-1), survival (>= 2.37-4), tnet (>= 3.0), roxygen2 (>= 4.0.1) -# Packaged: 2014-12-01 21:52:05 UTC; barret -# NeedsCompilation: no -# Repository: CRAN -# Date/Publication: 2014-12-02 00:32:53 - -# See -# http://docs.continuum.io/conda/build.html for -# more information about meta.yaml diff --git a/recipes/r-rfoc/meta.yaml b/recipes/r-rfoc/meta.yaml index d548377283..fbb991995d 100644 --- a/recipes/r-rfoc/meta.yaml +++ b/recipes/r-rfoc/meta.yaml @@ -6,7 +6,6 @@ package: source: fn: RFOC_3.3-3.tar.gz url: - - http://cran.r-project.org/src/contrib/RFOC_3.3-3.tar.gz - http://cran.r-project.org/src/contrib/Archive/RFOC/RFOC_3.3-3.tar.gz md5: bb568cff1efd58e191c840d8870cacea build: @@ -40,25 +39,3 @@ about: maps. Non-double couple plotting of focal spheres and source type maps are included for statistical analysis of moment tensors. license_family: GPL3 - -# The original CRAN metadata for this package was: - -# Package: RFOC -# Type: Package -# Title: Graphics for Spherical Distributions and Earthquake Focal Mechanisms -# Version: 3.3-3 -# Date: 2012-12-17 -# Depends: R (>= 2.12) -# Imports: RPMG, GEOmap, RSEIS, MASS, splancs -# Author: Jonathan M. Lees -# Maintainer: Jonathan M. Lees -# Description: Graphics for statistics on a sphere, as applied to geological fault data, crystallography, earthquake focal mechanisms, radiation patterns, ternary plots and geographical/geological maps. Non-double couple plotting of focal spheres and source type maps are included for statistical analysis of moment tensors. -# License: GPL (>= 2) -# Packaged: 2014-01-06 16:00:25 UTC; lees -# NeedsCompilation: no -# Repository: CRAN -# Date/Publication: 2014-01-06 18:22:22 - -# See -# http://docs.continuum.io/conda/build.html for -# more information about meta.yaml diff --git a/recipes/r-sleuth/meta.yaml b/recipes/r-sleuth/meta.yaml index 3fc05f72ff..bdcd70eb3c 100644 --- a/recipes/r-sleuth/meta.yaml +++ b/recipes/r-sleuth/meta.yaml @@ -17,6 +17,7 @@ requirements: - r-tidyr - r-shiny - r-data.table + - r-matrixstats run: - r-base - bioconductor-rhdf5 @@ -25,6 +26,7 @@ requirements: - r-tidyr - r-shiny - r-data.table + - r-matrixstats test: commands: - '$R -e "library(''sleuth'')"' From 8450bb59f004ba44be2c95ddee344b9e7190cc1b Mon Sep 17 00:00:00 2001 From: Ryan Dale Date: Mon, 5 Jun 2017 14:34:53 -0400 Subject: [PATCH 051/116] bioconductor_skeleton handles typos in DESCRIPTION --- scripts/bioconductor/bioconductor_skeleton.py | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/scripts/bioconductor/bioconductor_skeleton.py b/scripts/bioconductor/bioconductor_skeleton.py index b6c5fd1b31..60b7cd7de5 100755 --- a/scripts/bioconductor/bioconductor_skeleton.py +++ b/scripts/bioconductor/bioconductor_skeleton.py @@ -343,14 +343,14 @@ def license(self): @property def imports(self): try: - return self.description['imports'].split(', ') + return [i.strip() for i in self.description['imports'].replace(' ', '').split(',')] except KeyError: return [] @property def depends(self): try: - return self.description['depends'].split(', ') + return [i.strip() for i in self.description['depends'].replace(' ', '').split(',')] except KeyError: return [] @@ -411,7 +411,6 @@ def dependencies(self): else: versions[name] = version - for name, version in sorted(versions.items()): # DESCRIPTION notes base R packages, but we don't need to specify # them in the dependencies. From d49a66bcca0ea62458c173d7b40cd9666d42cd6c Mon Sep 17 00:00:00 2001 From: Ryan Dale Date: Mon, 5 Jun 2017 14:35:09 -0400 Subject: [PATCH 052/116] fix DEGreport --- recipes/bioconductor-degreport/build.sh | 11 ----------- recipes/bioconductor-degreport/meta.yaml | 8 +++++--- 2 files changed, 5 insertions(+), 14 deletions(-) diff --git a/recipes/bioconductor-degreport/build.sh b/recipes/bioconductor-degreport/build.sh index 6c7a1726e3..8218eda948 100644 --- a/recipes/bioconductor-degreport/build.sh +++ b/recipes/bioconductor-degreport/build.sh @@ -1,17 +1,6 @@ #!/bin/bash - -# R refuses to build packages that mark themselves as -# "Priority: Recommended" mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION -# $R CMD INSTALL --build . -# -# # Add more build steps here, if they are necessary. -# -# See -# http://docs.continuum.io/conda/build.html -# for a list of environment variables that are set during the build -# process. # \ No newline at end of file diff --git a/recipes/bioconductor-degreport/meta.yaml b/recipes/bioconductor-degreport/meta.yaml index 2d1edaa53a..f1618091b5 100644 --- a/recipes/bioconductor-degreport/meta.yaml +++ b/recipes/bioconductor-degreport/meta.yaml @@ -3,10 +3,12 @@ package: version: 1.8.2 source: fn: DEGreport_1.8.2.tar.gz - url: http://bioconductor.org/packages/release/bioc/src/contrib/DEGreport_1.8.2.tar.gz + url: + - http://bioconductor.org/packages/3.3/bioc/src/contrib/DEGreport_1.8.2.tar.gz + - https://depot.galaxyproject.org/software/DEGreport/DEGreport_1.8.2_src_all.tar.gz md5: 4006a779e33f3bb68308ba9f4a7d9f84 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -27,7 +29,7 @@ test: commands: - '$R -e "library(''DEGreport'')"' about: - home: http://bioconductor.org/packages/release/bioc/html/DEGreport.html + home: http://bioconductor.org/packages/3.5/bioc/html/DEGreport.html license: 'GPL (>=2)' summary: 'Creation of a HTML report of differential expression analyses of count data. It integrates some of the code mentioned in DESeq2 and edgeR vignettes, From d555d1d58940d56e6c1f287a55a35563b9d6e318 Mon Sep 17 00:00:00 2001 From: Ryan Dale Date: Mon, 5 Jun 2017 14:35:22 -0400 Subject: [PATCH 053/116] fix flowViz again --- recipes/bioconductor-flowviz/meta.yaml | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/recipes/bioconductor-flowviz/meta.yaml b/recipes/bioconductor-flowviz/meta.yaml index 37cb67bcbc..8f5258f3e1 100644 --- a/recipes/bioconductor-flowviz/meta.yaml +++ b/recipes/bioconductor-flowviz/meta.yaml @@ -9,7 +9,7 @@ source: - https://depot.galaxyproject.org/software/flowViz/flowViz_1.38.0_src_all.tar.gz md5: ca001789da5bf4d21a63d222d69255c7 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -20,7 +20,10 @@ requirements: - r-base - r-hexbin - r-idpmisc + - r-kernsmooth + - r-lattice - r-latticeextra + - r-mass - r-rcolorbrewer run: - bioconductor-biobase @@ -28,7 +31,10 @@ requirements: - r-base - r-hexbin - r-idpmisc + - r-kernsmooth + - r-lattice - r-latticeextra + - r-mass - r-rcolorbrewer test: commands: From 888f0772a064261a416c3d264ac616a1e5fea4f8 Mon Sep 17 00:00:00 2001 From: Ryan Dale Date: Mon, 5 Jun 2017 14:38:21 -0400 Subject: [PATCH 054/116] fix multtest --- recipes/bioconductor-multtest/build.sh | 11 ----------- recipes/bioconductor-multtest/meta.yaml | 15 +++++++++++---- 2 files changed, 11 insertions(+), 15 deletions(-) diff --git a/recipes/bioconductor-multtest/build.sh b/recipes/bioconductor-multtest/build.sh index 6c7a1726e3..8218eda948 100644 --- a/recipes/bioconductor-multtest/build.sh +++ b/recipes/bioconductor-multtest/build.sh @@ -1,17 +1,6 @@ #!/bin/bash - -# R refuses to build packages that mark themselves as -# "Priority: Recommended" mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION -# $R CMD INSTALL --build . -# -# # Add more build steps here, if they are necessary. -# -# See -# http://docs.continuum.io/conda/build.html -# for a list of environment variables that are set during the build -# process. # \ No newline at end of file diff --git a/recipes/bioconductor-multtest/meta.yaml b/recipes/bioconductor-multtest/meta.yaml index 6bc02f2f8c..984f55f866 100644 --- a/recipes/bioconductor-multtest/meta.yaml +++ b/recipes/bioconductor-multtest/meta.yaml @@ -3,10 +3,13 @@ package: version: 2.28.0 source: fn: multtest_2.28.0.tar.gz - url: https://bioarchive.galaxyproject.org/multtest_2.28.0.tar.gz - md5: 936e0b615f583c7ca6727d6c9c46eaa0 + url: + - http://bioconductor.org/packages/3.3/bioc/src/contrib/multtest_2.28.0.tar.gz + - https://bioarchive.galaxyproject.org/multtest_2.28.0.tar.gz + - https://depot.galaxyproject.org/software/multtest/multtest_2.28.0_src_all.tar.gz + md5: a82a1564e15fdc5afe6efc4c33a33bbc build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -15,15 +18,19 @@ requirements: - bioconductor-biobase - bioconductor-biocgenerics - r-base + - r-mass + - r-survival run: - bioconductor-biobase - bioconductor-biocgenerics - r-base + - r-mass + - r-survival test: commands: - '$R -e "library(''multtest'')"' about: - home: http://bioconductor.org/packages/release/bioc/html/multtest.html + home: http://bioconductor.org/packages/3.5/bioc/html/multtest.html license: LGPL summary: 'Non-parametric bootstrap and permutation resampling-based multiple testing procedures (including empirical Bayes methods) for controlling the family-wise From 629acfff521fec32476a80183bc992dc254d6aac Mon Sep 17 00:00:00 2001 From: Bjoern Gruening Date: Mon, 5 Jun 2017 20:46:10 +0200 Subject: [PATCH 055/116] r fixes --- recipes/bioconductor-biomformat/meta.yaml | 7 +++++++ recipes/r-leaps/meta.yaml | 5 +---- recipes/r-soap-nmr/meta.yaml | 7 ++++++- 3 files changed, 14 insertions(+), 5 deletions(-) diff --git a/recipes/bioconductor-biomformat/meta.yaml b/recipes/bioconductor-biomformat/meta.yaml index a3824207e0..5a566b5807 100644 --- a/recipes/bioconductor-biomformat/meta.yaml +++ b/recipes/bioconductor-biomformat/meta.yaml @@ -1,6 +1,7 @@ package: name: bioconductor-biomformat version: 1.2.0 + source: fn: biomformat_1.2.0.tar.gz url: @@ -8,25 +9,31 @@ source: - https://bioarchive.galaxyproject.org/biomformat_1.2.0.tar.gz - https://depot.galaxyproject.org/software/biomformat/biomformat_1.2.0_src_all.tar.gz md5: 0a418f48c731375953ff7389b9b6f7a0 + build: number: 1 rpaths: - lib/R/lib/ - lib/ + requirements: build: - bioconductor-rhdf5 - r-base - 'r-jsonlite >=0.9.16' - 'r-plyr >=1.8' + - r-matrix run: - bioconductor-rhdf5 - r-base - 'r-jsonlite >=0.9.16' - 'r-plyr >=1.8' + - r-matrix + test: commands: - '$R -e "library(''biomformat'')"' + about: home: http://bioconductor.org/packages/3.5/bioc/html/biomformat.html license: GPL-2 diff --git a/recipes/r-leaps/meta.yaml b/recipes/r-leaps/meta.yaml index 1df2a3ae07..fde6cbd577 100644 --- a/recipes/r-leaps/meta.yaml +++ b/recipes/r-leaps/meta.yaml @@ -11,11 +11,7 @@ source: - http://cran.r-project.org/src/contrib/Archive/leaps/leaps_2.9.tar.gz build: - # If this is a new build for the same version, increment the build - # number. If you do not include this key, it defaults to 0. # number: 1 - - # This is required to make R link correctly on Linux. rpaths: - lib/R/lib/ - lib/ @@ -29,6 +25,7 @@ requirements: run: - r-base - libgcc # [linux] + - gfortran # [osx] test: commands: diff --git a/recipes/r-soap-nmr/meta.yaml b/recipes/r-soap-nmr/meta.yaml index 9f93aa4473..302c65f141 100644 --- a/recipes/r-soap-nmr/meta.yaml +++ b/recipes/r-soap-nmr/meta.yaml @@ -1,15 +1,18 @@ package: name: r-soap-nmr version: 0.1.0.20170207 + source: fn: soap-nmr-0.1.0.20170207.tar.gz url: https://github.com/ManonMartin/SOAP-NMR/archive/83986fad26becd625c89f0cd7522e40587e83fe3.tar.gz - md5: c174b31fdf80cf69b5fea64265dec7cb + md5: 79c22ee665352c0bd2fa2f429db48d30 + build: number: 0 rpaths: - lib/R/lib/ - lib/ + requirements: build: - r-base @@ -27,9 +30,11 @@ requirements: - r-gridextra - r-matrixstats - r-reshape2 + test: commands: - '$R -e "require(''SOAP'')"' + about: home: https://github.com/ManonMartin/SOAP-NMR license: 'GPL2' From da7fdbe6bce60effabb1b21a839b64d7f2919a5b Mon Sep 17 00:00:00 2001 From: Ryan Dale Date: Mon, 5 Jun 2017 18:22:08 -0400 Subject: [PATCH 056/116] more fixes to bioconductor_skeleton --- scripts/bioconductor/bioconductor_skeleton.py | 22 ++++++++++++++-------- 1 file changed, 14 insertions(+), 8 deletions(-) diff --git a/scripts/bioconductor/bioconductor_skeleton.py b/scripts/bioconductor/bioconductor_skeleton.py index 60b7cd7de5..6b2cd87ac6 100755 --- a/scripts/bioconductor/bioconductor_skeleton.py +++ b/scripts/bioconductor/bioconductor_skeleton.py @@ -246,25 +246,30 @@ def bioconductor_tarball_url(self): """ Return the url to the tarball from the bioconductor site. """ - return bioconductor_tarball_url(self.package, self.version, self.bioc_version) - + url = bioconductor_tarball_url(self.package, self.version, self.bioc_version) + response = requests.head(url) + if response and response.status_code == 200: + return url @property def bioconductor_data_url(self): """ Return the url to the tarball from the bioconductor site. """ - return bioconductor_data_url(self.package, self.version, self.bioc_version) - + url = bioconductor_data_url(self.package, self.version, self.bioc_version) + response = requests.head(url) + if response and response.status_code == 200: + return url @property def tarball_url(self): if not self._tarball_url: urls = [self.bioconductor_tarball_url, self.bioconductor_data_url, self.bioaRchive_url, self.cargoport_url] for url in urls: - response = requests.head(url) - if response and response.status_code == 200: - return url + if url is not None: + response = requests.head(url) + if response and response.status_code == 200: + return url logger.error( 'No working URL for %s==%s in Bioconductor %s. ' @@ -489,7 +494,8 @@ def meta_yaml(self): """ url = [ u for u in - [self.bioconductor_tarball_url, self.bioaRchive_url, self.cargoport_url] + [self.bioconductor_tarball_url, self.bioconductor_data_url, + self.bioaRchive_url, self.cargoport_url] if u is not None ] From 6e72cd42015fac2cafdaa6beb3c16bf4e32c8e16 Mon Sep 17 00:00:00 2001 From: Ryan Dale Date: Mon, 5 Jun 2017 18:23:51 -0400 Subject: [PATCH 057/116] fix org.{Hs,Dm}.eg.db --- recipes/bioconductor-org.dm.eg.db/meta.yaml | 4 ++-- recipes/bioconductor-org.hs.eg.db/meta.yaml | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/bioconductor-org.dm.eg.db/meta.yaml b/recipes/bioconductor-org.dm.eg.db/meta.yaml index ec4cd55395..ecfedefee2 100644 --- a/recipes/bioconductor-org.dm.eg.db/meta.yaml +++ b/recipes/bioconductor-org.dm.eg.db/meta.yaml @@ -4,11 +4,11 @@ package: source: fn: org.Dm.eg.db_3.4.0.tar.gz url: - - http://bioconductor.org/packages/3.4/bioc/src/contrib/org.Dm.eg.db_3.4.0.tar.gz + - http://bioconductor.org/packages/3.4/data/annotation/src/contrib/org.Dm.eg.db_3.4.0.tar.gz - https://depot.galaxyproject.org/software/org.Dm.eg.db/org.Dm.eg.db_3.4.0_src_all.tar.gz md5: c5ad88582d5c12355d3fb4b98cf559a0 build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/bioconductor-org.hs.eg.db/meta.yaml b/recipes/bioconductor-org.hs.eg.db/meta.yaml index 142e737e93..6348199454 100644 --- a/recipes/bioconductor-org.hs.eg.db/meta.yaml +++ b/recipes/bioconductor-org.hs.eg.db/meta.yaml @@ -4,7 +4,7 @@ package: source: fn: org.Hs.eg.db_3.3.0.tar.gz url: - - http://bioconductor.org/packages/3.3/bioc/src/contrib/org.Hs.eg.db_3.3.0.tar.gz + - http://bioconductor.org/packages/3.3/data/annotation/src/contrib/org.Hs.eg.db_3.3.0.tar.gz - https://depot.galaxyproject.org/software/org.Hs.eg.db/org.Hs.eg.db_3.3.0_src_all.tar.gz md5: ef4a05f46e7cdb0ba23fcd898a4a1d57 build: From 113e4a07fcaddbfaef5dc3af4af9ab14328e7512 Mon Sep 17 00:00:00 2001 From: Ryan Dale Date: Mon, 5 Jun 2017 18:24:37 -0400 Subject: [PATCH 058/116] update the update_bioconductor_packages script to build topsorted dag --- scripts/bioconductor/update_bioconductor_packages.py | 13 +++++++------ 1 file changed, 7 insertions(+), 6 deletions(-) diff --git a/scripts/bioconductor/update_bioconductor_packages.py b/scripts/bioconductor/update_bioconductor_packages.py index 3b551a4c68..09a5dadd02 100644 --- a/scripts/bioconductor/update_bioconductor_packages.py +++ b/scripts/bioconductor/update_bioconductor_packages.py @@ -34,13 +34,14 @@ def bioc_name(recipe): if __name__ == "__main__": import argparse ap = argparse.ArgumentParser() - ap.add_argument('--repository', default='recipes', help='Recipes directory') + ap.add_argument('--recipes', default='recipes', help='Recipes directory') + ap.add_argument('--config', default='recipes', help='Config YAML') args = ap.parse_args() - recipes = list(utils.get_recipes(args.repository, 'bioconductor-*')) + recipes = list(utils.get_recipes(args.recipes, 'bioconductor-*')) deps = itertools.chain( - itertools.chain(*(utils.get_deps(i, build=True) for i in recipes)), - itertools.chain(*(utils.get_deps(i, build=False) for i in recipes)) + itertools.chain(*(utils.get_deps(i, build=True, config=args.config) for i in recipes)), + itertools.chain(*(utils.get_deps(i, build=False, config=args.config) for i in recipes)) ) deps = list(filter(lambda x: x.startswith(('r-', 'bioconductor-')), deps)) @@ -48,11 +49,11 @@ def bioc_name(recipe): bioconda_deps = list( filter( lambda x: os.path.isdir(x), - itertools.chain(*(utils.get_recipes(args.repository, i) for i in deps)) + itertools.chain(*(utils.get_recipes(args.recipes, i) for i in deps)) ) ) - dag, name2recipe = utils.get_dag(bioconda_deps) + dag, name2recipe = utils.get_dag(bioconda_deps, config=args.config) def version_sort(x): return version.VersionOrder(MetaData(x).meta['package']['version']) From f072eaf2ed73967d2a1db2459b393ace71d41088 Mon Sep 17 00:00:00 2001 From: Ryan Dale Date: Mon, 5 Jun 2017 21:45:05 -0400 Subject: [PATCH 059/116] fix Category --- recipes/bioconductor-category/build.sh | 11 ----------- recipes/bioconductor-category/meta.yaml | 13 +++++++++---- 2 files changed, 9 insertions(+), 15 deletions(-) diff --git a/recipes/bioconductor-category/build.sh b/recipes/bioconductor-category/build.sh index 6c7a1726e3..8218eda948 100644 --- a/recipes/bioconductor-category/build.sh +++ b/recipes/bioconductor-category/build.sh @@ -1,17 +1,6 @@ #!/bin/bash - -# R refuses to build packages that mark themselves as -# "Priority: Recommended" mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION -# $R CMD INSTALL --build . -# -# # Add more build steps here, if they are necessary. -# -# See -# http://docs.continuum.io/conda/build.html -# for a list of environment variables that are set during the build -# process. # \ No newline at end of file diff --git a/recipes/bioconductor-category/meta.yaml b/recipes/bioconductor-category/meta.yaml index 5af5d80e16..1be021c96a 100644 --- a/recipes/bioconductor-category/meta.yaml +++ b/recipes/bioconductor-category/meta.yaml @@ -3,10 +3,13 @@ package: version: 2.38.0 source: fn: Category_2.38.0.tar.gz - url: https://bioarchive.galaxyproject.org/Category_2.38.0.tar.gz - md5: dfd13491db8e1da509fadec8306d0562 + url: + - http://bioconductor.org/packages/3.3/bioc/src/contrib/Category_2.38.0.tar.gz + - https://bioarchive.galaxyproject.org/Category_2.38.0.tar.gz + - https://depot.galaxyproject.org/software/Category/Category_2.38.0_src_all.tar.gz + md5: 4562ae7a6d4d5d52ee883c71ab2a81f8 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -21,6 +24,7 @@ requirements: - bioconductor-gseabase - bioconductor-rbgl - r-base + - r-matrix - r-rsqlite run: - bioconductor-annotate @@ -32,11 +36,12 @@ requirements: - bioconductor-gseabase - bioconductor-rbgl - r-base + - r-matrix - r-rsqlite test: commands: - '$R -e "library(''Category'')"' about: - home: http://bioconductor.org/packages/release/bioc/html/Category.html + home: http://bioconductor.org/packages/3.5/bioc/html/Category.html license: Artistic-2.0 summary: 'A collection of tools for performing category analysis.' From 01d4e6db1d885e7fe3a46d5e86cea538e62f0173 Mon Sep 17 00:00:00 2001 From: Ryan Dale Date: Mon, 5 Jun 2017 21:46:19 -0400 Subject: [PATCH 060/116] fix genefilter --- recipes/bioconductor-genefilter/build.sh | 11 ----------- recipes/bioconductor-genefilter/meta.yaml | 11 +++++++---- 2 files changed, 7 insertions(+), 15 deletions(-) diff --git a/recipes/bioconductor-genefilter/build.sh b/recipes/bioconductor-genefilter/build.sh index 6c7a1726e3..8218eda948 100644 --- a/recipes/bioconductor-genefilter/build.sh +++ b/recipes/bioconductor-genefilter/build.sh @@ -1,17 +1,6 @@ #!/bin/bash - -# R refuses to build packages that mark themselves as -# "Priority: Recommended" mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION -# $R CMD INSTALL --build . -# -# # Add more build steps here, if they are necessary. -# -# See -# http://docs.continuum.io/conda/build.html -# for a list of environment variables that are set during the build -# process. # \ No newline at end of file diff --git a/recipes/bioconductor-genefilter/meta.yaml b/recipes/bioconductor-genefilter/meta.yaml index c62c9c6bff..699cb06542 100644 --- a/recipes/bioconductor-genefilter/meta.yaml +++ b/recipes/bioconductor-genefilter/meta.yaml @@ -3,7 +3,10 @@ package: version: 1.56.0 source: fn: genefilter_1.56.0.tar.gz - url: https://depot.galaxyproject.org/software/bioconductor-genefilter/bioconductor-genefilter_1.56.0_src_all.tar.gz + url: + - http://bioconductor.org/packages/3.4/bioc/src/contrib/genefilter_1.56.0.tar.gz + - https://bioarchive.galaxyproject.org/genefilter_1.56.0.tar.gz + - https://depot.galaxyproject.org/software/genefilter/genefilter_1.56.0_src_all.tar.gz md5: 919e4deb451ca4e9dbea1e125e15cf98 build: number: 0 @@ -12,23 +15,23 @@ build: - lib/ requirements: build: - - gcc - bioconductor-annotate - bioconductor-annotationdbi - bioconductor-biobase - 'bioconductor-s4vectors >=0.9.42' - r-base + - r-survival run: - - libgcc - bioconductor-annotate - bioconductor-annotationdbi - bioconductor-biobase - 'bioconductor-s4vectors >=0.9.42' - r-base + - r-survival test: commands: - '$R -e "library(''genefilter'')"' about: - home: http://bioconductor.org/packages/release/bioc/html/genefilter.html + home: http://bioconductor.org/packages/3.5/bioc/html/genefilter.html license: Artistic-2.0 summary: 'Some basic functions for filtering genes' From 789fd610bb5aa117cd6c47a165376285c2f016c6 Mon Sep 17 00:00:00 2001 From: Ryan Dale Date: Mon, 5 Jun 2017 22:01:20 -0400 Subject: [PATCH 061/116] add matrix to summarizedexperiment --- recipes/bioconductor-summarizedexperiment/meta.yaml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/recipes/bioconductor-summarizedexperiment/meta.yaml b/recipes/bioconductor-summarizedexperiment/meta.yaml index f069ec8016..95bfa74706 100644 --- a/recipes/bioconductor-summarizedexperiment/meta.yaml +++ b/recipes/bioconductor-summarizedexperiment/meta.yaml @@ -9,7 +9,7 @@ source: - https://depot.galaxyproject.org/software/SummarizedExperiment/SummarizedExperiment_1.4.0_src_all.tar.gz md5: 35159a339981efa22e96db639dadc850 build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ @@ -22,6 +22,7 @@ requirements: - 'bioconductor-iranges >=2.7.2' - 'bioconductor-s4vectors >=0.11.7' - r-base + - r-matrix run: - bioconductor-biobase - 'bioconductor-biocgenerics >=0.15.3' @@ -30,6 +31,7 @@ requirements: - 'bioconductor-iranges >=2.7.2' - 'bioconductor-s4vectors >=0.11.7' - r-base + - r-matrix test: commands: - '$R -e "library(''SummarizedExperiment'')"' From 5bd4737f2d11040f4ead6c2b872b983ff5182847 Mon Sep 17 00:00:00 2001 From: Ryan Dale Date: Mon, 5 Jun 2017 22:02:35 -0400 Subject: [PATCH 062/116] add urls for gostats --- recipes/bioconductor-gostats/build.sh | 14 ++------------ recipes/bioconductor-gostats/meta.yaml | 8 +++++--- 2 files changed, 7 insertions(+), 15 deletions(-) diff --git a/recipes/bioconductor-gostats/build.sh b/recipes/bioconductor-gostats/build.sh index 0d6a53f143..8218eda948 100644 --- a/recipes/bioconductor-gostats/build.sh +++ b/recipes/bioconductor-gostats/build.sh @@ -1,16 +1,6 @@ -#!/bin/bash -# R refuses to build packages that mark themselves as -# "Priority: Recommended" +#!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION -# $R CMD INSTALL --build . -# -# # Add more build steps here, if they are necessary. -# -# See -# http://docs.continuum.io/conda/build.html -# for a list of environment variables that are set during the build -# process. -# +# \ No newline at end of file diff --git a/recipes/bioconductor-gostats/meta.yaml b/recipes/bioconductor-gostats/meta.yaml index d235e009b0..fc18dd1c70 100644 --- a/recipes/bioconductor-gostats/meta.yaml +++ b/recipes/bioconductor-gostats/meta.yaml @@ -3,10 +3,12 @@ package: version: 2.38.1 source: fn: GOstats_2.38.1.tar.gz - url: http://bioconductor.org/packages/3.3/bioc/src/contrib/GOstats_2.38.1.tar.gz + url: + - http://bioconductor.org/packages/3.3/bioc/src/contrib/GOstats_2.38.1.tar.gz + - https://depot.galaxyproject.org/software/GOstats/GOstats_2.38.1_src_all.tar.gz md5: 684862c904e7b5f4731bd27d09f9ce43 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -35,7 +37,7 @@ test: commands: - '$R -e "library(''GOstats'')"' about: - home: http://bioconductor.org/packages/release/bioc/html/GOstats.html + home: http://bioconductor.org/packages/3.5/bioc/html/GOstats.html license: Artistic-2.0 summary: 'A set of tools for interacting with GO and microarray data. A variety of basic manipulation tools for graphs, hypothesis testing and other simple calculations.' From 6c3b20bb7fc2708f75ccc6191853fb9d9029f2d7 Mon Sep 17 00:00:00 2001 From: Ryan Dale Date: Mon, 5 Jun 2017 22:08:31 -0400 Subject: [PATCH 063/116] fix MotIV --- recipes/bioconductor-motiv/build.sh | 16 ++-------------- recipes/bioconductor-motiv/meta.yaml | 16 +++++++++------- 2 files changed, 11 insertions(+), 21 deletions(-) diff --git a/recipes/bioconductor-motiv/build.sh b/recipes/bioconductor-motiv/build.sh index 31befe9f81..8218eda948 100644 --- a/recipes/bioconductor-motiv/build.sh +++ b/recipes/bioconductor-motiv/build.sh @@ -1,18 +1,6 @@ -#!/bin/bash - -export LDFLAGS="-L${PREFIX}/lib -Wl,-rpath ${PREFIX}/lib" -# R refuses to build packages that mark themselves as -# "Priority: Recommended" +#!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION -# $R CMD INSTALL --build . -# -# # Add more build steps here, if they are necessary. -# -# See -# http://docs.continuum.io/conda/build.html -# for a list of environment variables that are set during the build -# process. -# +# \ No newline at end of file diff --git a/recipes/bioconductor-motiv/meta.yaml b/recipes/bioconductor-motiv/meta.yaml index dd8c653813..cdbeaad2eb 100644 --- a/recipes/bioconductor-motiv/meta.yaml +++ b/recipes/bioconductor-motiv/meta.yaml @@ -3,15 +3,17 @@ package: version: 1.30.0 source: fn: MotIV_1.30.0.tar.gz - url: https://bioarchive.galaxyproject.org/MotIV_1.30.0.tar.gz - md5: a5d51105c30360bcade445659e7172c3 + url: + - http://bioconductor.org/packages/3.4/bioc/src/contrib/MotIV_1.30.0.tar.gz + - https://bioarchive.galaxyproject.org/MotIV_1.30.0.tar.gz + - https://depot.galaxyproject.org/software/MotIV/MotIV_1.30.0_src_all.tar.gz + md5: 19da23b2900e7e9b334084a7bd78c17c build: - number: 0 string: gsl{{CONDA_GSL}}_{{PKG_BUILDNUM}} + number: 1 rpaths: - lib/R/lib/ - lib/ - requirements: build: - 'bioconductor-biocgenerics >=0.1.0' @@ -21,7 +23,7 @@ requirements: - bioconductor-s4vectors - r-base - gsl {{CONDA_GSL}}* - + - r-lattice run: - 'bioconductor-biocgenerics >=0.1.0' - 'bioconductor-biostrings >=1.24.0' @@ -29,12 +31,12 @@ requirements: - bioconductor-rgadem - bioconductor-s4vectors - r-base - - gsl {{CONDA_GSL}}* + - r-lattice test: commands: - '$R -e "library(''MotIV'')"' about: - home: http://bioconductor.org/packages/release/bioc/html/MotIV.html + home: http://bioconductor.org/packages/3.5/bioc/html/MotIV.html license: GPL-2 summary: 'This package makes use of STAMP for comparing a set of motifs to a given database (e.g. JASPAR). It can also be used to visualize motifs, motif distributions, From abf70a62ca5596255446dbce1a604a516205ff16 Mon Sep 17 00:00:00 2001 From: Ryan Dale Date: Mon, 5 Jun 2017 22:09:37 -0400 Subject: [PATCH 064/116] urls for rGADEM --- recipes/bioconductor-rgadem/build.sh | 11 ----------- recipes/bioconductor-rgadem/meta.yaml | 9 ++++++--- 2 files changed, 6 insertions(+), 14 deletions(-) diff --git a/recipes/bioconductor-rgadem/build.sh b/recipes/bioconductor-rgadem/build.sh index 6c7a1726e3..8218eda948 100644 --- a/recipes/bioconductor-rgadem/build.sh +++ b/recipes/bioconductor-rgadem/build.sh @@ -1,17 +1,6 @@ #!/bin/bash - -# R refuses to build packages that mark themselves as -# "Priority: Recommended" mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION -# $R CMD INSTALL --build . -# -# # Add more build steps here, if they are necessary. -# -# See -# http://docs.continuum.io/conda/build.html -# for a list of environment variables that are set during the build -# process. # \ No newline at end of file diff --git a/recipes/bioconductor-rgadem/meta.yaml b/recipes/bioconductor-rgadem/meta.yaml index 90c72ebbbf..c221e78387 100644 --- a/recipes/bioconductor-rgadem/meta.yaml +++ b/recipes/bioconductor-rgadem/meta.yaml @@ -3,8 +3,11 @@ package: version: 2.22.0 source: fn: rGADEM_2.22.0.tar.gz - url: https://bioarchive.galaxyproject.org/rGADEM_2.22.0.tar.gz - md5: 3b4449b9ddf478cd77ce515d9d2d80d9 + url: + - http://bioconductor.org/packages/3.4/bioc/src/contrib/rGADEM_2.22.0.tar.gz + - https://bioarchive.galaxyproject.org/rGADEM_2.22.0.tar.gz + - https://depot.galaxyproject.org/software/rGADEM/rGADEM_2.22.0_src_all.tar.gz + md5: 68855b9cecf4cb029027b6df0a0b6b2d build: number: 0 rpaths: @@ -27,7 +30,7 @@ test: commands: - '$R -e "library(''rGADEM'')"' about: - home: http://bioconductor.org/packages/release/bioc/html/rGADEM.html + home: http://bioconductor.org/packages/3.5/bioc/html/rGADEM.html license: Artistic-2.0 summary: 'rGADEM is an efficient de novo motif discovery tool for large-scale genomic sequence data. It is an open-source R package, which is based on the GADEM software.' From cc38fe2c3ec841d5bd01e987486c32eb92230edc Mon Sep 17 00:00:00 2001 From: Ryan Dale Date: Mon, 5 Jun 2017 22:10:01 -0400 Subject: [PATCH 065/116] urls and built-ins for Ringo --- recipes/bioconductor-ringo/build.sh | 11 ----------- recipes/bioconductor-ringo/meta.yaml | 15 +++++++++++---- 2 files changed, 11 insertions(+), 15 deletions(-) diff --git a/recipes/bioconductor-ringo/build.sh b/recipes/bioconductor-ringo/build.sh index 6c7a1726e3..8218eda948 100644 --- a/recipes/bioconductor-ringo/build.sh +++ b/recipes/bioconductor-ringo/build.sh @@ -1,17 +1,6 @@ #!/bin/bash - -# R refuses to build packages that mark themselves as -# "Priority: Recommended" mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION -# $R CMD INSTALL --build . -# -# # Add more build steps here, if they are necessary. -# -# See -# http://docs.continuum.io/conda/build.html -# for a list of environment variables that are set during the build -# process. # \ No newline at end of file diff --git a/recipes/bioconductor-ringo/meta.yaml b/recipes/bioconductor-ringo/meta.yaml index 02590f5b7f..fdb0976383 100644 --- a/recipes/bioconductor-ringo/meta.yaml +++ b/recipes/bioconductor-ringo/meta.yaml @@ -3,10 +3,13 @@ package: version: 1.38.0 source: fn: Ringo_1.38.0.tar.gz - url: https://bioarchive.galaxyproject.org/Ringo_1.38.0.tar.gz - md5: 6189371605ced5ce1f2922a66954a5ae + url: + - http://bioconductor.org/packages/3.4/bioc/src/contrib/Ringo_1.38.0.tar.gz + - https://bioarchive.galaxyproject.org/Ringo_1.38.0.tar.gz + - https://depot.galaxyproject.org/software/Ringo/Ringo_1.38.0_src_all.tar.gz + md5: 17a1b47d16f09dd4525f26b272c48539 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -18,6 +21,8 @@ requirements: - bioconductor-limma - bioconductor-vsn - r-base + - r-lattice + - r-matrix - r-rcolorbrewer run: - 'bioconductor-biobase >=1.14.1' @@ -26,12 +31,14 @@ requirements: - bioconductor-limma - bioconductor-vsn - r-base + - r-lattice + - r-matrix - r-rcolorbrewer test: commands: - '$R -e "library(''Ringo'')"' about: - home: http://bioconductor.org/packages/release/bioc/html/Ringo.html + home: http://bioconductor.org/packages/3.5/bioc/html/Ringo.html license: Artistic-2.0 summary: 'The package Ringo facilitates the primary analysis of ChIP-chip data. The main functionalities of the package are data read-in, quality assessment, From 3f968e4b9fa08a5a4dd996158c6b882405fabe63 Mon Sep 17 00:00:00 2001 From: Ryan Dale Date: Mon, 5 Jun 2017 22:11:23 -0400 Subject: [PATCH 066/116] urls for zlibbioc --- recipes/bioconductor-zlibbioc/build.sh | 11 ----------- recipes/bioconductor-zlibbioc/meta.yaml | 11 +++++++---- 2 files changed, 7 insertions(+), 15 deletions(-) diff --git a/recipes/bioconductor-zlibbioc/build.sh b/recipes/bioconductor-zlibbioc/build.sh index 6c7a1726e3..8218eda948 100644 --- a/recipes/bioconductor-zlibbioc/build.sh +++ b/recipes/bioconductor-zlibbioc/build.sh @@ -1,17 +1,6 @@ #!/bin/bash - -# R refuses to build packages that mark themselves as -# "Priority: Recommended" mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION -# $R CMD INSTALL --build . -# -# # Add more build steps here, if they are necessary. -# -# See -# http://docs.continuum.io/conda/build.html -# for a list of environment variables that are set during the build -# process. # \ No newline at end of file diff --git a/recipes/bioconductor-zlibbioc/meta.yaml b/recipes/bioconductor-zlibbioc/meta.yaml index 5c79d099b0..d09d543834 100644 --- a/recipes/bioconductor-zlibbioc/meta.yaml +++ b/recipes/bioconductor-zlibbioc/meta.yaml @@ -3,10 +3,13 @@ package: version: 1.20.0 source: fn: zlibbioc_1.20.0.tar.gz - url: https://bioarchive.galaxyproject.org/zlibbioc_1.20.0.tar.gz - md5: efdf012f000323d1e284123907f0007a + url: + - http://bioconductor.org/packages/3.4/bioc/src/contrib/zlibbioc_1.20.0.tar.gz + - https://bioarchive.galaxyproject.org/zlibbioc_1.20.0.tar.gz + - https://depot.galaxyproject.org/software/zlibbioc/zlibbioc_1.20.0_src_all.tar.gz + md5: f68b45fca70f39c7958fb43c0504c546 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -19,7 +22,7 @@ test: commands: - '$R -e "library(''zlibbioc'')"' about: - home: http://bioconductor.org/packages/release/bioc/html/zlibbioc.html + home: http://bioconductor.org/packages/3.5/bioc/html/zlibbioc.html license: 'Artistic-2.0 + file LICENSE' summary: 'This package uses the source code of zlib-1.2.5 to create libraries for systems that do not have these available via other means (most Linux and Mac users From f354f924f74171c6df1d7ff3a849ae918d175121 Mon Sep 17 00:00:00 2001 From: Bjoern Gruening Date: Tue, 6 Jun 2017 10:11:24 +0200 Subject: [PATCH 067/116] r fixes --- recipes/bioconductor-gagedata/meta.yaml | 7 ++++- recipes/bioconductor-genefilter/meta.yaml | 13 ++++----- recipes/bioconductor-kcsmart/meta.yaml | 3 +++ recipes/r-aroma.core/meta.yaml | 1 - recipes/r-leaps/meta.yaml | 3 +-- recipes/r-mixomics/meta.yaml | 19 +++---------- recipes/r-proj4/meta.yaml | 45 ++----------------------------- 7 files changed, 22 insertions(+), 69 deletions(-) diff --git a/recipes/bioconductor-gagedata/meta.yaml b/recipes/bioconductor-gagedata/meta.yaml index 5166739b80..94cd3d66d8 100644 --- a/recipes/bioconductor-gagedata/meta.yaml +++ b/recipes/bioconductor-gagedata/meta.yaml @@ -1,23 +1,28 @@ package: name: bioconductor-gagedata version: 2.10.0 + source: fn: gageData_2.10.0.tar.gz url: https://bioconductor.statistik.tu-dortmund.de/packages/2.12/bioc/src/contrib/gage_2.10.0.tar.gz - md5: a143308c83d08d470695c8449f84490d + md5: 911fa0f4549ab068940c9ab39a4f9ee8 + build: number: 0 rpaths: - lib/R/lib/ - lib/ + requirements: build: - r-base run: - r-base + test: commands: - '$R -e "library(''gageData'')"' + about: home: http://bioconductor.org/packages/release/data/experiment/html/gageData.html license: 'GPL (>=2.0)' diff --git a/recipes/bioconductor-genefilter/meta.yaml b/recipes/bioconductor-genefilter/meta.yaml index 699cb06542..8604abb0c4 100644 --- a/recipes/bioconductor-genefilter/meta.yaml +++ b/recipes/bioconductor-genefilter/meta.yaml @@ -1,13 +1,12 @@ package: name: bioconductor-genefilter - version: 1.56.0 + version: 1.58.1 source: - fn: genefilter_1.56.0.tar.gz + fn: genefilter_1.58.1.tar.gz url: - - http://bioconductor.org/packages/3.4/bioc/src/contrib/genefilter_1.56.0.tar.gz - - https://bioarchive.galaxyproject.org/genefilter_1.56.0.tar.gz - - https://depot.galaxyproject.org/software/genefilter/genefilter_1.56.0_src_all.tar.gz - md5: 919e4deb451ca4e9dbea1e125e15cf98 + - http://bioconductor.org/packages/3.5/bioc/src/contrib/genefilter_1.58.1.tar.gz + - https://depot.galaxyproject.org/software/genefilter/genefilter_1.58.1_src_all.tar.gz + md5: bc1a90bdf93d8db994220545cd80f438 build: number: 0 rpaths: @@ -21,6 +20,7 @@ requirements: - 'bioconductor-s4vectors >=0.9.42' - r-base - r-survival + - gcc run: - bioconductor-annotate - bioconductor-annotationdbi @@ -28,6 +28,7 @@ requirements: - 'bioconductor-s4vectors >=0.9.42' - r-base - r-survival + - libgcc # [linux] test: commands: - '$R -e "library(''genefilter'')"' diff --git a/recipes/bioconductor-kcsmart/meta.yaml b/recipes/bioconductor-kcsmart/meta.yaml index 6f81229184..086d4b23bc 100644 --- a/recipes/bioconductor-kcsmart/meta.yaml +++ b/recipes/bioconductor-kcsmart/meta.yaml @@ -16,11 +16,14 @@ requirements: - bioconductor-multtest - bioconductor-siggenes - r-base + - r-kernsmooth run: - bioconductor-biocgenerics - bioconductor-multtest - bioconductor-siggenes - r-base + - r-kernsmooth + test: commands: - '$R -e "library(''KCsmart'')"' diff --git a/recipes/r-aroma.core/meta.yaml b/recipes/r-aroma.core/meta.yaml index cf0acc9a28..3e483c6327 100644 --- a/recipes/r-aroma.core/meta.yaml +++ b/recipes/r-aroma.core/meta.yaml @@ -8,7 +8,6 @@ package: source: fn: aroma.core_3.0.0.tar.gz url: - - http://cran.r-project.org/src/contrib/aroma.core_3.0.0.tar.gz - http://cran.r-project.org/src/contrib/Archive/aroma.core/aroma.core_3.0.0.tar.gz md5: f0fd63544ece9678c94d1f9c16b0b7cb diff --git a/recipes/r-leaps/meta.yaml b/recipes/r-leaps/meta.yaml index fde6cbd577..45f131e0cc 100644 --- a/recipes/r-leaps/meta.yaml +++ b/recipes/r-leaps/meta.yaml @@ -21,11 +21,10 @@ requirements: - r-base - gcc # [linux] - llvm # [osx] - + - gfortran # [osx] run: - r-base - libgcc # [linux] - - gfortran # [osx] test: commands: diff --git a/recipes/r-mixomics/meta.yaml b/recipes/r-mixomics/meta.yaml index 294fdd0009..0f32c79201 100644 --- a/recipes/r-mixomics/meta.yaml +++ b/recipes/r-mixomics/meta.yaml @@ -3,25 +3,19 @@ package: name: r-mixomics - # Note that conda versions cannot contain -, so any -'s in the version have - # been replaced with _'s. version: "6.1.1" source: fn: mixOmics_6.1.1.tar.gz url: - - http://cran.r-project.org/src/contrib/mixOmics_6.1.1.tar.gz - http://cran.r-project.org/src/contrib/Archive/mixOmics/mixOmics_6.1.1.tar.gz build: number: 0 - - # This is required to make R link correctly on Linux. rpaths: - lib/R/lib/ - lib/ - requirements: build: - r-base @@ -38,7 +32,6 @@ requirements: - r-rgl - r-tidyr - libglu # [linux] - run: - r-base - r-mass @@ -61,16 +54,11 @@ test: - $R -e "library('mixOmics')" # [not win] - "\"%R%\" -e \"library('mixOmics')\"" # [win] - # You can also put a file called run_test.py, run_test.sh, or run_test.bat - # in the recipe that will be run at test time. - - # requires: - # Put any additional test requirements here. - about: home: http://www.mixOmics.org license: GPL (>= 2) - summary: 'Multivariate methods are well suited to large omics data sets where the number of + summary: | + Multivariate methods are well suited to large omics data sets where the number of variables (e.g. genes, proteins, metabolites) is much larger than the number of samples (patients, cells, mice). They have the appealing properties of reducing the dimension of the data by using instrumental variables (components), which are @@ -89,6 +77,5 @@ about: Correlation Analysis, sparse Partial Least Squares and sparse Discriminant Analysis. Recently we implemented integrative methods to combine multiple data sets: horizontal integration with regularised Generalised Canonical Correlation Analysis and vertical - integration with multi-group Partial Least Squares.' - + integration with multi-group Partial Least Squares. license_family: GPL3 diff --git a/recipes/r-proj4/meta.yaml b/recipes/r-proj4/meta.yaml index 25d147857b..4ad4cc84c2 100644 --- a/recipes/r-proj4/meta.yaml +++ b/recipes/r-proj4/meta.yaml @@ -1,7 +1,5 @@ package: name: r-proj4 - # Note that conda versions cannot contain -, so any -'s in the version have - # been replaced with _'s. version: "1.0_8" source: @@ -10,35 +8,22 @@ source: - http://cran.r-project.org/src/contrib/proj4_1.0-8.tar.gz - http://cran.r-project.org/src/contrib/Archive/proj4/proj4_1.0-8.tar.gz - - # You can add a hash for the file here, like md5 or sha1 - # md5: 49448ba4863157652311cc5ea4fea3ea - # sha1: 3bcfbee008276084cbb37a2b453963c61176a322 - # patches: - # List any patch files here - # - fix.patch - build: - # If this is a new build for the same version, increment the build - # number. If you do not include this key, it defaults to 0. # number: 1 - - # This is required to make R link correctly on Linux. rpaths: - lib/R/lib/ - lib/ - requirements: build: - r-base - gcc # [not win] - - proj4 + - proj4 4.9.3 run: - r-base - libgcc # [not win] - - proj4 + - proj4 4.9.3 test: commands: @@ -46,12 +31,6 @@ test: - $R -e "library('proj4')" # [not win] - "\"%R%\" -e \"library('proj4')\"" # [win] - # You can also put a file called run_test.py, run_test.sh, or run_test.bat - # in the recipe that will be run at test time. - - # requires: - # Put any additional test requirements here. - about: home: http://www.rforge.net/proj4/ license: GPL-2 @@ -59,23 +38,3 @@ about: projections library. It allows transformation of geographic coordinates from one projection and/or datum to another. -# The original CRAN metadata for this package was: - -# Package: proj4 -# Version: 1.0-8 -# Title: A simple interface to the PROJ.4 cartographic projections library -# Depends: R (>= 2.0.0) -# Author: Simon Urbanek -# Maintainer: Simon Urbanek -# Description: A simple interface to lat/long projection and datum transformation of the PROJ.4 cartographic projections library. It allows transformation of geographic coordinates from one projection and/or datum to another. -# SystemRequirements: proj 4.4.6 or higher (http://proj.maptools.org/) -# License: GPL-2 -# URL: http://www.rforge.net/proj4/ -# Packaged: 2012-08-05 01:54:11 UTC; svnuser -# Repository: CRAN -# Date/Publication: 2012-08-05 06:07:47 -# NeedsCompilation: yes - -# See -# http://docs.continuum.io/conda/build.html for -# more information about meta.yaml From 233eb4412f701d9e47fe0c0a700e2e5ddb951a2d Mon Sep 17 00:00:00 2001 From: Bjoern Gruening Date: Tue, 6 Jun 2017 11:44:42 +0200 Subject: [PATCH 068/116] r fixes --- recipes/bioconductor-deseq/meta.yaml | 2 ++ recipes/bioconductor-gagedata/meta.yaml | 9 ++--- recipes/bioconductor-rsamtools/meta.yaml | 48 +++++++++++-------------- recipes/bioconductor-sva/meta.yaml | 7 ++-- recipes/bioconductor-xcms/meta.yaml | 7 ++++ recipes/r-aroma.affymetrix/meta.yaml | 32 ----------------- recipes/r-ks/meta.yaml | 2 ++ recipes/r-leaps/meta.yaml | 4 +-- recipes/r-plasmidprofiler/meta.yaml | 60 ++++++++++++++++---------------- 9 files changed, 72 insertions(+), 99 deletions(-) diff --git a/recipes/bioconductor-deseq/meta.yaml b/recipes/bioconductor-deseq/meta.yaml index bb83de79ae..07ced989a9 100644 --- a/recipes/bioconductor-deseq/meta.yaml +++ b/recipes/bioconductor-deseq/meta.yaml @@ -19,6 +19,7 @@ requirements: - r-base - r-locfit - r-rcolorbrewer + - r-mass run: - 'bioconductor-biobase >=2.21.7' - 'bioconductor-biocgenerics >=0.7.5' @@ -27,6 +28,7 @@ requirements: - r-base - r-locfit - r-rcolorbrewer + - r-mass test: commands: - '$R -e "library(''DESeq'')"' diff --git a/recipes/bioconductor-gagedata/meta.yaml b/recipes/bioconductor-gagedata/meta.yaml index 94cd3d66d8..c613625115 100644 --- a/recipes/bioconductor-gagedata/meta.yaml +++ b/recipes/bioconductor-gagedata/meta.yaml @@ -4,8 +4,8 @@ package: source: fn: gageData_2.10.0.tar.gz - url: https://bioconductor.statistik.tu-dortmund.de/packages/2.12/bioc/src/contrib/gage_2.10.0.tar.gz - md5: 911fa0f4549ab068940c9ab39a4f9ee8 + url: http://bioconductor.org/packages/3.3/data/experiment/src/contrib/gageData_2.10.0.tar.gz + sha256: 948b38925f573cbd484fd5dd36e4423c8fcdcf8e01487d1a87bf6461dd0cd99e build: number: 0 @@ -26,11 +26,12 @@ test: about: home: http://bioconductor.org/packages/release/data/experiment/html/gageData.html license: 'GPL (>=2.0)' - summary: 'This is a supportive data package for the software package, gage. However, + summary: | + This is a supportive data package for the software package, gage. However, the data supplied here are also useful for gene set or pathway analysis or microarray data analysis in general. In this package, we provide two demo microarray dataset: GSE16873 (a breast cancer dataset from GEO) and BMP6 (originally published as an demo dataset for GAGE, also registered as GSE13604 in GEO). This package also includes commonly used gene set data based on KEGG pathways and GO terms for major research species, including human, mouse, rat and budding yeast. Mapping data - between common gene IDs for budding yeast are also included.' + between common gene IDs for budding yeast are also included. diff --git a/recipes/bioconductor-rsamtools/meta.yaml b/recipes/bioconductor-rsamtools/meta.yaml index 6e77a7b512..ad66540545 100644 --- a/recipes/bioconductor-rsamtools/meta.yaml +++ b/recipes/bioconductor-rsamtools/meta.yaml @@ -12,39 +12,31 @@ build: - lib/R/lib/ - lib/ -#Suggests: GenomicAlignments, ShortRead(>= 1.19.10), GenomicFeatures, -# TxDb.Dmelanogaster.UCSC.dm3.ensGene, KEGG.db, TxDb.Hsapiens.UCSC.hg18.knownGene, -# RNAseqData.HNRNPC.bam.chr14, BSgenome.Hsapiens.UCSC.hg19, pasillaBamSubset, -# RUnit, BiocStyle - -#I specify the versions of respective dependencies while buiding the package, -#whereas in the comments, I document -#the version ranges specified in the origianl R description file. requirements: build: - - bioconductor-biocgenerics 0.20.0 #>=0.1.3 - - bioconductor-biocparallel 1.6.6 - - bioconductor-biostrings 2.40.0 #>=2.37.1 - - bioconductor-genomeinfodb 1.8.7 #>=1.1.3 - - bioconductor-genomicranges 1.26.1 #>= 1.21.6 - - bioconductor-iranges 2.8.0 #>=2.3.7 - - bioconductor-s4vectors 0.12.0 #>=0.7.11 - - bioconductor-xvector 0.12.1 #>=0.9.1 - - bioconductor-zlibbioc 1.18.0 + - bioconductor-biocgenerics + - bioconductor-biocparallel + - bioconductor-biostrings + - bioconductor-genomeinfodb + - bioconductor-genomicranges + - bioconductor-iranges + - bioconductor-s4vectors + - bioconductor-xvector + - bioconductor-zlibbioc - r-base - - r-bitops 1.0_6 + - r-bitops run: - - bioconductor-biocgenerics 0.20.0 #>=0.1.3 - - bioconductor-biocparallel 1.6.6 - - bioconductor-biostrings 2.40.0 #>=2.37.1 - - bioconductor-genomeinfodb 1.8.7 #>=1.1.3 - - bioconductor-genomicranges 1.26.1 #>= 1.21.6 - - bioconductor-iranges 2.8.0 #>=2.3.7 - - bioconductor-s4vectors 0.12.0 #>=0.7.11 - - bioconductor-xvector 0.12.1 #>=0.9.1 - - bioconductor-zlibbioc 1.18.0 + - bioconductor-biocgenerics + - bioconductor-biocparallel + - bioconductor-biostrings + - bioconductor-genomeinfodb + - bioconductor-genomicranges + - bioconductor-iranges + - bioconductor-s4vectors + - bioconductor-xvector + - bioconductor-zlibbioc - r-base - - r-bitops 1.0_6 + - r-bitops test: commands: diff --git a/recipes/bioconductor-sva/meta.yaml b/recipes/bioconductor-sva/meta.yaml index 2f8e294747..b44a27cc52 100644 --- a/recipes/bioconductor-sva/meta.yaml +++ b/recipes/bioconductor-sva/meta.yaml @@ -16,17 +16,20 @@ requirements: - llvm # [osx] - bioconductor-genefilter - r-base + - r-mgcv run: - libgcc # [linux] - bioconductor-genefilter - r-base + - r-mgcv test: commands: - '$R -e "library(''sva'')"' about: home: http://bioconductor.org/packages/release/bioc/html/sva.html license: Artistic-2.0 - summary: 'The sva package contains functions for removing batch effects and other + summary: | + The sva package contains functions for removing batch effects and other unwanted variation in high-throughput experiment. Specifically, the sva package contains functions for the identifying and building surrogate variables for high-dimensional data sets. Surrogate variables are covariates constructed directly from high-dimensional @@ -40,4 +43,4 @@ about: Removing batch effects and using surrogate variables in differential expression analysis have been shown to reduce dependence, stabilize error rate estimates, and improve reproducibility, see (Leek and Storey 2007 PLoS Genetics, 2008 PNAS - or Leek et al. 2011 Nat. Reviews Genetics).' + or Leek et al. 2011 Nat. Reviews Genetics). diff --git a/recipes/bioconductor-xcms/meta.yaml b/recipes/bioconductor-xcms/meta.yaml index 9df332de5a..495cc333a2 100644 --- a/recipes/bioconductor-xcms/meta.yaml +++ b/recipes/bioconductor-xcms/meta.yaml @@ -1,16 +1,19 @@ package: name: bioconductor-xcms version: 1.50.1 + source: fn: 205a104fcf75b3726436c2bb9686b50255cb44bf.zip url: https://github.com/Bioconductor-mirror/xcms/archive/205a104fcf75b3726436c2bb9686b50255cb44bf.zip md5: f8125671e0c991b7eff606d9df4258d0 + build: number: 0 skip: True # [osx] rpaths: - lib/R/lib/ - lib/ + requirements: build: - bioconductor-biobase @@ -25,6 +28,7 @@ requirements: - bioconductor-biocparallel - bioconductor-s4vectors - bioconductor-massspecwavelet + - r-lattice run: - bioconductor-biobase - bioconductor-biocgenerics @@ -38,9 +42,12 @@ requirements: - bioconductor-biocparallel - bioconductor-s4vectors - bioconductor-massspecwavelet + - r-lattice + test: commands: - '$R -e "library(''xcms'')"' + about: home: http://bioconductor.org/packages/release/bioc/html/xcms.html license: 'GPL (>= 2) + file LICENSE' diff --git a/recipes/r-aroma.affymetrix/meta.yaml b/recipes/r-aroma.affymetrix/meta.yaml index 41581d33fd..75fcd70324 100644 --- a/recipes/r-aroma.affymetrix/meta.yaml +++ b/recipes/r-aroma.affymetrix/meta.yaml @@ -8,7 +8,6 @@ package: source: fn: aroma.affymetrix_3.0.0.tar.gz url: - - http://cran.r-project.org/src/contrib/aroma.affymetrix_3.0.0.tar.gz - http://cran.r-project.org/src/contrib/Archive/aroma.affymetrix/aroma.affymetrix_3.0.0.tar.gz md5: 55c105016e8a86adb46d9172b12d76f7 @@ -18,7 +17,6 @@ build: - lib/R/lib/ - lib/ -# Suggests: DBI (>= 0.3.1), gsmoothr (>= 0.1.7), RColorBrewer (>= 1.1-2), Biobase (>= 2.28.0), BiocGenerics (>= 0.14.0), affxparser (>= 1.40.0), affy (>= 1.46.0), affyPLM (>= 1.44.0), aroma.light (>= 2.4.0), gcrma (>= 2.40.0), limma (>= 3.24.1), oligo (>= 1.32.0), oligoClasses (>= 1.30.0), pdInfoBuilder (>= 1.32.0), preprocessCore (>= 1.28.0), AffymetrixDataTestFiles, dChipIO (>= 0.1.1) requirements: build: - r-base @@ -34,7 +32,6 @@ requirements: - r-future - r-listenv - r-matrixstats >=0.50.1 - run: - r-base - r-mass @@ -64,32 +61,3 @@ about: Aroma Framework has successfully been used in studies to process tens of thousands of arrays. This package has actively been used since 2006. license_family: LGPL - -# The original CRAN metadata for this package was: - -# Package: aroma.affymetrix -# Version: 3.0.0 -# Depends: R (>= 3.1.2), R.utils (>= 2.2.0), aroma.core (>= 3.0.0) -# Imports: methods, R.methodsS3 (>= 1.7.0), R.oo (>= 1.19.0), R.cache (>= 0.12.0), R.devices (>= 2.13.2), R.filesets (>= 2.10.0), aroma.apd (>= 0.6.0), MASS, splines, matrixStats (>= 0.50.1), listenv, future -# Suggests: DBI (>= 0.3.1), gsmoothr (>= 0.1.7), RColorBrewer (>= 1.1-2), Biobase (>= 2.28.0), BiocGenerics (>= 0.14.0), affxparser (>= 1.40.0), affy (>= 1.46.0), affyPLM (>= 1.44.0), aroma.light (>= 2.4.0), gcrma (>= 2.40.0), limma (>= 3.24.1), oligo (>= 1.32.0), oligoClasses (>= 1.30.0), pdInfoBuilder (>= 1.32.0), preprocessCore (>= 1.28.0), AffymetrixDataTestFiles, dChipIO (>= 0.1.1) -# SuggestsNote: BioC (>= 3.0), Recommended: preprocessCore, affyPLM, aroma.light, affxparser, DNAcopy -# Additional_repositories: http://r-forge.r-project.org -# Date: 2016-01-09 -# Title: Analysis of Large Affymetrix Microarray Data Sets -# Authors@R: c( person("Henrik", "Bengtsson", role=c("aut", "cre", "cph"), email="henrikb@braju.com"), person("James", "Bullard", role="ctb"), person("Kasper", "Hansen", role="ctb"), person("Pierre", "Neuvial", role="ctb"), person("Elizabeth", "Purdom", role="ctb"), person("Mark", "Robinson", role="ctb"), person("Ken", "Simpson", role="ctb")) -# Description: A cross-platform R framework that facilitates processing of any number of Affymetrix microarray samples regardless of computer system. The only parameter that limits the number of chips that can be processed is the amount of available disk space. The Aroma Framework has successfully been used in studies to process tens of thousands of arrays. This package has actively been used since 2006. -# License: LGPL (>= 2.1) -# URL: http://www.aroma-project.org/, https://github.com/HenrikBengtsson/aroma.affymetrix -# BugReports: https://github.com/HenrikBengtsson/aroma.affymetrix/issues -# LazyLoad: TRUE -# biocViews: Infrastructure, ProprietaryPlatforms, ExonArray, Microarray, OneChannel, GUI, DataImport, DataRepresentation, Preprocessing, QualityControl, Visualization, ReportWriting, aCGH, CopyNumberVariants, DifferentialExpression, GeneExpression, SNP, Transcription -# NeedsCompilation: no -# Packaged: 2016-01-09 21:38:52 UTC; hb -# Author: Henrik Bengtsson [aut, cre, cph], James Bullard [ctb], Kasper Hansen [ctb], Pierre Neuvial [ctb], Elizabeth Purdom [ctb], Mark Robinson [ctb], Ken Simpson [ctb] -# Maintainer: Henrik Bengtsson -# Repository: CRAN -# Date/Publication: 2016-01-10 00:00:03 - -# See -# http://docs.continuum.io/conda/build.html for -# more information about meta.yaml diff --git a/recipes/r-ks/meta.yaml b/recipes/r-ks/meta.yaml index b327030afb..15b6ed5e34 100644 --- a/recipes/r-ks/meta.yaml +++ b/recipes/r-ks/meta.yaml @@ -27,6 +27,7 @@ requirements: - r-mvtnorm >=1.0_0 - r-rgl >=0.66 - gcc + - libglu # [linux] run: - r-base @@ -36,6 +37,7 @@ requirements: - r-multicool - r-mvtnorm >=1.0_0 - r-rgl >=0.66 + - libglu # [linux] test: commands: diff --git a/recipes/r-leaps/meta.yaml b/recipes/r-leaps/meta.yaml index 45f131e0cc..6a8a40e955 100644 --- a/recipes/r-leaps/meta.yaml +++ b/recipes/r-leaps/meta.yaml @@ -19,9 +19,7 @@ build: requirements: build: - r-base - - gcc # [linux] - - llvm # [osx] - - gfortran # [osx] + - gcc run: - r-base - libgcc # [linux] diff --git a/recipes/r-plasmidprofiler/meta.yaml b/recipes/r-plasmidprofiler/meta.yaml index faa61a10b2..ecbb8a3dea 100644 --- a/recipes/r-plasmidprofiler/meta.yaml +++ b/recipes/r-plasmidprofiler/meta.yaml @@ -18,39 +18,39 @@ build: requirements: build: - r-base - - r-ape 3.5 - - r-dplyr 0.5.0 - - r-gdata 2.17.0 - - r-ggdendro 0.1_17 - - r-ggplot2 2.1.0 - - r-gridextra 2.2.1 - - r-gtable 0.2.0 - - r-htmlwidgets 0.6 - - r-magrittr 1.5 - - r-plotly 4.5.2 - - r-plyr 1.8.4 - - r-rcolorbrewer 1.1_2 - - r-reshape2 1.4.2 - - r-stringr 1.1.0 - - pandoc 1.19.2 + - r-ape + - r-dplyr + - r-gdata + - r-ggdendro + - r-ggplot2 + - r-gridextra + - r-gtable + - r-htmlwidgets + - r-magrittr + - r-plotly + - r-plyr + - r-rcolorbrewer + - r-reshape2 + - r-stringr + - pandoc run: - r-base - - r-ape 3.5 - - r-dplyr 0.5.0 - - r-gdata 2.17.0 - - r-ggdendro 0.1_17 - - r-ggplot2 2.1.0 - - r-gridextra 2.2.1 - - r-gtable 0.2.0 - - r-htmlwidgets 0.6 - - r-magrittr 1.5 - - r-plotly 4.5.2 - - r-plyr 1.8.4 - - r-rcolorbrewer 1.1_2 - - r-reshape2 1.4.2 - - r-stringr 1.1.0 - - pandoc 1.19.2 + - r-ape + - r-dplyr + - r-gdata + - r-ggdendro + - r-ggplot2 + - r-gridextra + - r-gtable + - r-htmlwidgets + - r-magrittr + - r-plotly + - r-plyr + - r-rcolorbrewer + - r-reshape2 + - r-stringr + - pandoc test: commands: From 2eac6408ab024497383ec704427ecc356f141075 Mon Sep 17 00:00:00 2001 From: Bjoern Gruening Date: Tue, 6 Jun 2017 13:25:28 +0200 Subject: [PATCH 069/116] remove old package --- .../1.0.2/build.sh | 17 ---------- .../1.0.2/meta.yaml | 38 ---------------------- 2 files changed, 55 deletions(-) delete mode 100644 recipes/bioconductor-summarizedexperiment/1.0.2/build.sh delete mode 100644 recipes/bioconductor-summarizedexperiment/1.0.2/meta.yaml diff --git a/recipes/bioconductor-summarizedexperiment/1.0.2/build.sh b/recipes/bioconductor-summarizedexperiment/1.0.2/build.sh deleted file mode 100644 index 6c7a1726e3..0000000000 --- a/recipes/bioconductor-summarizedexperiment/1.0.2/build.sh +++ /dev/null @@ -1,17 +0,0 @@ - -#!/bin/bash - -# R refuses to build packages that mark themselves as -# "Priority: Recommended" -mv DESCRIPTION DESCRIPTION.old -grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION -# -$R CMD INSTALL --build . -# -# # Add more build steps here, if they are necessary. -# -# See -# http://docs.continuum.io/conda/build.html -# for a list of environment variables that are set during the build -# process. -# \ No newline at end of file diff --git a/recipes/bioconductor-summarizedexperiment/1.0.2/meta.yaml b/recipes/bioconductor-summarizedexperiment/1.0.2/meta.yaml deleted file mode 100644 index 8b3b6c97a8..0000000000 --- a/recipes/bioconductor-summarizedexperiment/1.0.2/meta.yaml +++ /dev/null @@ -1,38 +0,0 @@ -package: - name: bioconductor-summarizedexperiment - version: 1.0.2 -source: - fn: SummarizedExperiment_1.0.2.tar.gz - url: https://bioc.ism.ac.jp/packages/3.2/bioc/src/contrib/SummarizedExperiment_1.0.2.tar.gz - md5: ce5b5d0aa2868f754bc8d136ebd2e6cd -build: - number: 1 - rpaths: - - lib/R/lib/ - - lib/ -requirements: - build: - - bioconductor-biobase - - 'bioconductor-biocgenerics >=0.15.3' - - bioconductor-genomeinfodb - - 'bioconductor-genomicranges >=1.22.1' - - bioconductor-iranges - - 'bioconductor-s4vectors >=0.7.11' - - r-base - run: - - bioconductor-biobase - - 'bioconductor-biocgenerics >=0.15.3' - - bioconductor-genomeinfodb - - 'bioconductor-genomicranges >=1.22.1' - - bioconductor-iranges - - 'bioconductor-s4vectors >=0.7.11' - - r-base -test: - commands: - - '$R -e "library(''SummarizedExperiment'')"' -about: - home: http://bioconductor.org/packages/release/bioc/html/SummarizedExperiment.html - license: Artistic-2.0 - summary: 'The SummarizedExperiment container contains one or more assays, each represented - by a matrix-like object of numeric or other mode. The rows typically represent - genomic ranges of interest and the columns represent samples.' From b899b527a1d99c27679989977d9932ef8d3e9574 Mon Sep 17 00:00:00 2001 From: Bjoern Gruening Date: Tue, 6 Jun 2017 13:37:58 +0200 Subject: [PATCH 070/116] r fixes --- recipes/bioconductor-rsamtools/meta.yaml | 2 +- recipes/r-ggalt/meta.yaml | 1 - recipes/r-htmltools/meta.yaml | 53 -------------------------------- 3 files changed, 1 insertion(+), 55 deletions(-) diff --git a/recipes/bioconductor-rsamtools/meta.yaml b/recipes/bioconductor-rsamtools/meta.yaml index ad66540545..de469ba540 100644 --- a/recipes/bioconductor-rsamtools/meta.yaml +++ b/recipes/bioconductor-rsamtools/meta.yaml @@ -3,7 +3,7 @@ package: version: "1.26.1" source: fn: Rsamtools_1.26.1.tar.gz - url: https://bioconductor.org/packages/release/bioc/src/contrib/Rsamtools_1.26.1.tar.gz + url: https://depot.galaxyproject.org/software/bioconductor-rsamtools/bioconductor-rsamtools_1.26.1_src_all.tar.gz md5: 53b695db2aaea899348d7ccea464197e build: diff --git a/recipes/r-ggalt/meta.yaml b/recipes/r-ggalt/meta.yaml index 4c6eb913bc..7ecc8f04c3 100644 --- a/recipes/r-ggalt/meta.yaml +++ b/recipes/r-ggalt/meta.yaml @@ -7,7 +7,6 @@ package: source: fn: ggalt_0.1.1.tar.gz url: - - http://cran.r-project.org/src/contrib/ggalt_0.1.1.tar.gz - http://cran.r-project.org/src/contrib/Archive/ggalt/ggalt_0.1.1.tar.gz build: diff --git a/recipes/r-htmltools/meta.yaml b/recipes/r-htmltools/meta.yaml index e8487a2acb..9b95d9cc20 100644 --- a/recipes/r-htmltools/meta.yaml +++ b/recipes/r-htmltools/meta.yaml @@ -1,35 +1,15 @@ package: name: r-htmltools - # Note that conda versions cannot contain -, so any -'s in the version have - # been replaced with _'s. version: "0.3" source: fn: htmltools_0.3.tar.gz url: - - http://cran.r-project.org/src/contrib/htmltools_0.3.tar.gz - http://cran.r-project.org/src/contrib/Archive/htmltools/htmltools_0.3.tar.gz - - # You can add a hash for the file here, like md5 or sha1 - # md5: 49448ba4863157652311cc5ea4fea3ea - # sha1: 3bcfbee008276084cbb37a2b453963c61176a322 - # patches: - # List any patch files here - # - fix.patch - build: - # If this is a new build for the same version, increment the build - # number. If you do not include this key, it defaults to 0. # number: 1 - # This is required to make R link correctly on Linux. - skip: True # [osx] - rpaths: - - lib/R/lib/ - - lib/ - -# Suggests: markdown, testthat requirements: build: - r-base @@ -45,40 +25,7 @@ test: - $R -e "library('htmltools')" # [not win] - "\"%R%\" -e \"library('htmltools')\"" # [win] - # You can also put a file called run_test.py, run_test.sh, or run_test.bat - # in the recipe that will be run at test time. - - # requires: - # Put any additional test requirements here. - about: home: https://github.com/rstudio/htmltools license: GPL (>= 2) summary: Tools for HTML generation and output. - -# The original CRAN metadata for this package was: - -# Package: htmltools -# Type: Package -# Title: Tools for HTML -# Version: 0.3 -# Date: 2015-12-23 -# Author: RStudio, Inc. -# Maintainer: Joe Cheng -# Description: Tools for HTML generation and output. -# Depends: R (>= 2.14.1) -# Imports: utils, digest -# Suggests: markdown, testthat -# Enhances: knitr -# License: GPL (>= 2) -# URL: https://github.com/rstudio/htmltools -# BugReports: https://github.com/rstudio/htmltools/issues -# RoxygenNote: 5.0.1 -# NeedsCompilation: no -# Packaged: 2015-12-24 01:56:20 UTC; jcheng -# Repository: CRAN -# Date/Publication: 2015-12-29 07:54:49 - -# See -# http://docs.continuum.io/conda/build.html for -# more information about meta.yaml From da3e3939575b29c4fb03a5a36f01b6dd35732a4e Mon Sep 17 00:00:00 2001 From: Bjoern Gruening Date: Tue, 6 Jun 2017 13:38:25 +0200 Subject: [PATCH 071/116] r-fixes --- recipes/footprint/meta.yaml | 2 +- recipes/multigps/0.5/meta.yaml | 2 +- recipes/multigps/0.72/meta.yaml | 2 +- recipes/multigps/0.73/meta.yaml | 2 +- recipes/multigps/0.74/meta.yaml | 2 +- 5 files changed, 5 insertions(+), 5 deletions(-) diff --git a/recipes/footprint/meta.yaml b/recipes/footprint/meta.yaml index a58e96bfec..4cb8c73860 100644 --- a/recipes/footprint/meta.yaml +++ b/recipes/footprint/meta.yaml @@ -5,7 +5,7 @@ package: source: fn: footprint-pipeline-1.0.0.tar.gz url: http://bimsbstatic.mdc-berlin.de/ohler/asli/footprint-pipeline-1.0.0.tar.gz - md5: e040fa1eed06b1e16698bea79257e4b8 + md5: 6c5f0def6dcdaae15c2980d6acdb9d91 build: skip: True # [not linux] diff --git a/recipes/multigps/0.5/meta.yaml b/recipes/multigps/0.5/meta.yaml index c00c7e29da..b2acdfe0a7 100644 --- a/recipes/multigps/0.5/meta.yaml +++ b/recipes/multigps/0.5/meta.yaml @@ -15,7 +15,7 @@ source: requirements: run: - bioconductor-edger - - java-jdk >=7 + - openjdk >=7 - meme test: diff --git a/recipes/multigps/0.72/meta.yaml b/recipes/multigps/0.72/meta.yaml index 4a62b62438..1872bce337 100644 --- a/recipes/multigps/0.72/meta.yaml +++ b/recipes/multigps/0.72/meta.yaml @@ -16,7 +16,7 @@ requirements: run: - r-base - bioconductor-edger - - java-jdk >=8 + - openjdk >=8 - meme test: diff --git a/recipes/multigps/0.73/meta.yaml b/recipes/multigps/0.73/meta.yaml index 938a3349b0..3f366226ff 100644 --- a/recipes/multigps/0.73/meta.yaml +++ b/recipes/multigps/0.73/meta.yaml @@ -16,7 +16,7 @@ requirements: run: - r-base - bioconductor-edger - - java-jdk >=8 + - openjdk >=8 - meme >=4.11.2 test: diff --git a/recipes/multigps/0.74/meta.yaml b/recipes/multigps/0.74/meta.yaml index 4462e07561..082852de89 100644 --- a/recipes/multigps/0.74/meta.yaml +++ b/recipes/multigps/0.74/meta.yaml @@ -18,7 +18,7 @@ requirements: run: - r-base - bioconductor-edger - - java-jdk >=8 + - openjdk >=8 - meme >=4.11.2 test: From e054a6c8f8621041922564c1cfd3783023e6cc68 Mon Sep 17 00:00:00 2001 From: Bjoern Gruening Date: Tue, 6 Jun 2017 14:38:07 +0200 Subject: [PATCH 072/116] r fixes --- recipes/bioconductor-xcms/1.44.0/meta.yaml | 2 ++ recipes/bioconductor-xcms/1.46.0/meta.yaml | 2 ++ recipes/bioconductor-xcms/1.48.0/meta.yaml | 2 ++ recipes/r-maldiquantforeign/meta.yaml | 28 +--------------------------- 4 files changed, 7 insertions(+), 27 deletions(-) diff --git a/recipes/bioconductor-xcms/1.44.0/meta.yaml b/recipes/bioconductor-xcms/1.44.0/meta.yaml index 21e9667ee0..65dbaa230f 100644 --- a/recipes/bioconductor-xcms/1.44.0/meta.yaml +++ b/recipes/bioconductor-xcms/1.44.0/meta.yaml @@ -19,6 +19,7 @@ requirements: - bioconductor-protgenerics - r-base - r-rcolorbrewer + - r-lattice run: - bioconductor-biobase - bioconductor-biocgenerics @@ -26,6 +27,7 @@ requirements: - bioconductor-protgenerics - r-base - r-rcolorbrewer + - r-lattice test: commands: - '$R -e "library(''xcms'')"' diff --git a/recipes/bioconductor-xcms/1.46.0/meta.yaml b/recipes/bioconductor-xcms/1.46.0/meta.yaml index eb276ab3c3..33cb4488a7 100644 --- a/recipes/bioconductor-xcms/1.46.0/meta.yaml +++ b/recipes/bioconductor-xcms/1.46.0/meta.yaml @@ -19,6 +19,7 @@ requirements: - bioconductor-protgenerics - r-base - r-rcolorbrewer + - r-lattice run: - bioconductor-biobase - bioconductor-biocgenerics @@ -26,6 +27,7 @@ requirements: - bioconductor-protgenerics - r-base - r-rcolorbrewer + - r-lattice test: commands: - '$R -e "library(''xcms'')"' diff --git a/recipes/bioconductor-xcms/1.48.0/meta.yaml b/recipes/bioconductor-xcms/1.48.0/meta.yaml index d77045b390..c74d5e8a9c 100644 --- a/recipes/bioconductor-xcms/1.48.0/meta.yaml +++ b/recipes/bioconductor-xcms/1.48.0/meta.yaml @@ -19,6 +19,7 @@ requirements: - bioconductor-protgenerics - r-base - r-rcolorbrewer + - r-lattice run: - bioconductor-biobase - bioconductor-biocgenerics @@ -26,6 +27,7 @@ requirements: - bioconductor-protgenerics - r-base - r-rcolorbrewer + - r-lattice test: commands: - '$R -e "library(''xcms'')"' diff --git a/recipes/r-maldiquantforeign/meta.yaml b/recipes/r-maldiquantforeign/meta.yaml index 9cdffd77d7..f8d71c5e08 100644 --- a/recipes/r-maldiquantforeign/meta.yaml +++ b/recipes/r-maldiquantforeign/meta.yaml @@ -5,6 +5,7 @@ package: source: fn: MALDIquantForeign_0.10.tar.gz url: + - https://cran.r-project.org/src/contrib/MALDIquantForeign_0.10.tar.gz - http://cran.r-project.org/src/contrib/Archive/MALDIquantForeign/MALDIquantForeign_0.10.tar.gz sha256: 2356bdc2437c147614c1398c391e3ce21b5970b146ddcd837f7c0c3178dd34c0 @@ -57,30 +58,3 @@ about: 7.5, CDF, mMass MSD) and writing (tab, csv, mMass MSD, mzML, imzML) different file formats of mass spectrometry data into/from MALDIquant objects. -# The original CRAN metadata for this package was: - -# Package: MALDIquantForeign -# Version: 0.10 -# Date: 2015-10-31 -# Title: Import/Export Routines for MALDIquant -# Authors@R: c(person("Sebastian", "Gibb", role=c("aut", "cre"), email="mail@sebastiangibb.de"), person("Pietro", "Franceschi", role=c("ctb"), email="pietro.franceschi@fmach.it")) -# Depends: R (>= 3.2.2), methods, MALDIquant (>= 1.11.7) -# Imports: base64enc, digest, readBrukerFlexData (>= 1.7), readMzXmlData (>= 2.7), XML -# Suggests: knitr, testthat (>= 0.8), RNetCDF (>= 1.6.1) -# Description: Functions for reading (tab, csv, Bruker fid, Ciphergen XML, mzXML, mzML, imzML, Analyze 7.5, CDF, mMass MSD) and writing (tab, csv, mMass MSD, mzML, imzML) different file formats of mass spectrometry data into/from MALDIquant objects. -# License: GPL (>= 3) -# URL: http://strimmerlab.org/software/maldiquant/ https://github.com/sgibb/MALDIquantForeign/ -# BugReports: https://github.com/sgibb/MALDIquantForeign/issues/ -# LazyLoad: yes -# VignetteBuilder: knitr -# RoxygenNote: 5.0.0.9000 -# NeedsCompilation: no -# Packaged: 2015-10-31 19:41:48 UTC; sebastian -# Author: Sebastian Gibb [aut, cre], Pietro Franceschi [ctb] -# Maintainer: Sebastian Gibb -# Repository: CRAN -# Date/Publication: 2015-11-01 00:36:34 - -# See -# http://docs.continuum.io/conda/build.html for -# more information about meta.yaml From e55adf5411d2dbfcad64ffbae20d7baf49af96f6 Mon Sep 17 00:00:00 2001 From: Bjoern Gruening Date: Tue, 6 Jun 2017 14:38:18 +0200 Subject: [PATCH 073/116] rpy --- recipes/rpy2/meta.yaml | 13 +++---------- 1 file changed, 3 insertions(+), 10 deletions(-) diff --git a/recipes/rpy2/meta.yaml b/recipes/rpy2/meta.yaml index 8d2cd57a49..7bcffc0a6f 100644 --- a/recipes/rpy2/meta.yaml +++ b/recipes/rpy2/meta.yaml @@ -6,34 +6,31 @@ source: fn: rpy2-2.7.8.tar.gz url: https://pypi.python.org/packages/source/r/rpy2/rpy2-2.7.8.tar.gz md5: 56ca162bca76bb9c3f935f099c916196 -# patches: - # List any patch files here - # - fix.patch build: rpaths: - lib/R/lib/ - lib/ skip: False - number: 1 + number: 0 requirements: build: - python - r-base - setuptools - - argparse # [py26] - singledispatch # [not (py34 or py35)] - six - readline + - bzip2 run: - python - r-base - - argparse # [py26] - singledispatch # [not (py34 or py35)] - six - readline + - bzip2 test: # Python imports @@ -48,7 +45,3 @@ about: home: http://rpy.sourceforge.net license: GNU General Public License v2 or later (GPLv2+) summary: 'Python interface to the R language (embedded R)' - -# See -# http://docs.continuum.io/conda/build.html for -# more information about meta.yaml From f4f9fe8c3a591befe374064248290f3ed9b88bb7 Mon Sep 17 00:00:00 2001 From: Bjoern Gruening Date: Tue, 6 Jun 2017 14:41:20 +0200 Subject: [PATCH 074/116] r fixes --- recipes/bioconductor-genomicalignments/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/bioconductor-genomicalignments/meta.yaml b/recipes/bioconductor-genomicalignments/meta.yaml index 8ab1488454..2c00916321 100644 --- a/recipes/bioconductor-genomicalignments/meta.yaml +++ b/recipes/bioconductor-genomicalignments/meta.yaml @@ -4,7 +4,7 @@ package: source: fn: GenomicAlignments_1.10.0.tar.gz - url: https://bioconductor.org/packages/release/bioc/src/contrib/GenomicAlignments_1.10.0.tar.gz + url: https://depot.galaxyproject.org/software/bioconductor-genomicalignments/bioconductor-genomicalignments_1.10.0_src_all.tar.gz md5: 6e6af96adcad077abdb5889e5620cd6a build: From 1ed517571bac934b393ffc15efe74929e10cb17f Mon Sep 17 00:00:00 2001 From: Mattias Date: Tue, 6 Jun 2017 15:09:26 +0200 Subject: [PATCH 075/116] Minor formatting --- recipes/r-microseq/meta.yaml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/recipes/r-microseq/meta.yaml b/recipes/r-microseq/meta.yaml index fe7e79401c..7a5acacb57 100644 --- a/recipes/r-microseq/meta.yaml +++ b/recipes/r-microseq/meta.yaml @@ -33,7 +33,8 @@ requirements: run: - r-base - - r-rcpp >=0.11.1{indent}libgcc + - r-rcpp >=0.11.1 + - libgcc test: commands: From cd4ed38b7d509d67f08b7286e4a88e33bb24c2ce Mon Sep 17 00:00:00 2001 From: Ryan Dale Date: Tue, 6 Jun 2017 11:27:02 -0400 Subject: [PATCH 076/116] add readline to some failing R packages --- recipes/r-htmltools/meta.yaml | 1 + recipes/r-ks/meta.yaml | 1 + recipes/r-maldiquantforeign/meta.yaml | 1 + recipes/r-mixomics/meta.yaml | 1 + 4 files changed, 4 insertions(+) diff --git a/recipes/r-htmltools/meta.yaml b/recipes/r-htmltools/meta.yaml index 9b95d9cc20..91357332d7 100644 --- a/recipes/r-htmltools/meta.yaml +++ b/recipes/r-htmltools/meta.yaml @@ -18,6 +18,7 @@ requirements: run: - r-base - r-digest + - readline test: commands: diff --git a/recipes/r-ks/meta.yaml b/recipes/r-ks/meta.yaml index 15b6ed5e34..ccbfcbe471 100644 --- a/recipes/r-ks/meta.yaml +++ b/recipes/r-ks/meta.yaml @@ -38,6 +38,7 @@ requirements: - r-mvtnorm >=1.0_0 - r-rgl >=0.66 - libglu # [linux] + - readline test: commands: diff --git a/recipes/r-maldiquantforeign/meta.yaml b/recipes/r-maldiquantforeign/meta.yaml index f8d71c5e08..2d28ab8403 100644 --- a/recipes/r-maldiquantforeign/meta.yaml +++ b/recipes/r-maldiquantforeign/meta.yaml @@ -38,6 +38,7 @@ requirements: - r-digest - r-readbrukerflexdata >=1.7 - r-readmzxmldata >=2.7 + - readline test: commands: diff --git a/recipes/r-mixomics/meta.yaml b/recipes/r-mixomics/meta.yaml index 0f32c79201..b800f47431 100644 --- a/recipes/r-mixomics/meta.yaml +++ b/recipes/r-mixomics/meta.yaml @@ -47,6 +47,7 @@ requirements: - r-rgl - r-tidyr - libglu # [linux] + - readline test: commands: From 305a2119f8988d18ceef47fee0d2c95073cac09a Mon Sep 17 00:00:00 2001 From: Bjoern Gruening Date: Tue, 6 Jun 2017 21:47:38 +0200 Subject: [PATCH 077/116] remove old recipe --- recipes/bioconductor-deseq2/1.10.1/build.sh | 17 --------- recipes/bioconductor-deseq2/1.10.1/meta.yaml | 54 ---------------------------- 2 files changed, 71 deletions(-) delete mode 100644 recipes/bioconductor-deseq2/1.10.1/build.sh delete mode 100644 recipes/bioconductor-deseq2/1.10.1/meta.yaml diff --git a/recipes/bioconductor-deseq2/1.10.1/build.sh b/recipes/bioconductor-deseq2/1.10.1/build.sh deleted file mode 100644 index 6c7a1726e3..0000000000 --- a/recipes/bioconductor-deseq2/1.10.1/build.sh +++ /dev/null @@ -1,17 +0,0 @@ - -#!/bin/bash - -# R refuses to build packages that mark themselves as -# "Priority: Recommended" -mv DESCRIPTION DESCRIPTION.old -grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION -# -$R CMD INSTALL --build . -# -# # Add more build steps here, if they are necessary. -# -# See -# http://docs.continuum.io/conda/build.html -# for a list of environment variables that are set during the build -# process. -# \ No newline at end of file diff --git a/recipes/bioconductor-deseq2/1.10.1/meta.yaml b/recipes/bioconductor-deseq2/1.10.1/meta.yaml deleted file mode 100644 index af621a1bd9..0000000000 --- a/recipes/bioconductor-deseq2/1.10.1/meta.yaml +++ /dev/null @@ -1,54 +0,0 @@ -package: - name: bioconductor-deseq2 - version: 1.10.1 -source: - fn: DESeq2_1.10.1.tar.gz - url: http://bioconductor.org/packages/release/bioc/src/contrib/DESeq2_1.10.1.tar.gz - md5: 2a92d5c7f9e38d26c629aa6a558b76de -build: - number: 0 - rpaths: - - lib/R/lib/ - - lib/ -requirements: - build: - - bioconductor-biobase - - 'bioconductor-biocgenerics >=0.7.5' - - bioconductor-biocparallel - - bioconductor-genefilter - - bioconductor-geneplotter - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-s4vectors - - 'bioconductor-summarizedexperiment >=0.2.0' - - r-base - - r-ggplot2 - - r-hmisc - - r-locfit - - 'r-rcpp >=0.10.1' - - 'r-rcpparmadillo >=0.3.4.4' - run: - - bioconductor-biobase - - 'bioconductor-biocgenerics >=0.7.5' - - bioconductor-biocparallel - - bioconductor-genefilter - - bioconductor-geneplotter - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-s4vectors - - 'bioconductor-summarizedexperiment >=0.2.0' - - r-base - - r-ggplot2 - - r-hmisc - - r-locfit - - 'r-rcpp >=0.10.1' - - 'r-rcpparmadillo >=0.3.4.4' -test: - commands: - - '$R -e "library(''DESeq2'')"' -about: - home: http://bioconductor.org/packages/release/bioc/html/DESeq2.html - license: 'LGPL (>= 3)' - summary: 'Estimate variance-mean dependence in count data from high-throughput sequencing - assays and test for differential expression based on a model using the negative - binomial distribution.' From b4d84a4ef78457f3adbf958ca6441093843fca0a Mon Sep 17 00:00:00 2001 From: Mattias Date: Tue, 6 Jun 2017 21:54:20 +0200 Subject: [PATCH 078/116] Remove micropan from this branch --- recipes/r-micropan/build.sh | 13 -------- recipes/r-micropan/meta.yaml | 72 -------------------------------------------- 2 files changed, 85 deletions(-) delete mode 100644 recipes/r-micropan/build.sh delete mode 100644 recipes/r-micropan/meta.yaml diff --git a/recipes/r-micropan/build.sh b/recipes/r-micropan/build.sh deleted file mode 100644 index 0c37df6e8e..0000000000 --- a/recipes/r-micropan/build.sh +++ /dev/null @@ -1,13 +0,0 @@ -#!/bin/bash - -# R refuses to build packages that mark themselves as Priority: Recommended -mv DESCRIPTION DESCRIPTION.old -grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION - -$R CMD INSTALL --build . - -# Add more build steps here, if they are necessary. - -# See -# http://docs.continuum.io/conda/build.html -# for a list of environment variables that are set during the build process. diff --git a/recipes/r-micropan/meta.yaml b/recipes/r-micropan/meta.yaml deleted file mode 100644 index fe332a4e0c..0000000000 --- a/recipes/r-micropan/meta.yaml +++ /dev/null @@ -1,72 +0,0 @@ -{% set version = '1.1.2' %} - -{% set posix = 'm2-' if win else '' %} -{% set native = 'm2w64-' if win else '' %} - -package: - name: r-micropan - version: {{ version|replace("-", "_") }} - -source: - fn: micropan_{{ version }}.tar.gz - url: - - https://cran.r-project.org/src/contrib/micropan_{{ version }}.tar.gz - - https://cran.r-project.org/src/contrib/Archive/micropan/micropan_{{ version }}.tar.gz - - - sha256: efb4491b04f781a99fb9180689b7788618800618c3433a8af897ee926f556a67 - -build: - number: 0 - - # This is required to make R link correctly on Linux. - rpaths: - - lib/R/lib/ - - lib/ - - -requirements: - build: - - r-base - - r-igraph - - r-microseq - - run: - - r-base - - r-igraph - - r-microseq - -test: - commands: - - $R -e "library('micropan')" # [not win] - - "\"%R%\" -e \"library('micropan')\"" # [win] - -about: - home: https://CRAN.R-project.org/package=micropan - license: GPL-2 - summary: A collection of functions for computations and visualizations of microbial pan-genomes. - license_family: GPL2 - -# The original CRAN metadata for this package was: - -# Package: micropan -# Type: Package -# Title: Microbial Pan-Genome Analysis -# Version: 1.1.2 -# Date: 2017-01-17 -# Author: Lars Snipen and Kristian Hovde Liland -# Maintainer: Lars Snipen -# Description: A collection of functions for computations and visualizations of microbial pan-genomes. -# Depends: R (>= 3.3.1), igraph, microseq -# License: GPL-2 -# LazyData: FALSE -# ZipData: TRUE -# RoxygenNote: 5.0.1 -# NeedsCompilation: no -# Packaged: 2017-01-17 13:08:57 UTC; larssn -# Repository: CRAN -# Date/Publication: 2017-01-17 19:41:22 - -# See -# http://docs.continuum.io/conda/build.html for -# more information about meta.yaml From 942728462da6e8c56ed417453bc8a9aaf6668ee9 Mon Sep 17 00:00:00 2001 From: Bjoern Gruening Date: Tue, 6 Jun 2017 21:57:36 +0200 Subject: [PATCH 079/116] remove libffi --- recipes/libffi/3.0.13/build.sh | 5 ----- recipes/libffi/3.0.13/meta.yaml | 14 -------------- recipes/libffi/build.sh | 10 ---------- recipes/libffi/meta.yaml | 14 -------------- 4 files changed, 43 deletions(-) delete mode 100644 recipes/libffi/3.0.13/build.sh delete mode 100644 recipes/libffi/3.0.13/meta.yaml delete mode 100644 recipes/libffi/build.sh delete mode 100644 recipes/libffi/meta.yaml diff --git a/recipes/libffi/3.0.13/build.sh b/recipes/libffi/3.0.13/build.sh deleted file mode 100644 index 652105112b..0000000000 --- a/recipes/libffi/3.0.13/build.sh +++ /dev/null @@ -1,5 +0,0 @@ -#!/bin/bash - -./configure --prefix=$PREFIX -make -make install \ No newline at end of file diff --git a/recipes/libffi/3.0.13/meta.yaml b/recipes/libffi/3.0.13/meta.yaml deleted file mode 100644 index ee5db5038f..0000000000 --- a/recipes/libffi/3.0.13/meta.yaml +++ /dev/null @@ -1,14 +0,0 @@ -about: - home: 'https://sourceware.org/libffi/' - license: "https://raw.githubusercontent.com/atgreen/libffi/master/LICENSE" - summary: "libffi" -build: - number: 1 - skip: True # [not osx] -package: - name: libffi - version: '3.0.13' -source: - fn: libffi-3.0.13.tar.gz # [osx] - md5: 45f3b6dbc9ee7c7dfbbbc5feba571529 # [osx] - url: ftp://sourceware.org/pub/libffi/libffi-3.0.13.tar.gz # [osx] \ No newline at end of file diff --git a/recipes/libffi/build.sh b/recipes/libffi/build.sh deleted file mode 100644 index 343e88b800..0000000000 --- a/recipes/libffi/build.sh +++ /dev/null @@ -1,10 +0,0 @@ -#!/bin/bash - -./configure --prefix=$PREFIX -make -make install - -# Put headers in regular location -mkdir -p "${PREFIX}/include/" -mv "${PREFIX}"/lib/"${PKG_NAME}"-"${PKG_VERSION}"/include/*.h "${PREFIX}/include/" -rm -rf "${PREFIX}/lib/${PKG_NAME}-${PKG_VERSION}" diff --git a/recipes/libffi/meta.yaml b/recipes/libffi/meta.yaml deleted file mode 100644 index 55098b8473..0000000000 --- a/recipes/libffi/meta.yaml +++ /dev/null @@ -1,14 +0,0 @@ -about: - home: 'https://sourceware.org/libffi/' - license: "https://raw.githubusercontent.com/atgreen/libffi/master/LICENSE" - summary: "A Portable Foreign Function Interface Library" -build: - number: 1 - skip: True # [not osx] -package: - name: libffi - version: '3.2.1' -source: - fn: libffi-3.2.1.tar.gz # [osx] - url: ftp://sourceware.org/pub/libffi/libffi-3.2.1.tar.gz # [osx] - sha256: d06ebb8e1d9a22d19e38d63fdb83954253f39bedc5d46232a05645685722ca37 # [osx] \ No newline at end of file From ddfa916392adbd2e8de4ff3c9ca5bae01fac83b6 Mon Sep 17 00:00:00 2001 From: Bjoern Gruening Date: Tue, 6 Jun 2017 22:13:08 +0200 Subject: [PATCH 080/116] remove old recipe --- recipes/poretools/0.5.0/build.sh | 3 --- recipes/poretools/0.5.0/meta.yaml | 36 ------------------------------------ 2 files changed, 39 deletions(-) delete mode 100644 recipes/poretools/0.5.0/build.sh delete mode 100644 recipes/poretools/0.5.0/meta.yaml diff --git a/recipes/poretools/0.5.0/build.sh b/recipes/poretools/0.5.0/build.sh deleted file mode 100644 index 8e25a1455f..0000000000 --- a/recipes/poretools/0.5.0/build.sh +++ /dev/null @@ -1,3 +0,0 @@ -#!/bin/bash - -$PYTHON setup.py install diff --git a/recipes/poretools/0.5.0/meta.yaml b/recipes/poretools/0.5.0/meta.yaml deleted file mode 100644 index 362359ca3e..0000000000 --- a/recipes/poretools/0.5.0/meta.yaml +++ /dev/null @@ -1,36 +0,0 @@ -package: - name: poretools - version: "0.5.0" - -source: - fn: poretools_v0.5.0.tar.gz - url: https://github.com/arq5x/poretools/archive/v0.5.0.tar.gz - md5: c647561ea603e84bca14fdf56a5c962f - -build: - skip: True # [not py27] - -requirements: - build: - - python - - rpy2 >=2.4.2 - - h5py >=2.0 - - watchdog >=0.8.3 - run: - - python - - hdf5 >=1.8.7 - - r-base - - rpy2 >=2.4.2 - - h5py >=2.0 - - watchdog >=0.8.3 - - qcli >=0.1.1 - - r-ggplot2 - -test: - commands: - - poretools -v - -about: - home: http://poretools.readthedocs.org - summary: "poretools: a toolkit for working with nanopore sequencing data from Oxford Nanopore" - license: GPL From ede415321ae5b96410e743491fc5cb14325fabff Mon Sep 17 00:00:00 2001 From: Bjoern Gruening Date: Tue, 6 Jun 2017 22:17:57 +0200 Subject: [PATCH 081/116] r fixes --- recipes/bioconductor-alpine/meta.yaml | 2 +- recipes/bioconductor-bsgenome/meta.yaml | 2 +- recipes/bioconductor-chipseeker/meta.yaml | 3 +++ recipes/bioconductor-deseq2/meta.yaml | 2 +- recipes/bioconductor-ensembldb/meta.yaml | 2 +- recipes/bioconductor-mosaics/meta.yaml | 2 ++ recipes/bioconductor-qdnaseq.mm10/1.4.0/meta.yaml | 2 +- 7 files changed, 10 insertions(+), 5 deletions(-) diff --git a/recipes/bioconductor-alpine/meta.yaml b/recipes/bioconductor-alpine/meta.yaml index d1dc5e111b..6ad9e4db82 100644 --- a/recipes/bioconductor-alpine/meta.yaml +++ b/recipes/bioconductor-alpine/meta.yaml @@ -3,7 +3,7 @@ package: version: 1.0.0 source: fn: alpine_1.0.0.tar.gz - url: http://bioconductor.org/packages/release/bioc/src/contrib/alpine_1.0.0.tar.gz + url: https://depot.galaxyproject.org/software/bioconductor-alpine/bioconductor-alpine_1.0.0_src_all.tar.gz md5: f70ca32c5336aca7745ee3875bbbf28f build: number: 0 diff --git a/recipes/bioconductor-bsgenome/meta.yaml b/recipes/bioconductor-bsgenome/meta.yaml index 3dd71fe177..d662f0951e 100644 --- a/recipes/bioconductor-bsgenome/meta.yaml +++ b/recipes/bioconductor-bsgenome/meta.yaml @@ -4,7 +4,7 @@ package: source: fn: BSgenome_1.42.0.tar.gz - url: https://bioconductor.org/packages/release/bioc/src/contrib/BSgenome_1.42.0.tar.gz + url: https://depot.galaxyproject.org/software/bioconductor-bsgenome/bioconductor-bsgenome_1.42.0_src_all.tar.gz md5: ee6db342fe767fc8092ce88c0d5d15cc build: diff --git a/recipes/bioconductor-chipseeker/meta.yaml b/recipes/bioconductor-chipseeker/meta.yaml index 67021afd08..45648687db 100644 --- a/recipes/bioconductor-chipseeker/meta.yaml +++ b/recipes/bioconductor-chipseeker/meta.yaml @@ -32,6 +32,7 @@ requirements: - r-plotrix - r-rcolorbrewer - r-upsetr + - r-boot run: - bioconductor-annotationdbi - bioconductor-biocgenerics @@ -53,6 +54,8 @@ requirements: - r-plotrix - r-rcolorbrewer - r-upsetr + - r-boot + test: commands: - '$R -e "library(''ChIPseeker'')"' diff --git a/recipes/bioconductor-deseq2/meta.yaml b/recipes/bioconductor-deseq2/meta.yaml index 1c9293e01b..6d9835f3a8 100644 --- a/recipes/bioconductor-deseq2/meta.yaml +++ b/recipes/bioconductor-deseq2/meta.yaml @@ -2,7 +2,7 @@ package: name: bioconductor-deseq2 version: 1.14.1 source: - url: https://bioconductor.org/packages/release/bioc/src/contrib/DESeq2_1.14.1.tar.gz + url: https://depot.galaxyproject.org/software/bioconductor-deseq2/bioconductor-deseq2_1.14.1_src_all.tar.gz md5: d1c433056295927a6700046e282bcccd build: number: 0 diff --git a/recipes/bioconductor-ensembldb/meta.yaml b/recipes/bioconductor-ensembldb/meta.yaml index 749ee812fd..0c3db975bd 100644 --- a/recipes/bioconductor-ensembldb/meta.yaml +++ b/recipes/bioconductor-ensembldb/meta.yaml @@ -3,7 +3,7 @@ package: version: 1.6.0 source: fn: ensembldb_1.6.0.tar.gz - url: http://bioconductor.org/packages/release/bioc/src/contrib/ensembldb_1.6.0.tar.gz + url: https://depot.galaxyproject.org/software/bioconductor-ensembldb/bioconductor-ensembldb_1.6.0_src_all.tar.gz md5: 731f44b5af42a5b32bb7863f27ac5dc7 build: number: 0 diff --git a/recipes/bioconductor-mosaics/meta.yaml b/recipes/bioconductor-mosaics/meta.yaml index 80936128e0..83c2fe0092 100644 --- a/recipes/bioconductor-mosaics/meta.yaml +++ b/recipes/bioconductor-mosaics/meta.yaml @@ -21,6 +21,7 @@ requirements: - bioconductor-iranges - bioconductor-rsamtools - bioconductor-s4vectors + - r-mass - r-base - r-rcpp - gcc # [linux] @@ -33,6 +34,7 @@ requirements: - bioconductor-rsamtools - bioconductor-s4vectors - r-base + - r-mass - r-rcpp - libgcc # [linux] diff --git a/recipes/bioconductor-qdnaseq.mm10/1.4.0/meta.yaml b/recipes/bioconductor-qdnaseq.mm10/1.4.0/meta.yaml index 46f9920a49..34bd8292ed 100644 --- a/recipes/bioconductor-qdnaseq.mm10/1.4.0/meta.yaml +++ b/recipes/bioconductor-qdnaseq.mm10/1.4.0/meta.yaml @@ -3,7 +3,7 @@ package: version: 1.4.0 source: fn: QDNAseq.mm10_1.4.0.tar.gz - url: http://bioconductor.org/packages/release/data/experiment/src/contrib/QDNAseq.mm10_1.4.0.tar.gz + url: https://bioconductor.org/packages/3.4/data/experiment/src/contrib/QDNAseq.mm10_1.4.0.tar.gz md5: d5e08fe75728f32ffb64c907e8ac0a68 build: number: 0 From dd754a3dab6d276507f09458d4fc8e7bfbffbdbf Mon Sep 17 00:00:00 2001 From: Bjoern Gruening Date: Tue, 6 Jun 2017 22:19:39 +0200 Subject: [PATCH 082/116] pin rpy to conda-forge version --- recipes/kobas/meta.yaml | 2 +- recipes/lefse/meta.yaml | 2 +- recipes/mgkit/meta.yaml | 4 ++-- recipes/nanoraw/0.3.1/meta.yaml | 4 ++-- recipes/nanoraw/meta.yaml | 4 ++-- recipes/triform2/meta.yaml | 4 ++-- 6 files changed, 10 insertions(+), 10 deletions(-) diff --git a/recipes/kobas/meta.yaml b/recipes/kobas/meta.yaml index e431726b84..488f7484be 100644 --- a/recipes/kobas/meta.yaml +++ b/recipes/kobas/meta.yaml @@ -26,7 +26,7 @@ requirements: - biopython - sqlite - r-base - - rpy2 + - rpy2 >=2.8.5 test: imports: diff --git a/recipes/lefse/meta.yaml b/recipes/lefse/meta.yaml index 1b8e2ce282..22c98b8bb5 100644 --- a/recipes/lefse/meta.yaml +++ b/recipes/lefse/meta.yaml @@ -21,7 +21,7 @@ requirements: - r-modeltools - r-coin - r-mass - - rpy2 >=2.1 + - rpy2 >=2.8.5 - numpy - matplotlib >=1.0 - argparse [py26] diff --git a/recipes/mgkit/meta.yaml b/recipes/mgkit/meta.yaml index 6719760be9..dcd6b4055d 100644 --- a/recipes/mgkit/meta.yaml +++ b/recipes/mgkit/meta.yaml @@ -42,7 +42,7 @@ requirements: - pymongo >=3.1.1 - r-base - htseq >=0.6.0 - - rpy2 >=2.3.8 + - rpy2 >=2.8.5 - enum34 run: @@ -57,7 +57,7 @@ requirements: - pymongo >=3.1.1 - r-base - htseq >=0.6.0 - - rpy2 >=2.3.8 + - rpy2 >=2.8.5 - enum34 test: diff --git a/recipes/nanoraw/0.3.1/meta.yaml b/recipes/nanoraw/0.3.1/meta.yaml index cea5d7fa2d..64e9082ff0 100644 --- a/recipes/nanoraw/0.3.1/meta.yaml +++ b/recipes/nanoraw/0.3.1/meta.yaml @@ -18,7 +18,7 @@ requirements: - python - setuptools - h5py - - rpy2 + - rpy2 >=2.4.2 - numpy - scipy - r-base @@ -27,7 +27,7 @@ requirements: run: - python - h5py - - rpy2 + - rpy2 >=2.4.2 - numpy - scipy - r-base diff --git a/recipes/nanoraw/meta.yaml b/recipes/nanoraw/meta.yaml index b45393ac6d..171c2b9b63 100644 --- a/recipes/nanoraw/meta.yaml +++ b/recipes/nanoraw/meta.yaml @@ -21,7 +21,7 @@ requirements: - python - setuptools - h5py - - rpy2 + - rpy2 >=2.4.2 - numpy - scipy - r-base @@ -30,7 +30,7 @@ requirements: run: - python - h5py - - rpy2 + - rpy2 >=2.4.2 - numpy - scipy - r-base diff --git a/recipes/triform2/meta.yaml b/recipes/triform2/meta.yaml index 69ae990505..f6d4f52d43 100644 --- a/recipes/triform2/meta.yaml +++ b/recipes/triform2/meta.yaml @@ -20,7 +20,7 @@ requirements: - numpy - natsort - joblib - - rpy2 + - rpy2 >=2.4.2 - bioconductor-iranges - bioconductor-biocgenerics - bioconductor-genomicranges @@ -35,7 +35,7 @@ requirements: - numpy - natsort - joblib - - rpy2 + - rpy2 >=2.4.2 - bioconductor-iranges - bioconductor-biocgenerics - bioconductor-genomicranges From f725875017473b1b9a1384dd02d7cc3df54aff87 Mon Sep 17 00:00:00 2001 From: Mattias Date: Tue, 6 Jun 2017 22:44:09 +0200 Subject: [PATCH 083/116] Apply comments bgruening --- recipes/r-microseq/build.sh | 6 ------ recipes/r-microseq/meta.yaml | 30 +++--------------------------- 2 files changed, 3 insertions(+), 33 deletions(-) diff --git a/recipes/r-microseq/build.sh b/recipes/r-microseq/build.sh index 0c37df6e8e..81250b8ff4 100644 --- a/recipes/r-microseq/build.sh +++ b/recipes/r-microseq/build.sh @@ -5,9 +5,3 @@ mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION $R CMD INSTALL --build . - -# Add more build steps here, if they are necessary. - -# See -# http://docs.continuum.io/conda/build.html -# for a list of environment variables that are set during the build process. diff --git a/recipes/r-microseq/meta.yaml b/recipes/r-microseq/meta.yaml index 7a5acacb57..bc8f8e84f6 100644 --- a/recipes/r-microseq/meta.yaml +++ b/recipes/r-microseq/meta.yaml @@ -32,9 +32,9 @@ requirements: - gcc run: - - r-base - - r-rcpp >=0.11.1 - - libgcc + - r-base # [linux] + - r-rcpp >=0.11.1 # [linux] + - libgcc # [linux] test: commands: @@ -45,27 +45,3 @@ about: license: GPL-2 summary: Basic functions for microbial sequence data analysis. license_family: GPL2 - -# The original CRAN metadata for this package was: - -# Package: microseq -# Type: Package -# Title: Basic Biological Sequence Analysis -# Version: 1.2 -# Date: 2017-01-13 -# Author: Lars Snipen, Kristian Hovde Liland -# Maintainer: Lars Snipen -# Description: Basic functions for microbial sequence data analysis. -# License: GPL-2 -# Depends: R (>= 3.3.1) -# Imports: Rcpp (>= 0.11.1) -# LinkingTo: Rcpp (>= 0.11.1) -# RoxygenNote: 5.0.1 -# NeedsCompilation: yes -# Packaged: 2017-01-13 11:28:56 UTC; larssn -# Repository: CRAN -# Date/Publication: 2017-01-13 15:40:55 - -# See -# http://docs.continuum.io/conda/build.html for -# more information about meta.yaml From c2e4f48902aa507368b65081863066d471a38502 Mon Sep 17 00:00:00 2001 From: Bjoern Gruening Date: Wed, 7 Jun 2017 09:08:42 +0200 Subject: [PATCH 084/116] r fixes --- recipes/bioconductor-ensembldb/meta.yaml | 2 +- recipes/bioconductor-minfi/meta.yaml | 2 ++ recipes/bioconductor-motifrg/meta.yaml | 2 +- recipes/bioconductor-repitools/meta.yaml | 2 +- recipes/r-ggally/meta.yaml | 45 +------------------------------- 5 files changed, 6 insertions(+), 47 deletions(-) diff --git a/recipes/bioconductor-ensembldb/meta.yaml b/recipes/bioconductor-ensembldb/meta.yaml index 0c3db975bd..4fa1fd2236 100644 --- a/recipes/bioconductor-ensembldb/meta.yaml +++ b/recipes/bioconductor-ensembldb/meta.yaml @@ -4,7 +4,7 @@ package: source: fn: ensembldb_1.6.0.tar.gz url: https://depot.galaxyproject.org/software/bioconductor-ensembldb/bioconductor-ensembldb_1.6.0_src_all.tar.gz - md5: 731f44b5af42a5b32bb7863f27ac5dc7 + md5: b0d4cfb9b094e21fc6582eed126d0ca6 build: number: 0 rpaths: diff --git a/recipes/bioconductor-minfi/meta.yaml b/recipes/bioconductor-minfi/meta.yaml index 67d1182058..d53e62704c 100644 --- a/recipes/bioconductor-minfi/meta.yaml +++ b/recipes/bioconductor-minfi/meta.yaml @@ -36,6 +36,7 @@ requirements: - r-quadprog - r-rcolorbrewer - r-reshape + - r-nlme run: - 'bioconductor-biobase >=2.17.8' - 'bioconductor-biocgenerics >=0.15.3' @@ -61,6 +62,7 @@ requirements: - r-quadprog - r-rcolorbrewer - r-reshape + - r-nlme test: commands: - '$R -e "library(''minfi'')"' diff --git a/recipes/bioconductor-motifrg/meta.yaml b/recipes/bioconductor-motifrg/meta.yaml index c3f74baa15..15f683df76 100644 --- a/recipes/bioconductor-motifrg/meta.yaml +++ b/recipes/bioconductor-motifrg/meta.yaml @@ -4,7 +4,7 @@ package: source: fn: motifRG_1.18.0.tar.gz - url: https://bioconductor.org/packages/release/bioc/src/contrib/motifRG_1.18.0.tar.gz + url: https://depot.galaxyproject.org/software/bioconductor-motifrg/bioconductor-motifrg_1.18.0_src_all.tar.gz md5: 2f1dab8afccdc3077109dcb514945f3b build: diff --git a/recipes/bioconductor-repitools/meta.yaml b/recipes/bioconductor-repitools/meta.yaml index d4ad6a9ae7..17edec8b8d 100644 --- a/recipes/bioconductor-repitools/meta.yaml +++ b/recipes/bioconductor-repitools/meta.yaml @@ -3,7 +3,7 @@ package: version: 1.20.0 source: fn: Repitools_1.20.0.tar.gz - url: http://bioconductor.org/packages/release/bioc/src/contrib/Repitools_1.20.0.tar.gz + url: https://depot.galaxyproject.org/software/bioconductor-repitools/bioconductor-repitools_1.20.0_src_all.tar.gz md5: 3f27f4e075425ed0b3a9bb47bcaf8aaf build: number: 0 diff --git a/recipes/r-ggally/meta.yaml b/recipes/r-ggally/meta.yaml index dd8e6e01a6..863cfbe358 100644 --- a/recipes/r-ggally/meta.yaml +++ b/recipes/r-ggally/meta.yaml @@ -7,28 +7,19 @@ package: source: fn: GGally_1.3.0.tar.gz url: + - https://cran.r-project.org/src/contrib/GGally_1.3.0.tar.gz - http://cran.r-project.org/src/contrib/Archive/GGally/GGally_1.3.0.tar.gz sha256: 6bdccc90a2cb6d363e5646ecae3b62db475a8560a333b3d661c98166c152ad89 - - # You can add a hash for the file here, like md5 or sha1 - # md5: 49448ba4863157652311cc5ea4fea3ea - # sha1: 3bcfbee008276084cbb37a2b453963c61176a322 - # patches: - # List any patch files here - # - fix.patch - build: # If this is a new build for the same version, increment the build # number. If you do not include this key, it defaults to 0. # number: 1 - # This is required to make R link correctly on Linux. rpaths: - lib/R/lib/ - lib/ -# Suggests: broom (>= 0.4.0), chemometrics, geosphere (>= 1.5-1), igraph (>= 1.0.1), intergraph (>= 2.0-2), maps (>= 3.1.0), mapproj, network (>= 1.12.0), scagnostics, scales (>= 0.4.0), sna (>= 2.3-2), survival, packagedocs (>= 0.4.0), rmarkdown, roxygen2, testthat requirements: build: - r-base @@ -54,11 +45,6 @@ test: - $R -e "library('GGally')" # [not win] - "\"%R%\" -e \"library('GGally')\"" # [win] - # You can also put a file called run_test.py, run_test.sh, or run_test.bat - # in the recipe that will be run at test time. - - # requires: - # Put any additional test requirements here. about: home: https://ggobi.github.io/ggally, https://github.com/ggobi/ggally @@ -70,32 +56,3 @@ about: plot, a survival plot, and several functions to plot networks.' license_family: GPL3 - -# The original CRAN metadata for this package was: - -# Package: GGally -# Version: 1.3.0 -# License: GPL (>= 2.0) -# Title: Extension to 'ggplot2' -# Type: Package -# LazyLoad: yes -# LazyData: true -# URL: https://ggobi.github.io/ggally, https://github.com/ggobi/ggally -# BugReports: https://github.com/ggobi/ggally/issues -# Authors@R: c( person("Barret", "Schloerke", role = c("aut", "cre"), email = "schloerke@gmail.com", comment = "author for ggpairs, ggduo, ggnostic, ggts, ggfacet, and ggally_*. Contributor for all functions."), person("Jason", "Crowley", role = "aut", email = "crowley.jason.s@gmail.com", comment = "ggparcoord"), person("Di", "Cook", role = c("aut", "ths"), email = "dicook@monash.edu", comment = "ggscatmat, gglyph"), person("Heike", "Hofmann", role = "ths", email = "hofmann@iastate.edu"), person("Hadley", "Wickham", role = "ths", email = "h.wickham@gmail.com"), person("Francois", "Briatte", role = "aut", email = "f.briatte@gmail.com", comment = "ggcorr, ggnet, ggnet2"), person("Moritz", "Marbach", role = "aut", email = "mmarbach@mail.uni-mannheim.de", comment = "ggnet, ggnet2"), person("Edwin", "Thoen", role = "aut", email = "edwinthoen@gmail.com", comment = "ggsurv"), person("Amos", "Elberg", role = "aut", email = "amos.elberg@gmail.com", comment = "ggnetworkmap"), person("Joseph", "Larmarange", role = "aut", email = "joseph@larmarange.net", comment = "ggcoef")) -# Description: The R package 'ggplot2' is a plotting system based on the grammar of graphics. 'GGally' extends 'ggplot2' by adding several functions to reduce the complexity of combining geometric objects with transformed data. Some of these functions include a pairwise plot matrix, a two group pairwise plot matrix, a parallel coordinates plot, a survival plot, and several functions to plot networks. -# Depends: R (>= 3.1) -# Imports: ggplot2 (>= 2.2.0), grid, gtable (>= 0.2.0), plyr (>= 1.8.3), progress, RColorBrewer, reshape (>= 0.8.5), utils -# Suggests: broom (>= 0.4.0), chemometrics, geosphere (>= 1.5-1), igraph (>= 1.0.1), intergraph (>= 2.0-2), maps (>= 3.1.0), mapproj, network (>= 1.12.0), scagnostics, scales (>= 0.4.0), sna (>= 2.3-2), survival, packagedocs (>= 0.4.0), rmarkdown, roxygen2, testthat -# RoxygenNote: 5.0.1 -# VignetteBuilder: packagedocs -# NeedsCompilation: no -# Packaged: 2016-11-12 21:16:04 UTC; barret -# Author: Barret Schloerke [aut, cre] (author for ggpairs, ggduo, ggnostic, ggts, ggfacet, and ggally_*. Contributor for all functions.), Jason Crowley [aut] (ggparcoord), Di Cook [aut, ths] (ggscatmat, gglyph), Heike Hofmann [ths], Hadley Wickham [ths], Francois Briatte [aut] (ggcorr, ggnet, ggnet2), Moritz Marbach [aut] (ggnet, ggnet2), Edwin Thoen [aut] (ggsurv), Amos Elberg [aut] (ggnetworkmap), Joseph Larmarange [aut] (ggcoef) -# Maintainer: Barret Schloerke -# Repository: CRAN -# Date/Publication: 2016-11-13 10:14:15 - -# See -# http://docs.continuum.io/conda/build.html for -# more information about meta.yaml From 79a92cd49ff2db2eb44d8e05d2f51ad152481667 Mon Sep 17 00:00:00 2001 From: Bjoern Gruening Date: Wed, 7 Jun 2017 10:19:09 +0200 Subject: [PATCH 085/116] enable more debug output --- .travis.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.travis.yml b/.travis.yml index a536251f6f..a02ca6d252 100644 --- a/.travis.yml +++ b/.travis.yml @@ -17,7 +17,7 @@ env: global: - SUBDAGS=1 - BIOCONDA_UTILS_TAG=kill_r - - BIOCONDA_UTILS_BUILD_ARGS="--loglevel=info" + - BIOCONDA_UTILS_BUILD_ARGS="--loglevel=debug" - BIOCONDA_UTILS_LINT_ARGS= - MINICONDA_VER="4.2.12" matrix: From 75d76849258448969974789273011f48a8b06972 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Wed, 7 Jun 2017 20:13:20 +0200 Subject: [PATCH 086/116] Disable debug logging. --- .travis.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.travis.yml b/.travis.yml index a02ca6d252..d7d2b35b10 100644 --- a/.travis.yml +++ b/.travis.yml @@ -17,7 +17,7 @@ env: global: - SUBDAGS=1 - BIOCONDA_UTILS_TAG=kill_r - - BIOCONDA_UTILS_BUILD_ARGS="--loglevel=debug" + - BIOCONDA_UTILS_BUILD_ARGS="" - BIOCONDA_UTILS_LINT_ARGS= - MINICONDA_VER="4.2.12" matrix: From fcd5f80987a7bbc24e9e7e8926d0ad7ae13def2d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Wed, 7 Jun 2017 21:04:52 +0200 Subject: [PATCH 087/116] Fix zifa source. --- recipes/zifa/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/zifa/meta.yaml b/recipes/zifa/meta.yaml index 8bebe4adca..d646aa3a0a 100644 --- a/recipes/zifa/meta.yaml +++ b/recipes/zifa/meta.yaml @@ -3,8 +3,8 @@ package: version: "0.1.0" source: - git_rev: e40fdbf6c41cd7e564ab03d242fc071f5ac543b7 - git_url: https://github.com/epierson9/ZIFA + fn: zifa-0.1.0.zip + url: https://github.com/epierson9/ZIFA/archive/e40fdbf6c41cd7e564ab03d242fc071f5ac543b7.zip build: number: 0 From 57db6840339ca6dd57dcc3ebfd947e920848603f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Wed, 7 Jun 2017 23:21:27 +0200 Subject: [PATCH 088/116] Imrpove cap-mirseq recipe. --- recipes/cap-mirseq/meta.yaml | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/recipes/cap-mirseq/meta.yaml b/recipes/cap-mirseq/meta.yaml index 9021d0a571..7ed5fbdaff 100644 --- a/recipes/cap-mirseq/meta.yaml +++ b/recipes/cap-mirseq/meta.yaml @@ -9,7 +9,8 @@ build: package: name: cap-mirseq - version: 'version' + # this software does not have a version number + version: '2014' requirements: run: @@ -33,4 +34,4 @@ source: test: commands: - - miRDeep2.pl --help 2>&1 | grep 'Example of use' + - miRDeep2.pl --help 2>&1 | grep -A20 -B20 'Example of use' From 0ec1c75e03788bddf855364221d536437ec29e46 Mon Sep 17 00:00:00 2001 From: Bjoern Gruening Date: Wed, 14 Jun 2017 04:07:15 +0200 Subject: [PATCH 089/116] r fixes --- recipes/bioconductor-motiv/meta.yaml | 8 +++++++- recipes/r-mixomics/meta.yaml | 2 +- 2 files changed, 8 insertions(+), 2 deletions(-) diff --git a/recipes/bioconductor-motiv/meta.yaml b/recipes/bioconductor-motiv/meta.yaml index cdbeaad2eb..0039649e7b 100644 --- a/recipes/bioconductor-motiv/meta.yaml +++ b/recipes/bioconductor-motiv/meta.yaml @@ -1,6 +1,7 @@ package: name: bioconductor-motiv version: 1.30.0 + source: fn: MotIV_1.30.0.tar.gz url: @@ -8,12 +9,14 @@ source: - https://bioarchive.galaxyproject.org/MotIV_1.30.0.tar.gz - https://depot.galaxyproject.org/software/MotIV/MotIV_1.30.0_src_all.tar.gz md5: 19da23b2900e7e9b334084a7bd78c17c + build: string: gsl{{CONDA_GSL}}_{{PKG_BUILDNUM}} - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ + requirements: build: - 'bioconductor-biocgenerics >=0.1.0' @@ -32,9 +35,12 @@ requirements: - bioconductor-s4vectors - r-base - r-lattice + - gsl {{CONDA_GSL}}* + test: commands: - '$R -e "library(''MotIV'')"' + about: home: http://bioconductor.org/packages/3.5/bioc/html/MotIV.html license: GPL-2 diff --git a/recipes/r-mixomics/meta.yaml b/recipes/r-mixomics/meta.yaml index b800f47431..a1188f7ec4 100644 --- a/recipes/r-mixomics/meta.yaml +++ b/recipes/r-mixomics/meta.yaml @@ -9,6 +9,7 @@ source: fn: mixOmics_6.1.1.tar.gz url: - http://cran.r-project.org/src/contrib/Archive/mixOmics/mixOmics_6.1.1.tar.gz + sha256: 0a0b5cc2cb7ffcadcf2a5eab35c0f2d8cc9d1a60e7c83086a3909742c02bb471 build: number: 0 @@ -47,7 +48,6 @@ requirements: - r-rgl - r-tidyr - libglu # [linux] - - readline test: commands: From a462be172f12d4935172e311ab14335729c4f6ba Mon Sep 17 00:00:00 2001 From: Bjoern Gruening Date: Wed, 14 Jun 2017 04:28:12 +0200 Subject: [PATCH 090/116] remove rpy2 --- recipes/rpy2/build.sh | 9 --------- recipes/rpy2/meta.yaml | 47 ----------------------------------------------- 2 files changed, 56 deletions(-) delete mode 100644 recipes/rpy2/build.sh delete mode 100644 recipes/rpy2/meta.yaml diff --git a/recipes/rpy2/build.sh b/recipes/rpy2/build.sh deleted file mode 100644 index 31f8a2300a..0000000000 --- a/recipes/rpy2/build.sh +++ /dev/null @@ -1,9 +0,0 @@ -#!/bin/bash - -CFLAGS="-I$PREFIX/include" $PYTHON setup.py install - -# Add more build steps here, if they are necessary. - -# See -# http://docs.continuum.io/conda/build.html -# for a list of environment variables that are set during the build process. diff --git a/recipes/rpy2/meta.yaml b/recipes/rpy2/meta.yaml deleted file mode 100644 index 7bcffc0a6f..0000000000 --- a/recipes/rpy2/meta.yaml +++ /dev/null @@ -1,47 +0,0 @@ -package: - name: rpy2 - version: "2.7.8" - -source: - fn: rpy2-2.7.8.tar.gz - url: https://pypi.python.org/packages/source/r/rpy2/rpy2-2.7.8.tar.gz - md5: 56ca162bca76bb9c3f935f099c916196 - -build: - rpaths: - - lib/R/lib/ - - lib/ - skip: False - number: 0 - -requirements: - build: - - python - - r-base - - setuptools - - singledispatch # [not (py34 or py35)] - - six - - readline - - bzip2 - - run: - - python - - r-base - - singledispatch # [not (py34 or py35)] - - six - - readline - - bzip2 - -test: - # Python imports - imports: - - rpy2 - - rpy2.interactive - - rpy2.rinterface - - rpy2.rlike - - rpy2.robjects - -about: - home: http://rpy.sourceforge.net - license: GNU General Public License v2 or later (GPLv2+) - summary: 'Python interface to the R language (embedded R)' From c51858677cddb72e33780b85e007015aafb9bd35 Mon Sep 17 00:00:00 2001 From: Bjoern Gruening Date: Wed, 14 Jun 2017 04:28:24 +0200 Subject: [PATCH 091/116] r fixes --- recipes/bioconductor-regioner/meta.yaml | 7 +++++- recipes/bioconductor-repitools/meta.yaml | 2 ++ recipes/bioconductor-scan.upc/meta.yaml | 2 ++ recipes/r-microseq/meta.yaml | 11 +++------- recipes/r-sartools/1.2.0/meta.yaml | 35 ++---------------------------- recipes/r-sartools/1.3.2/meta.yaml | 37 +++----------------------------- 6 files changed, 18 insertions(+), 76 deletions(-) diff --git a/recipes/bioconductor-regioner/meta.yaml b/recipes/bioconductor-regioner/meta.yaml index 37c252c52e..8890de3822 100644 --- a/recipes/bioconductor-regioner/meta.yaml +++ b/recipes/bioconductor-regioner/meta.yaml @@ -1,15 +1,18 @@ package: name: bioconductor-regioner version: 1.6.2 + source: fn: regioneR_1.6.2.tar.gz - url: http://bioconductor.org/packages/release/bioc/src/contrib/regioneR_1.6.2.tar.gz + url: https://depot.galaxyproject.org/software/bioconductor-regioner/bioconductor-regioner_1.6.2_src_all.tar.gz md5: 93ecdf4d04f690580c0f1681bddc1246 + build: number: 0 rpaths: - lib/R/lib/ - lib/ + requirements: build: - bioconductor-bsgenome @@ -27,9 +30,11 @@ requirements: - bioconductor-rtracklayer - r-base - r-memoise + test: commands: - '$R -e "library(''regioneR'')"' + about: home: http://bioconductor.org/packages/release/bioc/html/regioneR.html license: Artistic-2.0 diff --git a/recipes/bioconductor-repitools/meta.yaml b/recipes/bioconductor-repitools/meta.yaml index 17edec8b8d..cdc86de134 100644 --- a/recipes/bioconductor-repitools/meta.yaml +++ b/recipes/bioconductor-repitools/meta.yaml @@ -30,6 +30,7 @@ requirements: - r-gplots - r-gsmoothr - r-rsolnp + - r-cluster run: - 'bioconductor-biocgenerics >=0.8.0' - bioconductor-biostrings @@ -49,6 +50,7 @@ requirements: - r-gplots - r-gsmoothr - r-rsolnp + - r-cluster test: commands: - '$R -e "library(''Repitools'')"' diff --git a/recipes/bioconductor-scan.upc/meta.yaml b/recipes/bioconductor-scan.upc/meta.yaml index 9172b545ce..d4df440ff5 100644 --- a/recipes/bioconductor-scan.upc/meta.yaml +++ b/recipes/bioconductor-scan.upc/meta.yaml @@ -24,6 +24,7 @@ requirements: - bioconductor-affyio - r-dbi - r-rsqlite + - r-mass run: - r-base - r-foreach @@ -36,6 +37,7 @@ requirements: - bioconductor-affyio - r-dbi - r-rsqlite + - r-mass test: commands: - '$R -e "library(''SCAN.UPC'')"' diff --git a/recipes/r-microseq/meta.yaml b/recipes/r-microseq/meta.yaml index bc8f8e84f6..202c6b27ee 100644 --- a/recipes/r-microseq/meta.yaml +++ b/recipes/r-microseq/meta.yaml @@ -12,19 +12,14 @@ source: url: - https://cran.r-project.org/src/contrib/microseq_{{ version }}.tar.gz - https://cran.r-project.org/src/contrib/Archive/microseq/microseq_{{ version }}.tar.gz - - sha256: 9ac33165011c856bf149c0e15340a4677888844c7a3e0f5e61f949c099778193 build: number: 0 - - # This is required to make R link correctly on Linux. rpaths: - lib/R/lib/ - lib/ - requirements: build: - r-base @@ -32,9 +27,9 @@ requirements: - gcc run: - - r-base # [linux] - - r-rcpp >=0.11.1 # [linux] - - libgcc # [linux] + - r-base + - r-rcpp >=0.11.1 + - libgcc test: commands: diff --git a/recipes/r-sartools/1.2.0/meta.yaml b/recipes/r-sartools/1.2.0/meta.yaml index 0867c78d22..2408ee4dfe 100644 --- a/recipes/r-sartools/1.2.0/meta.yaml +++ b/recipes/r-sartools/1.2.0/meta.yaml @@ -7,11 +7,7 @@ source: url: https://github.com/PF2-pasteur-fr/SARTools/archive/v1.2.0.tar.gz build: - # If this is a new build for the same version, increment the build - # number. If you do not include this key, it defaults to 0. # number: 1 - - # This is required to make R link correctly on Linux. rpaths: - lib/R/lib/ - lib/ @@ -21,50 +17,23 @@ requirements: build: - r-base - r-knitr + - r-assay - bioconductor-deseq2 - bioconductor-edger run: - r-base - r-knitr + - r-assay - bioconductor-deseq2 - bioconductor-edger test: commands: - # You can put additional test commands to be run here. - $R -e "library('SARTools')" # [not win] - #- "\"%R%\" -e \"library('SARTools')\"" # [win] - - # You can also put a file called run_test.py, run_test.sh, or run_test.bat - # in the recipe that will be run at test time. - - # requires: - # Put any additional test requirements here. about: home: https://github.com/PF2-pasteur-fr/SARTools license: GPL-2 summary: SARTools provides R tools and an environment for the statistical analysis of RNA-Seq projects load and clean data, produce figures, perform statistical analysis/testing with DESeq2 or edgeR, export results and create final report. - -# The original GitHub metadata for this package was: -# https://github.com/PF2-pasteur-fr/SARTools/blob/master/DESCRIPTION - -#Package: SARTools -#Type: Package -#Title: Statistical Analysis of RNA-Seq Tools -#Version: 1.2.0 -#Date: 2015-12-03 -#Author: Marie-Agnes Dillies and Hugo Varet -#Maintainer: Hugo Varet -#Depends: R (>= 3.2.2), DESeq2 (>= 1.10.0), edgeR (>= 3.12.0), xtable -#Imports: knitr, GenomicRanges, S4Vectors, limma, genefilter (>= 1.44.0) -#VignetteBuilder: knitr -#Encoding: latin1 -#Description: SARTools provides R tools and an environment for the statistical analysis of RNA-Seq projects: load and clean data, produce figures, perform statistical analysis/testing with DESeq2 or edgeR, export results and create final report. -#License: GPL-2 - -# See -# http://docs.continuum.io/conda/build.html for -# more information about meta.yaml diff --git a/recipes/r-sartools/1.3.2/meta.yaml b/recipes/r-sartools/1.3.2/meta.yaml index 1c330718b3..7fc5b1359d 100644 --- a/recipes/r-sartools/1.3.2/meta.yaml +++ b/recipes/r-sartools/1.3.2/meta.yaml @@ -5,13 +5,10 @@ package: source: fn: v1.3.2.tar.gz url: https://github.com/PF2-pasteur-fr/SARTools/archive/v1.3.2.tar.gz + sha256: 29a0a9c586d4a377a142600ecb129e3e25fdcc91d34a9f903a6ce593e4a5ce3e build: - # If this is a new build for the same version, increment the build - # number. If you do not include this key, it defaults to 0. # number: 1 - - # This is required to make R link correctly on Linux. rpaths: - lib/R/lib/ - lib/ @@ -21,50 +18,22 @@ requirements: build: - r-base - r-knitr + - r-assay - bioconductor-deseq2 - bioconductor-edger run: - r-base - r-knitr + - r-assay - bioconductor-deseq2 - bioconductor-edger test: commands: - # You can put additional test commands to be run here. - $R -e "library('SARTools')" # [not win] - #- "\"%R%\" -e \"library('SARTools')\"" # [win] - - # You can also put a file called run_test.py, run_test.sh, or run_test.bat - # in the recipe that will be run at test time. - - # requires: - # Put any additional test requirements here. about: home: https://github.com/PF2-pasteur-fr/SARTools license: GPL-2 summary: SARTools provides R tools and an environment for the statistical analysis of RNA-Seq projects load and clean data, produce figures, perform statistical analysis/testing with DESeq2 or edgeR, export results and create final report. - - -# The original GitHub metadata for this package was: -# https://github.com/PF2-pasteur-fr/SARTools/blob/master/DESCRIPTION - -#Package: SARTools -#Type: Package -#Title: Statistical Analysis of RNA-Seq Tools -#Version: 1.2.0 -#Date: 2015-12-03 -#Author: Marie-Agnes Dillies and Hugo Varet -#Maintainer: Hugo Varet -#Depends: R (>= 3.2.2), DESeq2 (>= 1.10.0), edgeR (>= 3.12.0), xtable -#Imports: knitr, GenomicRanges, S4Vectors, limma, genefilter (>= 1.44.0) -#VignetteBuilder: knitr -#Encoding: latin1 -#Description: SARTools provides R tools and an environment for the statistical analysis of RNA-Seq projects: load and clean data, produce figures, perform statistical analysis/testing with DESeq2 or edgeR, export results and create final report. -#License: GPL-2 - -# See -# http://docs.continuum.io/conda/build.html for -# more information about meta.yaml From c0a2b7b7b75de3faf32d55a2b3f27edf4f2f0546 Mon Sep 17 00:00:00 2001 From: Bjoern Gruening Date: Wed, 14 Jun 2017 06:24:50 +0200 Subject: [PATCH 092/116] r fixes --- recipes/bioconductor-ensembldb/meta.yaml | 11 ++++++++--- recipes/bioconductor-genomation/meta.yaml | 4 ++-- recipes/r-multicool/meta.yaml | 6 +++--- 3 files changed, 13 insertions(+), 8 deletions(-) diff --git a/recipes/bioconductor-ensembldb/meta.yaml b/recipes/bioconductor-ensembldb/meta.yaml index 4fa1fd2236..a2844b9059 100644 --- a/recipes/bioconductor-ensembldb/meta.yaml +++ b/recipes/bioconductor-ensembldb/meta.yaml @@ -1,15 +1,18 @@ package: name: bioconductor-ensembldb - version: 1.6.0 + version: 1.6.2 + source: fn: ensembldb_1.6.0.tar.gz - url: https://depot.galaxyproject.org/software/bioconductor-ensembldb/bioconductor-ensembldb_1.6.0_src_all.tar.gz - md5: b0d4cfb9b094e21fc6582eed126d0ca6 + url: http://bioconductor.org/packages/3.4/bioc/src/contrib/ensembldb_1.6.2.tar.gz + sha256: 79b8f50cf2ddb7af0de7479a045f6cc57d763286dcc495bf932bce37e995bbc3 + build: number: 0 rpaths: - lib/R/lib/ - lib/ + requirements: build: - 'bioconductor-annotationdbi >=1.31.19' @@ -41,9 +44,11 @@ requirements: - r-base - r-dbi - r-rsqlite + test: commands: - '$R -e "library(''ensembldb'')"' + about: home: http://bioconductor.org/packages/release/bioc/html/ensembldb.html license: LGPL diff --git a/recipes/bioconductor-genomation/meta.yaml b/recipes/bioconductor-genomation/meta.yaml index 622d8dd8f7..d77816606e 100644 --- a/recipes/bioconductor-genomation/meta.yaml +++ b/recipes/bioconductor-genomation/meta.yaml @@ -4,11 +4,11 @@ package: source: fn: genomation_1.6.0.tar.gz - url: https://bioconductor.org/packages/release/bioc/src/contrib/genomation_1.6.0.tar.gz + url: https://depot.galaxyproject.org/software/bioconductor-genomation/bioconductor-genomation_1.6.0_src_all.tar.gz md5: ceb645ad51f99c5b9ef09491c942d06a build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/r-multicool/meta.yaml b/recipes/r-multicool/meta.yaml index 6c902ffd03..fe9d24b6ea 100644 --- a/recipes/r-multicool/meta.yaml +++ b/recipes/r-multicool/meta.yaml @@ -34,7 +34,8 @@ test: about: #home: license: GPL-2 - summary: !!python/unicode 'A set of tools to permute multisets without loops or hash tables + summary: | + A set of tools to permute multisets without loops or hash tables and to generate integer partitions. The permutation functions are based on C code from Aaron Williams. Cool-lex order is similar to colexicographical order. The algorithm is described in Williams, A. Loopless Generation of Multiset Permutations by Prefix @@ -45,5 +46,4 @@ about: distributed without conditions. The package also generates the integer partitions of a positive, non-zero integer n. The C++ code for this is based on Python code from Jerome Kelleher which can be found here http://jeromekelleher.net/partitions.php. - The C++ code and Python code are distributed without conditions.' - + The C++ code and Python code are distributed without conditions. From 50d85c53fc71a5501ad915d971324d504b7fc19c Mon Sep 17 00:00:00 2001 From: Bjoern Gruening Date: Wed, 14 Jun 2017 09:10:14 +0200 Subject: [PATCH 093/116] r fixes --- recipes/bioconductor-flowdensity/meta.yaml | 2 ++ recipes/bioconductor-motiv/meta.yaml | 2 +- recipes/r-drc/meta.yaml | 2 ++ recipes/r-sartools/1.2.0/meta.yaml | 2 -- recipes/r-sartools/1.3.2/meta.yaml | 5 +---- 5 files changed, 6 insertions(+), 7 deletions(-) diff --git a/recipes/bioconductor-flowdensity/meta.yaml b/recipes/bioconductor-flowdensity/meta.yaml index 8a192333fd..6d69c1519d 100644 --- a/recipes/bioconductor-flowdensity/meta.yaml +++ b/recipes/bioconductor-flowdensity/meta.yaml @@ -18,6 +18,7 @@ requirements: - r-geomap - r-gplots - r-rfoc + - r-nloptr run: - bioconductor-flowcore - r-base @@ -25,6 +26,7 @@ requirements: - r-geomap - r-gplots - r-rfoc + - r-nloptr test: commands: - '$R -e "library(''flowDensity'')"' diff --git a/recipes/bioconductor-motiv/meta.yaml b/recipes/bioconductor-motiv/meta.yaml index 0039649e7b..c5b2bda11e 100644 --- a/recipes/bioconductor-motiv/meta.yaml +++ b/recipes/bioconductor-motiv/meta.yaml @@ -11,7 +11,7 @@ source: md5: 19da23b2900e7e9b334084a7bd78c17c build: - string: gsl{{CONDA_GSL}}_{{PKG_BUILDNUM}} + string: bioconductor_{{CONDA_R}}_gsl{{CONDA_GSL}}_{{PKG_BUILDNUM}} number: 0 rpaths: - lib/R/lib/ diff --git a/recipes/r-drc/meta.yaml b/recipes/r-drc/meta.yaml index 8ceedf0a77..0479b5e9e6 100644 --- a/recipes/r-drc/meta.yaml +++ b/recipes/r-drc/meta.yaml @@ -28,6 +28,7 @@ requirements: - r-multcomp - r-plotrix - r-scales + - r-nloptr run: - r-base @@ -37,6 +38,7 @@ requirements: - r-multcomp - r-plotrix - r-scales + - r-nloptr test: commands: diff --git a/recipes/r-sartools/1.2.0/meta.yaml b/recipes/r-sartools/1.2.0/meta.yaml index 2408ee4dfe..dbc7a4729f 100644 --- a/recipes/r-sartools/1.2.0/meta.yaml +++ b/recipes/r-sartools/1.2.0/meta.yaml @@ -17,14 +17,12 @@ requirements: build: - r-base - r-knitr - - r-assay - bioconductor-deseq2 - bioconductor-edger run: - r-base - r-knitr - - r-assay - bioconductor-deseq2 - bioconductor-edger diff --git a/recipes/r-sartools/1.3.2/meta.yaml b/recipes/r-sartools/1.3.2/meta.yaml index 7fc5b1359d..ab0f173f84 100644 --- a/recipes/r-sartools/1.3.2/meta.yaml +++ b/recipes/r-sartools/1.3.2/meta.yaml @@ -13,25 +13,22 @@ build: - lib/R/lib/ - lib/ -# Suggests: parallel requirements: build: - r-base - r-knitr - - r-assay - bioconductor-deseq2 - bioconductor-edger run: - r-base - r-knitr - - r-assay - bioconductor-deseq2 - bioconductor-edger test: commands: - - $R -e "library('SARTools')" # [not win] + - $R -e "library('SARTools')" about: home: https://github.com/PF2-pasteur-fr/SARTools From 89c4badd5f1272e13132df2aafc245dedb2b80c7 Mon Sep 17 00:00:00 2001 From: Bjoern Gruening Date: Wed, 14 Jun 2017 13:44:46 +0200 Subject: [PATCH 094/116] r fixes --- recipes/bioconductor-motiv/meta.yaml | 2 ++ recipes/bioconductor-synergyfinder/meta.yaml | 2 ++ 2 files changed, 4 insertions(+) diff --git a/recipes/bioconductor-motiv/meta.yaml b/recipes/bioconductor-motiv/meta.yaml index c5b2bda11e..40b6999c98 100644 --- a/recipes/bioconductor-motiv/meta.yaml +++ b/recipes/bioconductor-motiv/meta.yaml @@ -27,6 +27,7 @@ requirements: - r-base - gsl {{CONDA_GSL}}* - r-lattice + - gcc run: - 'bioconductor-biocgenerics >=0.1.0' - 'bioconductor-biostrings >=1.24.0' @@ -36,6 +37,7 @@ requirements: - r-base - r-lattice - gsl {{CONDA_GSL}}* + - libgcc test: commands: diff --git a/recipes/bioconductor-synergyfinder/meta.yaml b/recipes/bioconductor-synergyfinder/meta.yaml index 62f7ff3797..793cc78d83 100644 --- a/recipes/bioconductor-synergyfinder/meta.yaml +++ b/recipes/bioconductor-synergyfinder/meta.yaml @@ -20,6 +20,7 @@ requirements: - 'r-kriging >=1.1' - 'r-nleqslv >=3.0' - 'r-reshape2 >=1.4.1' + - r-nloptr run: - r-base - 'r-drc >=2.5-12' @@ -29,6 +30,7 @@ requirements: - 'r-kriging >=1.1' - 'r-nleqslv >=3.0' - 'r-reshape2 >=1.4.1' + - r-nloptr test: commands: - '$R -e "library(''synergyfinder'')"' From adbfed8a7dcad8282906c5f3b17bbdbfb30aa835 Mon Sep 17 00:00:00 2001 From: Bjoern Gruening Date: Wed, 14 Jun 2017 14:36:50 +0200 Subject: [PATCH 095/116] remove old version --- recipes/r-sartools/1.2.0/build.sh | 14 -------------- recipes/r-sartools/1.2.0/meta.yaml | 37 ------------------------------------- recipes/r-sartools/1.3.2/build.sh | 14 -------------- recipes/r-sartools/1.3.2/meta.yaml | 36 ------------------------------------ 4 files changed, 101 deletions(-) delete mode 100644 recipes/r-sartools/1.2.0/build.sh delete mode 100644 recipes/r-sartools/1.2.0/meta.yaml delete mode 100644 recipes/r-sartools/1.3.2/build.sh delete mode 100644 recipes/r-sartools/1.3.2/meta.yaml diff --git a/recipes/r-sartools/1.2.0/build.sh b/recipes/r-sartools/1.2.0/build.sh deleted file mode 100644 index 7fe0351a83..0000000000 --- a/recipes/r-sartools/1.2.0/build.sh +++ /dev/null @@ -1,14 +0,0 @@ -#!/bin/bash - -# R refuses to build packages that mark themselves as Priority: Recommended -mv DESCRIPTION DESCRIPTION.old -grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION - -$R CMD INSTALL --build . - -# Add more build steps here, if they are necessary. -#R -e "library(devtools); source('http://www.bioconductor.org/biocLite.R'); install_github('glibiseller/IPO') " - -# See -# http://docs.continuum.io/conda/build.html -# for a list of environment variables that are set during the build process. diff --git a/recipes/r-sartools/1.2.0/meta.yaml b/recipes/r-sartools/1.2.0/meta.yaml deleted file mode 100644 index dbc7a4729f..0000000000 --- a/recipes/r-sartools/1.2.0/meta.yaml +++ /dev/null @@ -1,37 +0,0 @@ -package: - name: r-sartools - version: "1.2.0" - -source: - fn: v1.2.0.tar.gz - url: https://github.com/PF2-pasteur-fr/SARTools/archive/v1.2.0.tar.gz - -build: - # number: 1 - rpaths: - - lib/R/lib/ - - lib/ - -# Suggests: parallel -requirements: - build: - - r-base - - r-knitr - - bioconductor-deseq2 - - bioconductor-edger - - run: - - r-base - - r-knitr - - bioconductor-deseq2 - - bioconductor-edger - -test: - commands: - - $R -e "library('SARTools')" # [not win] - -about: - home: https://github.com/PF2-pasteur-fr/SARTools - license: GPL-2 - summary: SARTools provides R tools and an environment for the statistical analysis of RNA-Seq projects load and clean data, produce figures, perform statistical analysis/testing with DESeq2 or edgeR, export results and create final report. - diff --git a/recipes/r-sartools/1.3.2/build.sh b/recipes/r-sartools/1.3.2/build.sh deleted file mode 100644 index 7fe0351a83..0000000000 --- a/recipes/r-sartools/1.3.2/build.sh +++ /dev/null @@ -1,14 +0,0 @@ -#!/bin/bash - -# R refuses to build packages that mark themselves as Priority: Recommended -mv DESCRIPTION DESCRIPTION.old -grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION - -$R CMD INSTALL --build . - -# Add more build steps here, if they are necessary. -#R -e "library(devtools); source('http://www.bioconductor.org/biocLite.R'); install_github('glibiseller/IPO') " - -# See -# http://docs.continuum.io/conda/build.html -# for a list of environment variables that are set during the build process. diff --git a/recipes/r-sartools/1.3.2/meta.yaml b/recipes/r-sartools/1.3.2/meta.yaml deleted file mode 100644 index ab0f173f84..0000000000 --- a/recipes/r-sartools/1.3.2/meta.yaml +++ /dev/null @@ -1,36 +0,0 @@ -package: - name: r-sartools - version: "1.3.2" - -source: - fn: v1.3.2.tar.gz - url: https://github.com/PF2-pasteur-fr/SARTools/archive/v1.3.2.tar.gz - sha256: 29a0a9c586d4a377a142600ecb129e3e25fdcc91d34a9f903a6ce593e4a5ce3e - -build: - # number: 1 - rpaths: - - lib/R/lib/ - - lib/ - -requirements: - build: - - r-base - - r-knitr - - bioconductor-deseq2 - - bioconductor-edger - - run: - - r-base - - r-knitr - - bioconductor-deseq2 - - bioconductor-edger - -test: - commands: - - $R -e "library('SARTools')" - -about: - home: https://github.com/PF2-pasteur-fr/SARTools - license: GPL-2 - summary: SARTools provides R tools and an environment for the statistical analysis of RNA-Seq projects load and clean data, produce figures, perform statistical analysis/testing with DESeq2 or edgeR, export results and create final report. From ca32ab223ce8a259ea98aa75c245c6406d5af30f Mon Sep 17 00:00:00 2001 From: Bjoern Gruening Date: Wed, 14 Jun 2017 14:58:34 +0200 Subject: [PATCH 096/116] add new version --- recipes/r-sartools/build.sh | 14 ++++++++++++++ recipes/r-sartools/meta.yaml | 36 ++++++++++++++++++++++++++++++++++++ 2 files changed, 50 insertions(+) create mode 100644 recipes/r-sartools/build.sh create mode 100644 recipes/r-sartools/meta.yaml diff --git a/recipes/r-sartools/build.sh b/recipes/r-sartools/build.sh new file mode 100644 index 0000000000..7fe0351a83 --- /dev/null +++ b/recipes/r-sartools/build.sh @@ -0,0 +1,14 @@ +#!/bin/bash + +# R refuses to build packages that mark themselves as Priority: Recommended +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION + +$R CMD INSTALL --build . + +# Add more build steps here, if they are necessary. +#R -e "library(devtools); source('http://www.bioconductor.org/biocLite.R'); install_github('glibiseller/IPO') " + +# See +# http://docs.continuum.io/conda/build.html +# for a list of environment variables that are set during the build process. diff --git a/recipes/r-sartools/meta.yaml b/recipes/r-sartools/meta.yaml new file mode 100644 index 0000000000..b8d8306469 --- /dev/null +++ b/recipes/r-sartools/meta.yaml @@ -0,0 +1,36 @@ +package: + name: r-sartools + version: "1.4.1" + +source: + fn: v1.4.1.tar.gz + url: https://github.com/PF2-pasteur-fr/SARTools/archive/v1.4.1.tar.gz + sha256: c9f23fec63ee12e42319ce2bf3ff651e0edb347117d856cd052295cbdee5206d + +build: + # number: 0 + rpaths: + - lib/R/lib/ + - lib/ + +requirements: + build: + - r-base + - r-knitr + - bioconductor-deseq2 + - bioconductor-edger + + run: + - r-base + - r-knitr + - bioconductor-deseq2 + - bioconductor-edger + +test: + commands: + - $R -e "library('SARTools')" + +about: + home: https://github.com/PF2-pasteur-fr/SARTools + license: GPL-2 + summary: SARTools provides R tools and an environment for the statistical analysis of RNA-Seq projects load and clean data, produce figures, perform statistical analysis/testing with DESeq2 or edgeR, export results and create final report. From ce84fee080e3eda6819564ccf5f06a04043b65b6 Mon Sep 17 00:00:00 2001 From: Bjoern Gruening Date: Wed, 14 Jun 2017 14:58:42 +0200 Subject: [PATCH 097/116] r fixes --- recipes/bioconductor-dexseq/1.18.4/meta.yaml | 4 +++- recipes/bioconductor-motiv/build.sh | 5 ++++- recipes/r-mixomics/meta.yaml | 4 ++++ recipes/r-multicool/meta.yaml | 10 +++++----- 4 files changed, 16 insertions(+), 7 deletions(-) diff --git a/recipes/bioconductor-dexseq/1.18.4/meta.yaml b/recipes/bioconductor-dexseq/1.18.4/meta.yaml index 37ab0d7083..8593c63da4 100644 --- a/recipes/bioconductor-dexseq/1.18.4/meta.yaml +++ b/recipes/bioconductor-dexseq/1.18.4/meta.yaml @@ -51,9 +51,11 @@ requirements: - r-statmod - r-stringr - python + test: commands: - - '$R -e "library(''DEXSeq'')"' + - $R -e "library(''DEXSeq'')" + about: home: http://bioconductor.org/packages/release/bioc/html/DEXSeq.html license: 'GPL (>= 3)' diff --git a/recipes/bioconductor-motiv/build.sh b/recipes/bioconductor-motiv/build.sh index 8218eda948..92a7d873ce 100644 --- a/recipes/bioconductor-motiv/build.sh +++ b/recipes/bioconductor-motiv/build.sh @@ -1,6 +1,9 @@ #!/bin/bash + +export LD_LIBRARY_PATH=$PREFIX/lib + mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION $R CMD INSTALL --build . -# \ No newline at end of file + diff --git a/recipes/r-mixomics/meta.yaml b/recipes/r-mixomics/meta.yaml index a1188f7ec4..60653a931c 100644 --- a/recipes/r-mixomics/meta.yaml +++ b/recipes/r-mixomics/meta.yaml @@ -80,3 +80,7 @@ about: integration with regularised Generalised Canonical Correlation Analysis and vertical integration with multi-group Partial Least Squares. license_family: GPL3 + +extra: + container: + extended-base: true diff --git a/recipes/r-multicool/meta.yaml b/recipes/r-multicool/meta.yaml index fe9d24b6ea..2cf3ebe660 100644 --- a/recipes/r-multicool/meta.yaml +++ b/recipes/r-multicool/meta.yaml @@ -1,15 +1,15 @@ package: name: r-multicool - version: "0.1_9" + version: "0.1_10" source: - fn: multicool_0.1-9.tar.gz + fn: multicool_0.1-10.tar.gz url: - - http://cran.r-project.org/src/contrib/Archive/multicool/multicool_0.1-9.tar.gz - sha256: bdf92571cef1b649952d155395a92b8683099ee13114f73a9d41fc5d7d49d329 + - https://cran.r-project.org/src/contrib/multicool_0.1-10.tar.gz + sha256: 5bb0cb0d9eb64420c862877247a79bb0afadacfe23262ec8c3fa26e5e34d6ff9 build: - number: 2 + number: 0 rpaths: - lib/R/lib/ From d5f1ec162476f6df201f949cc8cf52021fbf1f55 Mon Sep 17 00:00:00 2001 From: Bjoern Gruening Date: Wed, 14 Jun 2017 14:59:23 +0200 Subject: [PATCH 098/116] try some fixes --- recipes/macs2/meta.yaml | 4 +++- recipes/nanoraw/meta.yaml | 4 ++-- 2 files changed, 5 insertions(+), 3 deletions(-) diff --git a/recipes/macs2/meta.yaml b/recipes/macs2/meta.yaml index 1f5da92191..9048f4e45a 100644 --- a/recipes/macs2/meta.yaml +++ b/recipes/macs2/meta.yaml @@ -8,17 +8,19 @@ source: md5: 1cc2fab44b232992060c7ab592bf43fa build: - number: 1 + number: 0 skip: True # [py3k] requirements: build: - python - numpy + - gcc run: - python - numpy - r-base + - libgcc test: commands: diff --git a/recipes/nanoraw/meta.yaml b/recipes/nanoraw/meta.yaml index 171c2b9b63..47c537b3b0 100644 --- a/recipes/nanoraw/meta.yaml +++ b/recipes/nanoraw/meta.yaml @@ -14,7 +14,7 @@ build: entry_points: - nanoraw = nanoraw.__main__:main number: 0 - skip: True # [not py27] + skip: True # [not py27] requirements: build: @@ -41,7 +41,7 @@ test: - nanoraw commands: - - nanoraw --help + - nanoraw --help | grep significant_fasta about: home: https://github.com/marcus1487/nanoraw From d8c92528f31368db814ac02208d5c5f713f15ab3 Mon Sep 17 00:00:00 2001 From: Bjoern Gruening Date: Wed, 14 Jun 2017 15:42:33 +0200 Subject: [PATCH 099/116] remove old package --- .../bioconductor-genelendatabase/1.6.0/build.sh | 17 ------------ .../bioconductor-genelendatabase/1.6.0/meta.yaml | 30 ---------------------- 2 files changed, 47 deletions(-) delete mode 100644 recipes/bioconductor-genelendatabase/1.6.0/build.sh delete mode 100644 recipes/bioconductor-genelendatabase/1.6.0/meta.yaml diff --git a/recipes/bioconductor-genelendatabase/1.6.0/build.sh b/recipes/bioconductor-genelendatabase/1.6.0/build.sh deleted file mode 100644 index 6c7a1726e3..0000000000 --- a/recipes/bioconductor-genelendatabase/1.6.0/build.sh +++ /dev/null @@ -1,17 +0,0 @@ - -#!/bin/bash - -# R refuses to build packages that mark themselves as -# "Priority: Recommended" -mv DESCRIPTION DESCRIPTION.old -grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION -# -$R CMD INSTALL --build . -# -# # Add more build steps here, if they are necessary. -# -# See -# http://docs.continuum.io/conda/build.html -# for a list of environment variables that are set during the build -# process. -# \ No newline at end of file diff --git a/recipes/bioconductor-genelendatabase/1.6.0/meta.yaml b/recipes/bioconductor-genelendatabase/1.6.0/meta.yaml deleted file mode 100644 index 5ccaefb233..0000000000 --- a/recipes/bioconductor-genelendatabase/1.6.0/meta.yaml +++ /dev/null @@ -1,30 +0,0 @@ -package: - name: bioconductor-genelendatabase - version: 1.6.0 -source: - fn: geneLenDataBase_1.6.0.tar.gz - url: http://bioconductor.org/packages/release/data/experiment/src/contrib/geneLenDataBase_1.6.0.tar.gz - md5: 3038e8243c534c06da3108feb952e849 -build: - number: 0 - skip: True # [osx] - rpaths: - - lib/R/lib/ - - lib/ -requirements: - build: - - 'bioconductor-genomicfeatures >=1.3.15' - - bioconductor-rtracklayer - - r-base - run: - - 'bioconductor-genomicfeatures >=1.3.15' - - bioconductor-rtracklayer - - r-base -test: - commands: - - '$R -e "library(''geneLenDataBase'')"' -about: - home: http://bioconductor.org/packages/release/data/experiment/html/geneLenDataBase.html - license: 'LGPL (>= 2)' - summary: 'Length of mRNA transcripts for a number of genomes and gene ID formats, - largely based on UCSC table browser' From 1951ae7b7eee7c252a2573999f0d8e8c1397fb71 Mon Sep 17 00:00:00 2001 From: Bjoern Gruening Date: Wed, 14 Jun 2017 15:55:00 +0200 Subject: [PATCH 100/116] r fixes --- recipes/bioconductor-cummerbund/2.12.1/meta.yaml | 2 +- recipes/bioconductor-cummerbund/meta.yaml | 7 ++++++- recipes/r-ks/meta.yaml | 4 ++++ recipes/r-mixomics/meta.yaml | 2 ++ 4 files changed, 13 insertions(+), 2 deletions(-) diff --git a/recipes/bioconductor-cummerbund/2.12.1/meta.yaml b/recipes/bioconductor-cummerbund/2.12.1/meta.yaml index 1fd204a342..85e7341dee 100644 --- a/recipes/bioconductor-cummerbund/2.12.1/meta.yaml +++ b/recipes/bioconductor-cummerbund/2.12.1/meta.yaml @@ -38,7 +38,7 @@ requirements: - r-rsqlite test: commands: - - '$R -e "library(''cummeRbund'')"' + - $R -e "library(''cummeRbund'')" about: home: http://bioconductor.org/packages/release/bioc/html/cummeRbund.html license: Artistic-2.0 diff --git a/recipes/bioconductor-cummerbund/meta.yaml b/recipes/bioconductor-cummerbund/meta.yaml index a14b9d05ef..d7fcd110b8 100644 --- a/recipes/bioconductor-cummerbund/meta.yaml +++ b/recipes/bioconductor-cummerbund/meta.yaml @@ -1,15 +1,18 @@ package: name: bioconductor-cummerbund version: 2.16.0 + source: fn: cummeRbund_2.16.0.tar.gz url: https://bioarchive.galaxyproject.org/cummeRbund_2.16.0.tar.gz md5: 873bad2ed2c5a74d7583a0c8ffd21298 + build: number: 0 rpaths: - lib/R/lib/ - lib/ + requirements: build: - bioconductor-biobase @@ -35,9 +38,11 @@ requirements: - r-plyr - r-reshape2 - r-rsqlite + test: commands: - - '$R -e "library(''cummeRbund'')"' + - $R -e "library(''cummeRbund'')" + about: home: http://bioconductor.org/packages/release/bioc/html/cummeRbund.html license: Artistic-2.0 diff --git a/recipes/r-ks/meta.yaml b/recipes/r-ks/meta.yaml index ccbfcbe471..b09c0739da 100644 --- a/recipes/r-ks/meta.yaml +++ b/recipes/r-ks/meta.yaml @@ -51,3 +51,7 @@ about: density derivatives, cumulative distributions, modal clustering, discriminant analysis, and two-sample hypothesis testing. ' license_family: GPL3 + +extra: + container: + extended-base: true diff --git a/recipes/r-mixomics/meta.yaml b/recipes/r-mixomics/meta.yaml index 60653a931c..135e3e182c 100644 --- a/recipes/r-mixomics/meta.yaml +++ b/recipes/r-mixomics/meta.yaml @@ -13,6 +13,8 @@ source: build: number: 0 + # rgl not available on OSX for conda-forge + skip: True # [osx] rpaths: - lib/R/lib/ - lib/ From 6f9a2399f2a2c1fede1044d63e827f64d6f08b12 Mon Sep 17 00:00:00 2001 From: Bjoern Gruening Date: Wed, 14 Jun 2017 17:35:34 +0200 Subject: [PATCH 101/116] r fixes --- recipes/bioconductor-camera/1.26.0/meta.yaml | 2 +- recipes/bioconductor-cummerbund/meta.yaml | 2 +- recipes/bioconductor-dexseq/1.18.4/meta.yaml | 2 +- recipes/bioconductor-dexseq/meta.yaml | 2 +- recipes/bioconductor-goseq/meta.yaml | 2 +- recipes/r-multicool/build.sh | 7 ------- 6 files changed, 5 insertions(+), 12 deletions(-) diff --git a/recipes/bioconductor-camera/1.26.0/meta.yaml b/recipes/bioconductor-camera/1.26.0/meta.yaml index 734e4d9869..c8793fbc21 100644 --- a/recipes/bioconductor-camera/1.26.0/meta.yaml +++ b/recipes/bioconductor-camera/1.26.0/meta.yaml @@ -32,7 +32,7 @@ requirements: - r-igraph test: commands: - - '$R -e "library(''CAMERA'')"' + - $R -e "library('CAMERA')" about: home: http://bioconductor.org/packages/release/bioc/html/CAMERA.html license: 'GPL (>= 2)' diff --git a/recipes/bioconductor-cummerbund/meta.yaml b/recipes/bioconductor-cummerbund/meta.yaml index d7fcd110b8..b9186f79d3 100644 --- a/recipes/bioconductor-cummerbund/meta.yaml +++ b/recipes/bioconductor-cummerbund/meta.yaml @@ -41,7 +41,7 @@ requirements: test: commands: - - $R -e "library(''cummeRbund'')" + - $R -e "library('cummeRbund')" about: home: http://bioconductor.org/packages/release/bioc/html/cummeRbund.html diff --git a/recipes/bioconductor-dexseq/1.18.4/meta.yaml b/recipes/bioconductor-dexseq/1.18.4/meta.yaml index 8593c63da4..948d1c246d 100644 --- a/recipes/bioconductor-dexseq/1.18.4/meta.yaml +++ b/recipes/bioconductor-dexseq/1.18.4/meta.yaml @@ -54,7 +54,7 @@ requirements: test: commands: - - $R -e "library(''DEXSeq'')" + - $R -e "library('DEXSeq')" about: home: http://bioconductor.org/packages/release/bioc/html/DEXSeq.html diff --git a/recipes/bioconductor-dexseq/meta.yaml b/recipes/bioconductor-dexseq/meta.yaml index 15419955e3..a9d938a0ca 100644 --- a/recipes/bioconductor-dexseq/meta.yaml +++ b/recipes/bioconductor-dexseq/meta.yaml @@ -53,7 +53,7 @@ requirements: - python test: commands: - - '$R -e "library(''DEXSeq'')"' + - $R -e "library('DEXSeq')" about: home: https://bioconductor.org/packages/release/bioc/html/DEXSeq.html license: 'GPL (>= 3)' diff --git a/recipes/bioconductor-goseq/meta.yaml b/recipes/bioconductor-goseq/meta.yaml index f84f4e58d7..eda17e17ab 100644 --- a/recipes/bioconductor-goseq/meta.yaml +++ b/recipes/bioconductor-goseq/meta.yaml @@ -2,7 +2,7 @@ package: name: bioconductor-goseq version: 1.26.0 source: - url: https://bioconductor.org/packages/release/bioc/src/contrib/goseq_1.26.0.tar.gz + url: https://depot.galaxyproject.org/software/bioconductor-goseq/bioconductor-goseq_1.26.0_src_all.tar.gz md5: da46e940cc1cf1f624a06c908f07f910 build: number: 0 diff --git a/recipes/r-multicool/build.sh b/recipes/r-multicool/build.sh index 0c37df6e8e..32bc29aa16 100644 --- a/recipes/r-multicool/build.sh +++ b/recipes/r-multicool/build.sh @@ -1,13 +1,6 @@ #!/bin/bash -# R refuses to build packages that mark themselves as Priority: Recommended mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION $R CMD INSTALL --build . - -# Add more build steps here, if they are necessary. - -# See -# http://docs.continuum.io/conda/build.html -# for a list of environment variables that are set during the build process. From 347b9801237689ec2a9e3acc13d8dba3eccade32 Mon Sep 17 00:00:00 2001 From: Bjoern Gruening Date: Wed, 14 Jun 2017 17:54:46 +0200 Subject: [PATCH 102/116] skip this recipe, as it has to strict pinning --- recipes/cgat-scripts/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/cgat-scripts/meta.yaml b/recipes/cgat-scripts/meta.yaml index f9ee6a37ec..81ee26f0f9 100644 --- a/recipes/cgat-scripts/meta.yaml +++ b/recipes/cgat-scripts/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.2.6" %} + {% set version = "0.2.6" %} package: name: cgat-scripts @@ -9,7 +9,7 @@ source: md5: 44f4abc43180440a22883c0f93312338 build: - skip: True # [not py27 or osx] + skip: True number: 0 entry_points: - cgat = CGAT.cgat:main From b868ceeb7df7c63a485081b9bfcf055c0a1563cd Mon Sep 17 00:00:00 2001 From: Bjoern Gruening Date: Thu, 15 Jun 2017 00:31:34 +0200 Subject: [PATCH 103/116] r fixes --- recipes/bioconductor-cexor/meta.yaml | 13 ++++++++----- recipes/bioconductor-motiv/build.sh | 6 ++++++ 2 files changed, 14 insertions(+), 5 deletions(-) diff --git a/recipes/bioconductor-cexor/meta.yaml b/recipes/bioconductor-cexor/meta.yaml index 5b7d1babae..38cacddceb 100644 --- a/recipes/bioconductor-cexor/meta.yaml +++ b/recipes/bioconductor-cexor/meta.yaml @@ -1,15 +1,18 @@ package: name: bioconductor-cexor - version: 1.8.0 + version: 1.14.0 + source: - fn: CexoR_1.8.0.tar.gz - url: https://bioarchive.galaxyproject.org/CexoR_1.8.0.tar.gz - md5: c5c013196a0f746623218b96824b4c9a + fn: CexoR_1.14.0.tar.gz + url: http://bioconductor.org/packages/release/bioc/src/contrib/CexoR_1.14.0.tar.gz + sha256: a45fed681bcbe9f6845b6ccd92b312fda8ec221f771861fa6127adb7e6546373 + build: number: 0 rpaths: - lib/R/lib/ - lib/ + requirements: build: - bioconductor-genomation @@ -35,7 +38,7 @@ requirements: - r-rcolorbrewer test: commands: - - '$R -e "library(''CexoR'')"' + - $R -e "library('CexoR')" about: home: http://bioconductor.org/packages/release/bioc/html/CexoR.html license: 'Artistic-2.0 | GPL-2 + file LICENSE' diff --git a/recipes/bioconductor-motiv/build.sh b/recipes/bioconductor-motiv/build.sh index 92a7d873ce..9b821879d2 100644 --- a/recipes/bioconductor-motiv/build.sh +++ b/recipes/bioconductor-motiv/build.sh @@ -1,6 +1,12 @@ #!/bin/bash +export CFLAGS="$(gsl-config --cflags)" +export LDFLAGS="$(gsl-config --libs)" + +# For whatever reason, it can't link to gsl correctly without this on OS X. +export DYLD_FALLBACK_LIBRARY_PATH=$PREFIX/lib + export LD_LIBRARY_PATH=$PREFIX/lib mv DESCRIPTION DESCRIPTION.old From 0d360e578c3286d2d071637e4ef454155fa60e95 Mon Sep 17 00:00:00 2001 From: Bjoern Gruening Date: Thu, 15 Jun 2017 03:56:12 +0200 Subject: [PATCH 104/116] remove old nanoraw package --- recipes/nanoraw/0.3.1/build.sh | 9 -------- recipes/nanoraw/0.3.1/meta.yaml | 48 ----------------------------------------- 2 files changed, 57 deletions(-) delete mode 100644 recipes/nanoraw/0.3.1/build.sh delete mode 100644 recipes/nanoraw/0.3.1/meta.yaml diff --git a/recipes/nanoraw/0.3.1/build.sh b/recipes/nanoraw/0.3.1/build.sh deleted file mode 100644 index 3f50b74e1b..0000000000 --- a/recipes/nanoraw/0.3.1/build.sh +++ /dev/null @@ -1,9 +0,0 @@ -#!/bin/bash - -$PYTHON setup.py install - -# Add more build steps here, if they are necessary. - -# See -# http://docs.continuum.io/conda/build.html -# for a list of environment variables that are set during the build process. diff --git a/recipes/nanoraw/0.3.1/meta.yaml b/recipes/nanoraw/0.3.1/meta.yaml deleted file mode 100644 index 64e9082ff0..0000000000 --- a/recipes/nanoraw/0.3.1/meta.yaml +++ /dev/null @@ -1,48 +0,0 @@ -package: - name: nanoraw - version: "0.3.1" - -source: - fn: nanoraw-0.3.1.tar.gz - url: https://pypi.python.org/packages/ae/5f/229de76718d161c6cb3cb29f6decab2adc444dd8c43b55d5354a7b2c91e7/nanoraw-0.3.1.tar.gz - md5: 992a56b78c49b53885446f2ec5612506 - -build: - entry_points: - - nanoraw = nanoraw.__main__:main - number: 0 - skip: True # [not py27] - -requirements: - build: - - python - - setuptools - - h5py - - rpy2 >=2.4.2 - - numpy - - scipy - - r-base - - r-ggplot2 - - run: - - python - - h5py - - rpy2 >=2.4.2 - - numpy - - scipy - - r-base - - r-ggplot2 - -test: - imports: - - nanoraw - - commands: - - nanoraw --help - -about: - home: https://github.com/marcus1487/nanoraw - license: BSD - summary: 'Analysis of nanopore sequencing data.' - license_family: BSD - From a4a5ab956d0250f511196ed122fd23abdefaac4a Mon Sep 17 00:00:00 2001 From: Bjoern Gruening Date: Thu, 15 Jun 2017 04:50:14 +0200 Subject: [PATCH 105/116] fix osx version --- recipes/macs2/build.sh | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/recipes/macs2/build.sh b/recipes/macs2/build.sh index cb1d4a48fa..bc0c93b15e 100644 --- a/recipes/macs2/build.sh +++ b/recipes/macs2/build.sh @@ -1,5 +1,9 @@ #!/bin/bash +if [[ `uname` == 'Darwin' ]]; then + export MACOSX_DEPLOYMENT_TARGET=10.9 +fi + # From setup.py: User must check GCC, if >= 4.6, use -Ofast, otherwise -O3. GCCVERSION=$( gcc -dumpversion ) GCCVERSION_MAJOR=$(echo $GCCVERSION | awk 'BEGIN {FS="."}; {print $1}') From 6d44bf52af37457651c1df42eab9562a193c4720 Mon Sep 17 00:00:00 2001 From: Bjoern Gruening Date: Thu, 15 Jun 2017 04:51:20 +0200 Subject: [PATCH 106/116] r fixes --- recipes/r-multicool/meta.yaml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/recipes/r-multicool/meta.yaml b/recipes/r-multicool/meta.yaml index 2cf3ebe660..a4348018b6 100644 --- a/recipes/r-multicool/meta.yaml +++ b/recipes/r-multicool/meta.yaml @@ -20,7 +20,8 @@ requirements: build: - r-base - r-rcpp >=0.11.2 - - gcc + - gcc # [not osx] + - llvm # [osx] run: - r-base From e2988918afab5820bd12bca1445535ade81b98ce Mon Sep 17 00:00:00 2001 From: Bjoern Gruening Date: Thu, 15 Jun 2017 08:58:15 +0200 Subject: [PATCH 107/116] r fixes --- recipes/r-ggally/meta.yaml | 1 - 1 file changed, 1 deletion(-) diff --git a/recipes/r-ggally/meta.yaml b/recipes/r-ggally/meta.yaml index 863cfbe358..449618bd06 100644 --- a/recipes/r-ggally/meta.yaml +++ b/recipes/r-ggally/meta.yaml @@ -7,7 +7,6 @@ package: source: fn: GGally_1.3.0.tar.gz url: - - https://cran.r-project.org/src/contrib/GGally_1.3.0.tar.gz - http://cran.r-project.org/src/contrib/Archive/GGally/GGally_1.3.0.tar.gz sha256: 6bdccc90a2cb6d363e5646ecae3b62db475a8560a333b3d661c98166c152ad89 From c2a6e0aabff789ee35b6ddda38df2f5f919e9946 Mon Sep 17 00:00:00 2001 From: Bjoern Gruening Date: Thu, 15 Jun 2017 08:59:58 +0200 Subject: [PATCH 108/116] remove older releases --- recipes/bioconductor-camera/1.22.0/build.sh | 17 ------------ recipes/bioconductor-camera/1.22.0/meta.yaml | 40 ---------------------------- recipes/bioconductor-camera/1.26.0/build.sh | 17 ------------ recipes/bioconductor-camera/1.26.0/meta.yaml | 40 ---------------------------- 4 files changed, 114 deletions(-) delete mode 100644 recipes/bioconductor-camera/1.22.0/build.sh delete mode 100644 recipes/bioconductor-camera/1.22.0/meta.yaml delete mode 100644 recipes/bioconductor-camera/1.26.0/build.sh delete mode 100644 recipes/bioconductor-camera/1.26.0/meta.yaml diff --git a/recipes/bioconductor-camera/1.22.0/build.sh b/recipes/bioconductor-camera/1.22.0/build.sh deleted file mode 100644 index 6c7a1726e3..0000000000 --- a/recipes/bioconductor-camera/1.22.0/build.sh +++ /dev/null @@ -1,17 +0,0 @@ - -#!/bin/bash - -# R refuses to build packages that mark themselves as -# "Priority: Recommended" -mv DESCRIPTION DESCRIPTION.old -grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION -# -$R CMD INSTALL --build . -# -# # Add more build steps here, if they are necessary. -# -# See -# http://docs.continuum.io/conda/build.html -# for a list of environment variables that are set during the build -# process. -# \ No newline at end of file diff --git a/recipes/bioconductor-camera/1.22.0/meta.yaml b/recipes/bioconductor-camera/1.22.0/meta.yaml deleted file mode 100644 index f96c7dde2a..0000000000 --- a/recipes/bioconductor-camera/1.22.0/meta.yaml +++ /dev/null @@ -1,40 +0,0 @@ -package: - name: bioconductor-camera - version: 1.22.0 -source: - fn: CAMERA_1.22.0.tar.gz - url: https://bioarchive.galaxyproject.org/CAMERA_1.22.0.tar.gz - md5: c570d514518bf667fbbc65c93a1ecf0a -build: - number: 1 - skip: True # [osx] - rpaths: - - lib/R/lib/ - - lib/ -requirements: - build: - - bioconductor-biobase - - bioconductor-graph - - bioconductor-rbgl - - 'bioconductor-xcms >=1.13.5' - - r-base - - r-hmisc - - gmp - - r-igraph - run: - - bioconductor-biobase - - bioconductor-graph - - bioconductor-rbgl - - 'bioconductor-xcms >=1.13.5' - - r-base - - r-hmisc - - gmp - - r-igraph -test: - commands: - - '$R -e "library(''CAMERA'')"' -about: - home: http://bioconductor.org/packages/release/bioc/html/CAMERA.html - license: 'GPL (>= 2)' - summary: 'Annotation of peaklists generated by xcms, rule based annotation of isotopes - and adducts, EIC correlation based tagging of unknown adducts and fragments' diff --git a/recipes/bioconductor-camera/1.26.0/build.sh b/recipes/bioconductor-camera/1.26.0/build.sh deleted file mode 100644 index 6c7a1726e3..0000000000 --- a/recipes/bioconductor-camera/1.26.0/build.sh +++ /dev/null @@ -1,17 +0,0 @@ - -#!/bin/bash - -# R refuses to build packages that mark themselves as -# "Priority: Recommended" -mv DESCRIPTION DESCRIPTION.old -grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION -# -$R CMD INSTALL --build . -# -# # Add more build steps here, if they are necessary. -# -# See -# http://docs.continuum.io/conda/build.html -# for a list of environment variables that are set during the build -# process. -# \ No newline at end of file diff --git a/recipes/bioconductor-camera/1.26.0/meta.yaml b/recipes/bioconductor-camera/1.26.0/meta.yaml deleted file mode 100644 index c8793fbc21..0000000000 --- a/recipes/bioconductor-camera/1.26.0/meta.yaml +++ /dev/null @@ -1,40 +0,0 @@ -package: - name: bioconductor-camera - version: 1.26.0 -source: - fn: CAMERA_1.26.0.tar.gz - url: https://bioarchive.galaxyproject.org/CAMERA_1.26.0.tar.gz - md5: 2b928ca28bf0ec22b40a6ec61ec0be99 -build: - number: 1 - skip: True # [osx] - rpaths: - - lib/R/lib/ - - lib/ -requirements: - build: - - bioconductor-biobase - - bioconductor-graph - - bioconductor-rbgl - - 'bioconductor-xcms >=1.13.5' - - r-base - - r-hmisc - - gmp - - r-igraph - run: - - bioconductor-biobase - - bioconductor-graph - - bioconductor-rbgl - - 'bioconductor-xcms >=1.13.5' - - r-base - - r-hmisc - - gmp - - r-igraph -test: - commands: - - $R -e "library('CAMERA')" -about: - home: http://bioconductor.org/packages/release/bioc/html/CAMERA.html - license: 'GPL (>= 2)' - summary: 'Annotation of peaklists generated by xcms, rule based annotation of isotopes - and adducts, EIC correlation based tagging of unknown adducts and fragments' From c3edb341b499438f42081c982899d97ed1ba5e83 Mon Sep 17 00:00:00 2001 From: Bjoern Gruening Date: Thu, 15 Jun 2017 10:13:41 +0200 Subject: [PATCH 109/116] this pkg is a bioc package --- recipes/r-ipo/build.sh | 14 ------- recipes/r-ipo/meta.yaml | 106 ------------------------------------------------ 2 files changed, 120 deletions(-) delete mode 100644 recipes/r-ipo/build.sh delete mode 100644 recipes/r-ipo/meta.yaml diff --git a/recipes/r-ipo/build.sh b/recipes/r-ipo/build.sh deleted file mode 100644 index 7fe0351a83..0000000000 --- a/recipes/r-ipo/build.sh +++ /dev/null @@ -1,14 +0,0 @@ -#!/bin/bash - -# R refuses to build packages that mark themselves as Priority: Recommended -mv DESCRIPTION DESCRIPTION.old -grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION - -$R CMD INSTALL --build . - -# Add more build steps here, if they are necessary. -#R -e "library(devtools); source('http://www.bioconductor.org/biocLite.R'); install_github('glibiseller/IPO') " - -# See -# http://docs.continuum.io/conda/build.html -# for a list of environment variables that are set during the build process. diff --git a/recipes/r-ipo/meta.yaml b/recipes/r-ipo/meta.yaml deleted file mode 100644 index 9986dc2fcc..0000000000 --- a/recipes/r-ipo/meta.yaml +++ /dev/null @@ -1,106 +0,0 @@ -package: - name: r-ipo - version: "1.7.5" - -source: - fn: 3e99def7e2ad455c075edf65c1923a76583c911b.tar.gz - url: https://github.com/glibiseller/IPO/archive/3e99def7e2ad455c075edf65c1923a76583c911b.tar.gz - -build: - skip: True # [osx] - # If this is a new build for the same version, increment the build - # number. If you do not include this key, it defaults to 0. - # number: 1 - - # This is required to make R link correctly on Linux. - rpaths: - - lib/R/lib/ - - lib/ - -# Suggests: parallel -requirements: - build: - - r-base - - bioconductor-xcms - - r-rsm - - bioconductor-camera - #- libnetcdf 4.2.1.1 - - run: - - r-base - - bioconductor-xcms - - r-rsm - - bioconductor-camera - #- libnetcdf 4.2.1.1 - -test: - commands: - # You can put additional test commands to be run here. - - $R -e "library('IPO')" # [not win] - #- "\"%R%\" -e \"library('IPO')\"" # [win] - - # You can also put a file called run_test.py, run_test.sh, or run_test.bat - # in the recipe that will be run at test time. - - # requires: - # Put any additional test requirements here. - -about: - home: https://github.com/glibiseller/IPO - license: GPL (>= 2) + file LICENSE - summary: The outcome of XCMS data processing strongly depends on the - parameter settings. IPO ('Isotopologue Parameter Optimization') is a parameter - optimization tool that is applicable for different kinds of samples and liquid - chromatography coupled to high resolution mass spectrometry devices, fast and - free of labeling steps. IPO uses natural, stable 13C isotopes to calculate a - peak picking score. Retention time correction is optimized by minimizing the - relative retention time differences within features and grouping parameters are - optimized by maximizing the number of features showing exactly one peak from - each injection of a pooled sample. The different parameter settings are achieved - by design of experiment. The resulting scores are evaluated using response - surface models. - - -# The original GitHub metadata for this package was: -# https://github.com/glibiseller/IPO/blob/master/DESCRIPTION - -#Package: IPO -#Type: Package -#Title: Automated Optimization of XCMS Data Processing parameters -#Version: 1.7.5 -#Date: 2016-04-15 -#Author: Libiseller, Gunnar -# Magnes, Christoph -#Maintainer: Riebenbauer, Thomas -#Depends: -# xcms, -# rsm, -# CAMERA -#Suggests: -# RUnit, -# BiocGenerics, -# msdata, -# mtbls2, -# knitr -#Enhances: parallel -#VignetteBuilder: knitr -#Description: The outcome of XCMS data processing strongly depends on the -# parameter settings. IPO ('Isotopologue Parameter Optimization') is a parameter -# optimization tool that is applicable for different kinds of samples and liquid -# chromatography coupled to high resolution mass spectrometry devices, fast and -# free of labeling steps. IPO uses natural, stable 13C isotopes to calculate a -# peak picking score. Retention time correction is optimized by minimizing the -# relative retention time differences within features and grouping parameters are -# optimized by maximizing the number of features showing exactly one peak from -# each injection of a pooled sample. The different parameter settings are achieved -# by design of experiment. The resulting scores are evaluated using response -# surface models. -#License: GPL (>= 2) + file LICENSE -#URL: https://github.com/glibiseller/IPO -#BugReports: https://github.com/glibiseller/IPOs/issues/new -#biocViews: Metabolomics, MassSpectrometry -#RoxygenNote: 5.0.1 - -# See -# http://docs.continuum.io/conda/build.html for -# more information about meta.yaml From 022751af723a6159a9debf256c925621bb9c7292 Mon Sep 17 00:00:00 2001 From: Bjoern Gruening Date: Thu, 15 Jun 2017 10:28:54 +0200 Subject: [PATCH 110/116] r fixes --- recipes/bioconductor-motiv/meta.yaml | 6 ++++-- recipes/r-ggally/0.5.0/meta.yaml | 13 +------------ recipes/r-ggally/meta.yaml | 2 +- recipes/r-multicool/build.sh | 5 +++++ 4 files changed, 11 insertions(+), 15 deletions(-) diff --git a/recipes/bioconductor-motiv/meta.yaml b/recipes/bioconductor-motiv/meta.yaml index 40b6999c98..384e0328b2 100644 --- a/recipes/bioconductor-motiv/meta.yaml +++ b/recipes/bioconductor-motiv/meta.yaml @@ -27,7 +27,9 @@ requirements: - r-base - gsl {{CONDA_GSL}}* - r-lattice - - gcc + - gcc # [linux] + - llvm # [osx] + run: - 'bioconductor-biocgenerics >=0.1.0' - 'bioconductor-biostrings >=1.24.0' @@ -37,7 +39,7 @@ requirements: - r-base - r-lattice - gsl {{CONDA_GSL}}* - - libgcc + - libgcc # [linux] test: commands: diff --git a/recipes/r-ggally/0.5.0/meta.yaml b/recipes/r-ggally/0.5.0/meta.yaml index beb7eb8bc6..9b58624280 100644 --- a/recipes/r-ggally/0.5.0/meta.yaml +++ b/recipes/r-ggally/0.5.0/meta.yaml @@ -5,20 +5,15 @@ package: source: fn: GGally_0.5.0.tar.gz url: - - https://cran.r-project.org/src/contrib/GGally_1.3.0.tar.gz - http://cran.r-project.org/src/contrib/Archive/GGally/GGally_0.5.0.tar.gz + sha256: b138c38ccc0ed654bc00024c1c784cf92d9c7572c80823e13e349ce814463d02 build: - # If this is a new build for the same version, increment the build - # number. If you do not include this key, it defaults to 0. # number: 1 - - # This is required to make R link correctly on Linux. rpaths: - lib/R/lib/ - lib/ -# Suggests: arm (>= 1.7), intergraph (>= 2.0-0), network (>= 1.7.2), RColorBrewer (>= 1.0-5), scales (>= 0.2.3), scagnostics (>= 0.2-4), sna (>= 2.3-1), survival (>= 2.37-4), tnet (>= 3.0), roxygen2 (>= 4.0.1) requirements: build: - r-base @@ -44,12 +39,6 @@ test: - $R -e "library('GGally')" # [not win] - "\"%R%\" -e \"library('GGally')\"" # [win] - # You can also put a file called run_test.py, run_test.sh, or run_test.bat - # in the recipe that will be run at test time. - - # requires: - # Put any additional test requirements here. - about: #home: license: GPL (>= 2.0) diff --git a/recipes/r-ggally/meta.yaml b/recipes/r-ggally/meta.yaml index 449618bd06..2a049dc2c1 100644 --- a/recipes/r-ggally/meta.yaml +++ b/recipes/r-ggally/meta.yaml @@ -7,7 +7,7 @@ package: source: fn: GGally_1.3.0.tar.gz url: - - http://cran.r-project.org/src/contrib/Archive/GGally/GGally_1.3.0.tar.gz + - https://cran.r-project.org/src/contrib/Archive/GGally/GGally_1.3.0.tar.gz sha256: 6bdccc90a2cb6d363e5646ecae3b62db475a8560a333b3d661c98166c152ad89 build: diff --git a/recipes/r-multicool/build.sh b/recipes/r-multicool/build.sh index 32bc29aa16..a30e93faef 100644 --- a/recipes/r-multicool/build.sh +++ b/recipes/r-multicool/build.sh @@ -1,5 +1,10 @@ #!/bin/bash +if [ "$(uname)" == "Darwin" ]; then + CXXFLAGS="$CXXFLAGS -fno-common" +fi + + mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION From 5b786d285aa340367c7439b150c7e2aeb6c06d1a Mon Sep 17 00:00:00 2001 From: Bjoern Gruening Date: Thu, 15 Jun 2017 12:32:54 +0200 Subject: [PATCH 111/116] remove old r-ggally version --- recipes/r-ggally/0.5.0/build.sh | 13 ----------- recipes/r-ggally/0.5.0/meta.yaml | 47 ---------------------------------------- 2 files changed, 60 deletions(-) delete mode 100644 recipes/r-ggally/0.5.0/build.sh delete mode 100644 recipes/r-ggally/0.5.0/meta.yaml diff --git a/recipes/r-ggally/0.5.0/build.sh b/recipes/r-ggally/0.5.0/build.sh deleted file mode 100644 index 0c37df6e8e..0000000000 --- a/recipes/r-ggally/0.5.0/build.sh +++ /dev/null @@ -1,13 +0,0 @@ -#!/bin/bash - -# R refuses to build packages that mark themselves as Priority: Recommended -mv DESCRIPTION DESCRIPTION.old -grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION - -$R CMD INSTALL --build . - -# Add more build steps here, if they are necessary. - -# See -# http://docs.continuum.io/conda/build.html -# for a list of environment variables that are set during the build process. diff --git a/recipes/r-ggally/0.5.0/meta.yaml b/recipes/r-ggally/0.5.0/meta.yaml deleted file mode 100644 index 9b58624280..0000000000 --- a/recipes/r-ggally/0.5.0/meta.yaml +++ /dev/null @@ -1,47 +0,0 @@ -package: - name: r-ggally - version: "0.5.0" - -source: - fn: GGally_0.5.0.tar.gz - url: - - http://cran.r-project.org/src/contrib/Archive/GGally/GGally_0.5.0.tar.gz - sha256: b138c38ccc0ed654bc00024c1c784cf92d9c7572c80823e13e349ce814463d02 - -build: - # number: 1 - rpaths: - - lib/R/lib/ - - lib/ - -requirements: - build: - - r-base - - r-ggplot2 >=1.0.0 - - r-gtable >=0.1.2 - - r-plyr >=1.8 - - r-reshape >=0.8.4 - - r-stringr >=0.6.2 - - r-progress - - run: - - r-base - - r-ggplot2 >=1.0.0 - - r-gtable >=0.1.2 - - r-plyr >=1.8 - - r-reshape >=0.8.4 - - r-stringr >=0.6.2 - - r-progress - -test: - commands: - # You can put additional test commands to be run here. - - $R -e "library('GGally')" # [not win] - - "\"%R%\" -e \"library('GGally')\"" # [win] - -about: - #home: - license: GPL (>= 2.0) - summary: !!python/unicode 'GGally is designed to be a helper to ggplot2. It contains templates - for different plots to be combined into a plot matrix, a parallel coordinate plot - function, as well as a function for making a network plot.' From 6f62239406df0901ba79e30405dfa1b1c7ce9ce6 Mon Sep 17 00:00:00 2001 From: Bjoern Gruening Date: Thu, 15 Jun 2017 13:27:51 +0200 Subject: [PATCH 112/116] readd older version --- recipes/r-ggally/0.5.0/build.sh | 13 +++++++++++ recipes/r-ggally/0.5.0/meta.yaml | 47 ++++++++++++++++++++++++++++++++++++++++ 2 files changed, 60 insertions(+) create mode 100644 recipes/r-ggally/0.5.0/build.sh create mode 100644 recipes/r-ggally/0.5.0/meta.yaml diff --git a/recipes/r-ggally/0.5.0/build.sh b/recipes/r-ggally/0.5.0/build.sh new file mode 100644 index 0000000000..0c37df6e8e --- /dev/null +++ b/recipes/r-ggally/0.5.0/build.sh @@ -0,0 +1,13 @@ +#!/bin/bash + +# R refuses to build packages that mark themselves as Priority: Recommended +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION + +$R CMD INSTALL --build . + +# Add more build steps here, if they are necessary. + +# See +# http://docs.continuum.io/conda/build.html +# for a list of environment variables that are set during the build process. diff --git a/recipes/r-ggally/0.5.0/meta.yaml b/recipes/r-ggally/0.5.0/meta.yaml new file mode 100644 index 0000000000..9b58624280 --- /dev/null +++ b/recipes/r-ggally/0.5.0/meta.yaml @@ -0,0 +1,47 @@ +package: + name: r-ggally + version: "0.5.0" + +source: + fn: GGally_0.5.0.tar.gz + url: + - http://cran.r-project.org/src/contrib/Archive/GGally/GGally_0.5.0.tar.gz + sha256: b138c38ccc0ed654bc00024c1c784cf92d9c7572c80823e13e349ce814463d02 + +build: + # number: 1 + rpaths: + - lib/R/lib/ + - lib/ + +requirements: + build: + - r-base + - r-ggplot2 >=1.0.0 + - r-gtable >=0.1.2 + - r-plyr >=1.8 + - r-reshape >=0.8.4 + - r-stringr >=0.6.2 + - r-progress + + run: + - r-base + - r-ggplot2 >=1.0.0 + - r-gtable >=0.1.2 + - r-plyr >=1.8 + - r-reshape >=0.8.4 + - r-stringr >=0.6.2 + - r-progress + +test: + commands: + # You can put additional test commands to be run here. + - $R -e "library('GGally')" # [not win] + - "\"%R%\" -e \"library('GGally')\"" # [win] + +about: + #home: + license: GPL (>= 2.0) + summary: !!python/unicode 'GGally is designed to be a helper to ggplot2. It contains templates + for different plots to be combined into a plot matrix, a parallel coordinate plot + function, as well as a function for making a network plot.' From 117c8341573f799a61dcbe7cbfef96616e6189af Mon Sep 17 00:00:00 2001 From: Bjoern Gruening Date: Thu, 15 Jun 2017 13:28:42 +0200 Subject: [PATCH 113/116] add R blacklist again --- config.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/config.yml b/config.yml index e4c4b6475e..04d1d5aa7b 100644 --- a/config.yml +++ b/config.yml @@ -1,5 +1,6 @@ env_matrix: "scripts/env_matrix.yml" blacklists: + - "sorted-r-blacklist" - "build-fail-blacklist" - "boost-1.61-migration-blacklist" - "perl-unable-to-find-blacklist" From 02d8eef7fb9a2ed448f51a2c6da9b9c1b3edfc78 Mon Sep 17 00:00:00 2001 From: Bjoern Gruening Date: Thu, 15 Jun 2017 13:29:26 +0200 Subject: [PATCH 114/116] update blacklist --- sorted-r-blacklist | 53 +++++++++++++++++++++++++++++------------------------ 1 file changed, 29 insertions(+), 24 deletions(-) diff --git a/sorted-r-blacklist b/sorted-r-blacklist index 1c2ff29346..25464a2100 100644 --- a/sorted-r-blacklist +++ b/sorted-r-blacklist @@ -3,12 +3,6 @@ recipes/cap-mirseq -# TODO: older limma packages should stay blacklisted until we can track down stable -# URLs for these versions. -recipes/bioconductor-limma/3.26.7 -recipes/bioconductor-limma/3.28.6 -recipes/bioconductor-limma/3.28.2 - # TODO: r-ks has error related to rgl recipes/r-ks @@ -22,20 +16,20 @@ recipes/r-hdrcde recipes/r-rainbow # TODO: r-mutoss has the same problem as r-phonr: it loops indefinitely on osx. -recipes/r-mutoss +#recipes/r-mutoss # TODO: older s4vectors should stay blacklisted until we can track down stable # version for 0.8.7 -recipes/bioconductor-s4vectors/0.8.7 +#recipes/bioconductor-s4vectors/0.8.7 # TODO: older versions o bioconductor-iranges need stable URLS -recipes/bioconductor-iranges/2.4.7 -recipes/bioconductor-iranges/2.4.6 +#recipes/bioconductor-iranges/2.4.7 +#recipes/bioconductor-iranges/2.4.6 -recipes/bioconductor-summarizedexperiment/1.0.2 -recipes/bioconductor-deseq2/1.10.1 -recipes/bioconductor-genelendatabase/1.6.0 +#recipes/bioconductor-summarizedexperiment/1.0.2 +#recipes/bioconductor-deseq2/1.10.1 +#recipes/bioconductor-genelendatabase/1.6.0 # TODO: bioconductor-qdnaseq depends on bioconductor-dnacopy which has some # gfortran issues @@ -52,25 +46,36 @@ recipes/bioconductor-genelendatabase/1.6.0 recipes/bioconductor-bubbletree # DEPRECATE: r-knitr exists in main R channel -recipes/r-knitr +#recipes/r-knitr # TODO: When building, complains that: # Error : object ‘assay’ is not exported by 'namespace:GenomicRanges' # ERROR: lazy loading failed for package ‘SARTools’ # # Maybe it needs an earlier version of bioconductor-genomicranges? -recipes/r-sartools/1.2.0 - -# DEPRECATE: r-readr exists in main R channel -recipes/r-readr +#recipes/r-sartools/1.2.0 # TODO: bioconductor-cexor needs specific version of genomicranges? -recipes/bioconductor-cexor +#recipes/bioconductor-cexor + + + +########################################## +r-maldiquantforeign +bioconductor-ggbio -# TODO: r-phonr seems to loop indefinitely when trying to build. -recipes/r-phonr -recipes/bioconductor-mmdiff +bioconductor-cummerbund +bioconductor-goseq +bioconductor-isomirs +bioconductor-motifbreakr +bioconductor-fourcseq +bioconductor-motifstack +mgkit +bioconductor-motiv +r-ggally +bioconductor-dexseq +r-spp +r-histonehmm +recipes/r-multicool -# try disabling to avoid osx timeouts -recipes/triform2 From 3f2eca212085badee21a918eec80b5557bf26e2d Mon Sep 17 00:00:00 2001 From: Bjoern Gruening Date: Thu, 15 Jun 2017 17:57:34 +0200 Subject: [PATCH 115/116] blacklist the rest of the packages --- sorted-r-blacklist | 29 +++++++++++++---------------- 1 file changed, 13 insertions(+), 16 deletions(-) diff --git a/sorted-r-blacklist b/sorted-r-blacklist index 25464a2100..9fb8cdddbc 100644 --- a/sorted-r-blacklist +++ b/sorted-r-blacklist @@ -61,21 +61,18 @@ recipes/bioconductor-bubbletree ########################################## -r-maldiquantforeign -bioconductor-ggbio - - -bioconductor-cummerbund -bioconductor-goseq -bioconductor-isomirs -bioconductor-motifbreakr -bioconductor-fourcseq -bioconductor-motifstack -mgkit -bioconductor-motiv -r-ggally -bioconductor-dexseq -r-spp -r-histonehmm +recipes/r-maldiquantforeign + +recipes/bioconductor-cummerbund +recipes/bioconductor-goseq +recipes/bioconductor-isomirs +recipes/bioconductor-motifbreakr +recipes/bioconductor-motifstack +recipes/mgkit +recipes/bioconductor-motiv +recipes/r-ggally +recipes/bioconductor-dexseq +recipes/r-spp +recipes/r-histonehmm recipes/r-multicool From 53a22e3b6a533836439973a1dd750ccb6cbca691 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= Date: Thu, 15 Jun 2017 20:58:20 +0200 Subject: [PATCH 116/116] Change back to master branch --- .travis.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.travis.yml b/.travis.yml index d7d2b35b10..a9515727ff 100644 --- a/.travis.yml +++ b/.travis.yml @@ -16,8 +16,8 @@ script: scripts/travis-run.sh env: global: - SUBDAGS=1 - - BIOCONDA_UTILS_TAG=kill_r - - BIOCONDA_UTILS_BUILD_ARGS="" + - BIOCONDA_UTILS_TAG=master + - BIOCONDA_UTILS_BUILD_ARGS="--loglevel=info" - BIOCONDA_UTILS_LINT_ARGS= - MINICONDA_VER="4.2.12" matrix: