From fd2ecba171e1ffbfb94f65bc698e11c80852ba7e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= Date: Thu, 15 Jun 2017 22:06:55 +0200 Subject: [PATCH] R rebuild against R 3.3.2 from conda-forge (#4972) * Add R package micropan * Add R package microseq * start rebuilding for R 3.3.2 without the r-channel * change channel order * various fixes * various fixes * fixes to bioc packages * fixes * remove blacklist * multiple fixes * multiple fixes * fixes * r fixes * change r to r-base * change r to r-base * change r to r-base * url fix * r fixes * r fixes * remove irganes 2.4.7 * r fixes * r fixes * r fixes * remove older version * r fixes * r fixes * r fixes * r fixes * r fixes * r fixes * r fixes * r fixes * rename folder * remove recipe * update bioc skeleton; fix tximport & biomformat * r fixes * fix syntax * r fixes * r fixes * update flowViz recipe * fix BiocStyle recipe * fix org.Hs.eg.db * fix bioconductor_skeleton to auto-find data packages * fix SummarizedExperiment * fix BiocParallel * fix fastseg * fix org.Dm.eg.db * R 3.3.2 has a different set of default packages * fix bioconductor-biomformat * r fixes * bioconductor_skeleton handles typos in DESCRIPTION * fix DEGreport * fix flowViz again * fix multtest * r fixes * more fixes to bioconductor_skeleton * fix org.{Hs,Dm}.eg.db * update the update_bioconductor_packages script to build topsorted dag * fix Category * fix genefilter * add matrix to summarizedexperiment * add urls for gostats * fix MotIV * urls for rGADEM * urls and built-ins for Ringo * urls for zlibbioc * r fixes * r fixes * remove old package * r fixes * r-fixes * r fixes * rpy * r fixes * Minor formatting * add readline to some failing R packages * remove old recipe * Remove micropan from this branch * remove libffi * remove old recipe * r fixes * pin rpy to conda-forge version * Apply comments bgruening * r fixes * enable more debug output * Disable debug logging. * Fix zifa source. * Imrpove cap-mirseq recipe. * r fixes * remove rpy2 * r fixes * r fixes * r fixes * r fixes * remove old version * add new version * r fixes * try some fixes * remove old package * r fixes * r fixes * skip this recipe, as it has to strict pinning * r fixes * remove old nanoraw package * fix osx version * r fixes * r fixes * remove older releases * this pkg is a bioc package * r fixes * remove old r-ggally version * readd older version * add R blacklist again * update blacklist * blacklist the rest of the packages * Change back to master branch --- config.yml | 3 +- recipes/bcbio-rnaseq/meta.yaml | 2 +- recipes/bioconductor-affy/meta.yaml | 4 +- recipes/bioconductor-affyio/meta.yaml | 4 +- recipes/bioconductor-alpine/meta.yaml | 6 +- recipes/bioconductor-annotate/meta.yaml | 4 +- recipes/bioconductor-annotationdbi/meta.yaml | 4 +- recipes/bioconductor-annotationforge/meta.yaml | 4 +- recipes/bioconductor-annotationhub/meta.yaml | 4 +- recipes/bioconductor-aroma.light/meta.yaml | 4 +- 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recipes/{r-ipo => r-sartools}/build.sh | 0 recipes/r-sartools/meta.yaml | 36 +++++++ recipes/r-scatterplot3d/meta.yaml | 6 +- recipes/r-scrm/meta.yaml | 34 +------ recipes/r-segmented/meta.yaml | 1 - recipes/r-sendmailr/meta.yaml | 4 +- recipes/r-seqinr/meta.yaml | 5 +- recipes/r-sets/meta.yaml | 1 - recipes/r-shape/meta.yaml | 4 +- recipes/r-signal/meta.yaml | 4 +- recipes/r-skellam/meta.yaml | 4 +- recipes/r-sleuth/meta.yaml | 6 +- recipes/r-snow/meta.yaml | 5 +- recipes/r-snowfall/meta.yaml | 4 +- recipes/r-soap-nmr/meta.yaml | 11 ++- recipes/r-sparql/meta.yaml | 4 +- recipes/r-spdep/meta.yaml | 5 +- recipes/r-speaq/meta.yaml | 1 - recipes/r-speedglm/meta.yaml | 21 +--- recipes/r-splancs/meta.yaml | 38 ++------ 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 | 5 +- recipes/r-vegan/2.3_0/meta.yaml | 4 +- recipes/r-vegan/2.3_3/meta.yaml | 5 +- recipes/r-vegan/2.3_4/meta.yaml | 33 +++---- recipes/r-venndiagram/meta.yaml | 35 +------ recipes/r-viridis/meta.yaml | 5 +- 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 +- recipes/r-yaml/meta.yaml | 43 +-------- recipes/rpy2/build.sh | 9 -- recipes/rpy2/meta.yaml | 54 ----------- recipes/rseqc/meta.yaml | 2 +- recipes/seq2hla/meta.yaml | 2 +- recipes/triform2/meta.yaml | 8 +- recipes/tssar/meta.yaml | 4 +- recipes/zifa/meta.yaml | 4 +- scripts/bioconductor/bioconductor_skeleton.py | 22 +++-- .../bioconductor/update_bioconductor_packages.py | 13 +-- scripts/env_matrix.yml | 2 +- sorted-r-blacklist | 50 +++++----- 503 files changed, 1632 insertions(+), 4158 deletions(-) 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 delete mode 100644 recipes/bioconductor-deseq2/1.10.1/build.sh delete mode 100644 recipes/bioconductor-deseq2/1.10.1/meta.yaml delete mode 100644 recipes/bioconductor-genelendatabase/1.6.0/build.sh delete mode 100644 recipes/bioconductor-genelendatabase/1.6.0/meta.yaml delete mode 100644 recipes/bioconductor-iranges/2.4.6/build.sh delete mode 100644 recipes/bioconductor-iranges/2.4.6/meta.yaml delete mode 100644 recipes/bioconductor-iranges/2.4.7/build.sh delete mode 100644 recipes/bioconductor-iranges/2.4.7/meta.yaml delete mode 100644 recipes/bioconductor-limma/3.26.7/build.sh delete mode 100644 recipes/bioconductor-limma/3.26.7/meta.yaml rename recipes/{bioconductor-camera/1.22.0 => bioconductor-limma/3.28.10}/build.sh (100%) create mode 100644 recipes/bioconductor-limma/3.28.10/meta.yaml delete mode 100644 recipes/bioconductor-limma/3.28.6/build.sh delete mode 100644 recipes/bioconductor-limma/3.28.6/meta.yaml delete mode 100644 recipes/bioconductor-summarizedexperiment/1.0.2/build.sh delete mode 100644 recipes/bioconductor-summarizedexperiment/1.0.2/meta.yaml 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 delete mode 100644 recipes/nanoraw/0.3.1/build.sh delete mode 100644 recipes/nanoraw/0.3.1/meta.yaml delete mode 100644 recipes/poretools/0.5.0/build.sh delete mode 100644 recipes/poretools/0.5.0/meta.yaml delete mode 100644 recipes/r-ipo/meta.yaml create mode 100644 recipes/r-microseq/build.sh create mode 100644 recipes/r-microseq/meta.yaml 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 rename recipes/{r-ipo => r-sartools}/build.sh (100%) create mode 100644 recipes/r-sartools/meta.yaml delete mode 100644 recipes/rpy2/build.sh delete mode 100644 recipes/rpy2/meta.yaml diff --git a/config.yml b/config.yml index cb1943760d..04d1d5aa7b 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 + - defaults docker_client_version: '1.20' 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/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..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 @@ -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-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-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-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: - '$R -e "library(''Biobase'')"' + about: home: https://bioconductor.org/packages/release/bioc/html/Biobase.html license: Artistic-2.0 diff --git a/recipes/bioconductor-biocinstaller/meta.yaml b/recipes/bioconductor-biocinstaller/meta.yaml index 6e37cc68cc..e88d9fcb36 100644 --- a/recipes/bioconductor-biocinstaller/meta.yaml +++ b/recipes/bioconductor-biocinstaller/meta.yaml @@ -1,25 +1,29 @@ package: name: bioconductor-biocinstaller - version: 1.22.3 + version: 1.24.0 + source: - fn: BiocInstaller_1.22.3.tar.gz - url: http://bioconductor.org/packages/release/bioc/src/contrib/BiocInstaller_1.22.3.tar.gz - md5: b4547d5fd23d431f2e9ce78a1f619bac + fn: BiocInstaller_1.24.0.tar.gz + url: https://bioarchive.galaxyproject.org/BiocInstaller_1.24.0.tar.gz + sha256: 74d89e27db12d216cd22d99e12372f3e1ffbad5eb71ab6f446ab7190cbcb7943 + build: number: 0 rpaths: - lib/R/lib/ - lib/ + requirements: build: - - r + - r-base run: - - r + - r-base + test: commands: - '$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-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 -# $R CMD INSTALL --build . -# -# # Add more build steps here, if they are necessary. -# -# See -# http://docs.continuum.io/conda/build.html -# for a list of environment variables that are set during the build -# process. # \ No newline at end of file diff --git a/recipes/bioconductor-biocparallel/meta.yaml b/recipes/bioconductor-biocparallel/meta.yaml index 6fe42a0a69..c9a2e405f0 100644 --- a/recipes/bioconductor-biocparallel/meta.yaml +++ b/recipes/bioconductor-biocparallel/meta.yaml @@ -3,27 +3,29 @@ package: version: 1.6.6 source: fn: BiocParallel_1.6.6.tar.gz - url: http://bioconductor.org/packages/release/bioc/src/contrib/BiocParallel_1.6.6.tar.gz + url: + - http://bioconductor.org/packages/3.3/bioc/src/contrib/BiocParallel_1.6.6.tar.gz + - https://depot.galaxyproject.org/software/BiocParallel/BiocParallel_1.6.6_src_all.tar.gz md5: 445ec78a20e348d678d2e7b8dc5b4354 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ requirements: build: - - r + - r-base - r-futile.logger - r-snow run: - - r + - r-base - r-futile.logger - r-snow test: commands: - '$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.' 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 -# $R CMD INSTALL --build . -# -# # Add more build steps here, if they are necessary. -# -# See -# http://docs.continuum.io/conda/build.html -# for a list of environment variables that are set during the build -# process. # \ No newline at end of file diff --git a/recipes/bioconductor-biocstyle/meta.yaml b/recipes/bioconductor-biocstyle/meta.yaml index 26b1470aed..ff555f2cc0 100644 --- a/recipes/bioconductor-biocstyle/meta.yaml +++ b/recipes/bioconductor-biocstyle/meta.yaml @@ -3,23 +3,25 @@ package: version: 2.0.3 source: fn: BiocStyle_2.0.3.tar.gz - url: http://bioconductor.org/packages/release/bioc/src/contrib/BiocStyle_2.0.3.tar.gz + url: + - http://bioconductor.org/packages/3.3/bioc/src/contrib/BiocStyle_2.0.3.tar.gz + - https://depot.galaxyproject.org/software/BiocStyle/BiocStyle_2.0.3_src_all.tar.gz md5: 426dcf23e33d0d29b10b6d40cae2054e build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ requirements: build: - - r + - r-base run: - - r + - r-base test: commands: - '$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.' 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/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 -# $R CMD INSTALL --build . -# -# # Add more build steps here, if they are necessary. -# -# See -# http://docs.continuum.io/conda/build.html -# for a list of environment variables that are set during the build -# process. # \ No newline at end of file diff --git a/recipes/bioconductor-biomformat/meta.yaml b/recipes/bioconductor-biomformat/meta.yaml index 9be7272faf..e521dfbb62 100644 --- a/recipes/bioconductor-biomformat/meta.yaml +++ b/recipes/bioconductor-biomformat/meta.yaml @@ -1,31 +1,43 @@ package: name: bioconductor-biomformat version: 1.2.0 + source: fn: biomformat_1.2.0.tar.gz - url: https://bioarchive.galaxyproject.org/biomformat_1.2.0.tar.gz - md5: 2e9efdd64bf09eecdc3699018203c18e + url: + - http://bioconductor.org/packages/3.4/bioc/src/contrib/biomformat_1.2.0.tar.gz + - https://bioarchive.galaxyproject.org/biomformat_1.2.0.tar.gz + - https://depot.galaxyproject.org/software/biomformat/biomformat_1.2.0_src_all.tar.gz + md5: 0a418f48c731375953ff7389b9b6f7a0 + build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + requirements: build: - bioconductor-rhdf5 - - r + - r-base - 'r-jsonlite >=0.9.16' + - 'r-matrix >=1.2' - 'r-plyr >=1.8' + - r-matrix run: - bioconductor-rhdf5 - - r + - r-base - 'r-jsonlite >=0.9.16' + - 'r-matrix >=1.2' - 'r-plyr >=1.8' + - r-matrix + test: commands: - '$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-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-bsgenome/meta.yaml b/recipes/bioconductor-bsgenome/meta.yaml index 54bd5d4b8b..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: @@ -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-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 deleted file mode 100644 index 1f75bf85b9..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 - - r-hmisc - - gmp - - r-igraph - run: - - bioconductor-biobase - - bioconductor-graph - - bioconductor-rbgl - - 'bioconductor-xcms >=1.13.5' - - r - - 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 -# -$R CMD INSTALL --build . -# -# # Add more build steps here, if they are necessary. -# -# See -# http://docs.continuum.io/conda/build.html -# for a list of environment variables that are set during the build -# process. -# \ No newline at end of file diff --git a/recipes/bioconductor-camera/1.26.0/meta.yaml b/recipes/bioconductor-camera/1.26.0/meta.yaml deleted file mode 100644 index 82c2f90ae9..0000000000 --- a/recipes/bioconductor-camera/1.26.0/meta.yaml +++ /dev/null @@ -1,40 +0,0 @@ -package: - name: bioconductor-camera - version: 1.26.0 -source: - fn: CAMERA_1.26.0.tar.gz - url: https://bioarchive.galaxyproject.org/CAMERA_1.26.0.tar.gz - md5: 2b928ca28bf0ec22b40a6ec61ec0be99 -build: - number: 1 - skip: True # [osx] - rpaths: - - lib/R/lib/ - - lib/ -requirements: - build: - - bioconductor-biobase - - bioconductor-graph - - bioconductor-rbgl - - 'bioconductor-xcms >=1.13.5' - - r - - r-hmisc - - gmp - - r-igraph - run: - - bioconductor-biobase - - bioconductor-graph - - bioconductor-rbgl - - 'bioconductor-xcms >=1.13.5' - - r - - r-hmisc - - gmp - - r-igraph -test: - commands: - - '$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/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..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 @@ -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/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 -# $R CMD INSTALL --build . -# -# # Add more build steps here, if they are necessary. -# -# See -# http://docs.continuum.io/conda/build.html -# for a list of environment variables that are set during the build -# process. # \ No newline at end of file diff --git a/recipes/bioconductor-category/meta.yaml b/recipes/bioconductor-category/meta.yaml index be52a1221b..1be021c96a 100644 --- a/recipes/bioconductor-category/meta.yaml +++ b/recipes/bioconductor-category/meta.yaml @@ -3,10 +3,13 @@ package: version: 2.38.0 source: fn: Category_2.38.0.tar.gz - url: https://bioarchive.galaxyproject.org/Category_2.38.0.tar.gz - md5: dfd13491db8e1da509fadec8306d0562 + url: + - http://bioconductor.org/packages/3.3/bioc/src/contrib/Category_2.38.0.tar.gz + - https://bioarchive.galaxyproject.org/Category_2.38.0.tar.gz + - https://depot.galaxyproject.org/software/Category/Category_2.38.0_src_all.tar.gz + md5: 4562ae7a6d4d5d52ee883c71ab2a81f8 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,7 +23,8 @@ requirements: - bioconductor-graph - bioconductor-gseabase - bioconductor-rbgl - - r + - r-base + - r-matrix - r-rsqlite run: - bioconductor-annotate @@ -31,12 +35,13 @@ requirements: - bioconductor-graph - bioconductor-gseabase - bioconductor-rbgl - - r + - r-base + - r-matrix - r-rsqlite test: commands: - '$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.' diff --git a/recipes/bioconductor-cexor/meta.yaml b/recipes/bioconductor-cexor/meta.yaml index f73243c8bc..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 @@ -19,7 +22,7 @@ requirements: - bioconductor-rsamtools - bioconductor-rtracklayer - bioconductor-s4vectors - - r + - r-base - r-idr - r-rcolorbrewer run: @@ -30,12 +33,12 @@ requirements: - bioconductor-rsamtools - bioconductor-rtracklayer - bioconductor-s4vectors - - r + - r-base - r-idr - r-rcolorbrewer test: commands: - - '$R -e "library(''CexoR'')"' + - $R -e "library('CexoR')" about: home: http://bioconductor.org/packages/release/bioc/html/CexoR.html license: 'Artistic-2.0 | GPL-2 + file LICENSE' diff --git a/recipes/bioconductor-cghbase/meta.yaml b/recipes/bioconductor-cghbase/meta.yaml index 35cb28e728..12b8ee9b65 100644 --- a/recipes/bioconductor-cghbase/meta.yaml +++ b/recipes/bioconductor-cghbase/meta.yaml @@ -14,11 +14,11 @@ requirements: build: - 'bioconductor-biobase >=2.5.5' - bioconductor-marray - - r + - r-base run: - 'bioconductor-biobase >=2.5.5' - bioconductor-marray - - r + - r-base test: commands: - '$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..45648687db 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 @@ -32,6 +32,7 @@ requirements: - r-plotrix - r-rcolorbrewer - r-upsetr + - r-boot run: - bioconductor-annotationdbi - bioconductor-biocgenerics @@ -43,7 +44,7 @@ requirements: - bioconductor-rtracklayer - 'bioconductor-s4vectors >=0.9.25' - bioconductor-txdb.hsapiens.ucsc.hg19.knowngene - - r + - r-base - r-dplyr - r-ggplot2 - r-gplots @@ -53,6 +54,8 @@ requirements: - r-plotrix - r-rcolorbrewer - r-upsetr + - r-boot + test: commands: - '$R -e "library(''ChIPseeker'')"' 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..85e7341dee 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 @@ -38,7 +38,7 @@ requirements: - r-rsqlite test: commands: - - '$R -e "library(''cummeRbund'')"' + - $R -e "library(''cummeRbund'')" about: home: http://bioconductor.org/packages/release/bioc/html/cummeRbund.html license: Artistic-2.0 diff --git a/recipes/bioconductor-cummerbund/2.8.2/meta.yaml b/recipes/bioconductor-cummerbund/2.8.2/meta.yaml index e2d7e0b95b..3c886aae44 100644 --- a/recipes/bioconductor-cummerbund/2.8.2/meta.yaml +++ b/recipes/bioconductor-cummerbund/2.8.2/meta.yaml @@ -18,7 +18,7 @@ requirements: - bioconductor-gviz - bioconductor-rtracklayer - bioconductor-s4vectors - - r + - r-base - r-fastcluster - r-ggplot2 - r-plyr @@ -30,7 +30,7 @@ requirements: - bioconductor-gviz - bioconductor-rtracklayer - bioconductor-s4vectors - - r + - r-base - r-fastcluster - r-ggplot2 - r-plyr diff --git a/recipes/bioconductor-cummerbund/meta.yaml b/recipes/bioconductor-cummerbund/meta.yaml index 9bef6fd3a5..b9186f79d3 100644 --- a/recipes/bioconductor-cummerbund/meta.yaml +++ b/recipes/bioconductor-cummerbund/meta.yaml @@ -1,15 +1,18 @@ package: name: bioconductor-cummerbund version: 2.16.0 + source: fn: cummeRbund_2.16.0.tar.gz url: https://bioarchive.galaxyproject.org/cummeRbund_2.16.0.tar.gz md5: 873bad2ed2c5a74d7583a0c8ffd21298 + build: number: 0 rpaths: - lib/R/lib/ - lib/ + requirements: build: - bioconductor-biobase @@ -17,7 +20,7 @@ requirements: - bioconductor-gviz - bioconductor-rtracklayer - 'bioconductor-s4vectors >=0.9.25' - - r + - r-base - r-fastcluster - r-ggplot2 - r-plyr @@ -29,15 +32,17 @@ requirements: - bioconductor-gviz - bioconductor-rtracklayer - 'bioconductor-s4vectors >=0.9.25' - - r + - r-base - r-fastcluster - r-ggplot2 - r-plyr - r-reshape2 - r-rsqlite + test: commands: - - '$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/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/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 -# $R CMD INSTALL --build . -# -# # Add more build steps here, if they are necessary. -# -# See -# http://docs.continuum.io/conda/build.html -# for a list of environment variables that are set during the build -# process. # \ No newline at end of file diff --git a/recipes/bioconductor-degreport/meta.yaml b/recipes/bioconductor-degreport/meta.yaml index d0a1a8c2d0..f1618091b5 100644 --- a/recipes/bioconductor-degreport/meta.yaml +++ b/recipes/bioconductor-degreport/meta.yaml @@ -3,10 +3,12 @@ package: version: 1.8.2 source: fn: DEGreport_1.8.2.tar.gz - url: http://bioconductor.org/packages/release/bioc/src/contrib/DEGreport_1.8.2.tar.gz + url: + - http://bioconductor.org/packages/3.3/bioc/src/contrib/DEGreport_1.8.2.tar.gz + - https://depot.galaxyproject.org/software/DEGreport/DEGreport_1.8.2_src_all.tar.gz md5: 4006a779e33f3bb68308ba9f4a7d9f84 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -14,20 +16,20 @@ requirements: build: - bioconductor-biocgenerics - bioconductor-edger - - r + - r-base - r-ggplot2 - r-plyr run: - bioconductor-biocgenerics - bioconductor-edger - - r + - r-base - r-ggplot2 - r-plyr test: commands: - '$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, diff --git a/recipes/bioconductor-deseq/meta.yaml b/recipes/bioconductor-deseq/meta.yaml index fddb9a4147..07ced989a9 100644 --- a/recipes/bioconductor-deseq/meta.yaml +++ b/recipes/bioconductor-deseq/meta.yaml @@ -16,17 +16,19 @@ requirements: - 'bioconductor-biocgenerics >=0.7.5' - bioconductor-genefilter - bioconductor-geneplotter - - r + - r-base - r-locfit - r-rcolorbrewer + - r-mass run: - 'bioconductor-biobase >=2.21.7' - 'bioconductor-biocgenerics >=0.7.5' - bioconductor-genefilter - bioconductor-geneplotter - - r + - r-base - r-locfit - r-rcolorbrewer + - r-mass test: commands: - '$R -e "library(''DESeq'')"' diff --git a/recipes/bioconductor-deseq2/1.10.1/build.sh b/recipes/bioconductor-deseq2/1.10.1/build.sh deleted file mode 100644 index 6c7a1726e3..0000000000 --- a/recipes/bioconductor-deseq2/1.10.1/build.sh +++ /dev/null @@ -1,17 +0,0 @@ - -#!/bin/bash - -# R refuses to build packages that mark themselves as -# "Priority: Recommended" -mv DESCRIPTION DESCRIPTION.old -grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION -# -$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 e01836bb90..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 - - 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 - - r-ggplot2 - - r-hmisc - - r-locfit - - 'r-rcpp >=0.10.1' - - 'r-rcpparmadillo >=0.3.4.4' -test: - commands: - - '$R -e "library(''DESeq2'')"' -about: - home: http://bioconductor.org/packages/release/bioc/html/DESeq2.html - license: 'LGPL (>= 3)' - summary: 'Estimate variance-mean dependence in count data from high-throughput sequencing - assays and test for differential expression based on a model using the negative - binomial distribution.' diff --git a/recipes/bioconductor-deseq2/meta.yaml b/recipes/bioconductor-deseq2/meta.yaml index 1c9293e01b..6d9835f3a8 100644 --- a/recipes/bioconductor-deseq2/meta.yaml +++ b/recipes/bioconductor-deseq2/meta.yaml @@ -2,7 +2,7 @@ package: name: bioconductor-deseq2 version: 1.14.1 source: - url: https://bioconductor.org/packages/release/bioc/src/contrib/DESeq2_1.14.1.tar.gz + url: https://depot.galaxyproject.org/software/bioconductor-deseq2/bioconductor-deseq2_1.14.1_src_all.tar.gz md5: d1c433056295927a6700046e282bcccd build: number: 0 diff --git a/recipes/bioconductor-dexseq/1.18.4/meta.yaml b/recipes/bioconductor-dexseq/1.18.4/meta.yaml index efee167a07..948d1c246d 100644 --- a/recipes/bioconductor-dexseq/1.18.4/meta.yaml +++ b/recipes/bioconductor-dexseq/1.18.4/meta.yaml @@ -26,7 +26,7 @@ requirements: - bioconductor-rsamtools - bioconductor-s4vectors - bioconductor-summarizedexperiment - - r + - r-base - r-hwriter - r-rcolorbrewer - r-statmod @@ -45,15 +45,17 @@ requirements: - bioconductor-rsamtools - bioconductor-s4vectors - bioconductor-summarizedexperiment - - r + - r-base - r-hwriter - r-rcolorbrewer - r-statmod - r-stringr - python + test: commands: - - '$R -e "library(''DEXSeq'')"' + - $R -e "library('DEXSeq')" + about: home: http://bioconductor.org/packages/release/bioc/html/DEXSeq.html license: 'GPL (>= 3)' diff --git a/recipes/bioconductor-dexseq/meta.yaml b/recipes/bioconductor-dexseq/meta.yaml index 15419955e3..a9d938a0ca 100644 --- a/recipes/bioconductor-dexseq/meta.yaml +++ b/recipes/bioconductor-dexseq/meta.yaml @@ -53,7 +53,7 @@ requirements: - python test: commands: - - '$R -e "library(''DEXSeq'')"' + - $R -e "library('DEXSeq')" about: home: https://bioconductor.org/packages/release/bioc/html/DEXSeq.html license: 'GPL (>= 3)' diff --git a/recipes/bioconductor-diffbind/meta.yaml b/recipes/bioconductor-diffbind/meta.yaml index 909dd7a9f0..2552d2c16d 100644 --- a/recipes/bioconductor-diffbind/meta.yaml +++ b/recipes/bioconductor-diffbind/meta.yaml @@ -30,7 +30,7 @@ requirements: - bioconductor-summarizedexperiment - bioconductor-systempiper - bioconductor-zlibbioc - - r + - r-base - r-amap - r-dplyr - r-gplots @@ -52,7 +52,7 @@ requirements: - bioconductor-summarizedexperiment - bioconductor-systempiper - bioconductor-zlibbioc - - r + - r-base - r-amap - r-dplyr - r-gplots diff --git a/recipes/bioconductor-dnacopy/meta.yaml b/recipes/bioconductor-dnacopy/meta.yaml index 046d5e8872..e5a86d1447 100644 --- a/recipes/bioconductor-dnacopy/meta.yaml +++ b/recipes/bioconductor-dnacopy/meta.yaml @@ -12,10 +12,10 @@ build: - lib/ requirements: build: - - r + - r-base - gcc run: - - r + - r-base test: commands: - '$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: - '$R -e "library(''DO.db'')"' diff --git a/recipes/bioconductor-dose/meta.yaml b/recipes/bioconductor-dose/meta.yaml index 62791575a4..feb46b61b0 100644 --- a/recipes/bioconductor-dose/meta.yaml +++ b/recipes/bioconductor-dose/meta.yaml @@ -16,7 +16,7 @@ requirements: - bioconductor-do.db - bioconductor-gosemsim - bioconductor-qvalue - - r + - r-base - r-ggplot2 - r-igraph - r-plyr @@ -28,7 +28,7 @@ requirements: - bioconductor-do.db - bioconductor-gosemsim - bioconductor-qvalue - - r + - r-base - r-ggplot2 - r-igraph - r-plyr diff --git a/recipes/bioconductor-dupradar/meta.yaml b/recipes/bioconductor-dupradar/meta.yaml index 709c09186a..b4c09b3d7f 100644 --- a/recipes/bioconductor-dupradar/meta.yaml +++ b/recipes/bioconductor-dupradar/meta.yaml @@ -3,8 +3,8 @@ package: version: 1.2.2 source: fn: dupRadar_1.2.2.tar.gz - url: http://bioconductor.org/packages/release/bioc/src/contrib/dupRadar_1.2.2.tar.gz - md5: 2c4527c61a83bdcaa9fb46c9865ae3a6 + url: http://www.imsbio.co.jp/RGM-files/R_BC/download/dupRadar_1.2.2.tar.gz + sha256: 0c6a907efe9035dc6ba386160f9f7fb47b18b39e8a2dcfeecb2743f14ad607d8 build: number: 0 rpaths: @@ -13,10 +13,10 @@ build: requirements: build: - 'bioconductor-rsubread >=1.14.1' - - 'r' + - r-base run: - 'bioconductor-rsubread >=1.14.1' - - 'r' + - r-base test: commands: - '$R -e "library(''dupRadar'')"' diff --git a/recipes/bioconductor-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: - '$R -e "library(''edgeR'')"' diff --git a/recipes/bioconductor-edger/meta.yaml b/recipes/bioconductor-edger/meta.yaml index e8a5c6f1cc..7ba3992242 100644 --- a/recipes/bioconductor-edger/meta.yaml +++ b/recipes/bioconductor-edger/meta.yaml @@ -2,7 +2,7 @@ package: name: bioconductor-edger version: 3.16.5 source: - url: https://bioconductor.org/packages/release/bioc/src/contrib/edgeR_3.16.5.tar.gz + url: https://depot.galaxyproject.org/software/bioconductor-edger/bioconductor-edger_3.16.5_src_all.tar.gz md5: 7fa050082478fb13173ee758342a6861 build: number: 0 diff --git a/recipes/bioconductor-ensembldb/meta.yaml b/recipes/bioconductor-ensembldb/meta.yaml index 9904287d60..a2844b9059 100644 --- a/recipes/bioconductor-ensembldb/meta.yaml +++ b/recipes/bioconductor-ensembldb/meta.yaml @@ -1,15 +1,18 @@ package: name: bioconductor-ensembldb - version: 1.6.0 + version: 1.6.2 + source: fn: ensembldb_1.6.0.tar.gz - url: http://bioconductor.org/packages/release/bioc/src/contrib/ensembldb_1.6.0.tar.gz - md5: 731f44b5af42a5b32bb7863f27ac5dc7 + url: http://bioconductor.org/packages/3.4/bioc/src/contrib/ensembldb_1.6.2.tar.gz + sha256: 79b8f50cf2ddb7af0de7479a045f6cc57d763286dcc495bf932bce37e995bbc3 + build: number: 0 rpaths: - lib/R/lib/ - lib/ + requirements: build: - 'bioconductor-annotationdbi >=1.31.19' @@ -23,7 +26,7 @@ requirements: - bioconductor-rsamtools - bioconductor-rtracklayer - bioconductor-s4vectors - - r + - r-base - r-dbi - r-rsqlite run: @@ -38,12 +41,14 @@ requirements: - bioconductor-rsamtools - bioconductor-rtracklayer - bioconductor-s4vectors - - r + - r-base - r-dbi - r-rsqlite + test: commands: - '$R -e "library(''ensembldb'')"' + about: home: http://bioconductor.org/packages/release/bioc/html/ensembldb.html license: LGPL diff --git a/recipes/bioconductor-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 -# $R CMD INSTALL --build . -# -# # Add more build steps here, if they are necessary. -# -# See -# http://docs.continuum.io/conda/build.html -# for a list of environment variables that are set during the build -# process. # \ No newline at end of file diff --git a/recipes/bioconductor-fastseg/meta.yaml b/recipes/bioconductor-fastseg/meta.yaml index b3d96c45a1..4df2fd72d8 100644 --- a/recipes/bioconductor-fastseg/meta.yaml +++ b/recipes/bioconductor-fastseg/meta.yaml @@ -3,10 +3,13 @@ package: version: 1.20.0 source: fn: fastseg_1.20.0.tar.gz - url: http://bioconductor.org/packages/release/bioc/src/contrib/fastseg_1.20.0.tar.gz + url: + - http://bioconductor.org/packages/3.4/bioc/src/contrib/fastseg_1.20.0.tar.gz + - https://bioarchive.galaxyproject.org/fastseg_1.20.0.tar.gz + - https://depot.galaxyproject.org/software/fastseg/fastseg_1.20.0_src_all.tar.gz md5: 1840f449546b1d89983e95a6280006c1 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -17,19 +20,19 @@ requirements: - bioconductor-genomicranges - bioconductor-iranges - bioconductor-s4vectors - - r + - r-base run: - bioconductor-biobase - bioconductor-biocgenerics - bioconductor-genomicranges - bioconductor-iranges - bioconductor-s4vectors - - r + - r-base test: commands: - '$R -e "library(''fastseg'')"' 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 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..6d69c1519d 100644 --- a/recipes/bioconductor-flowdensity/meta.yaml +++ b/recipes/bioconductor-flowdensity/meta.yaml @@ -13,18 +13,20 @@ build: requirements: build: - bioconductor-flowcore - - r + - r-base - r-car - r-geomap - r-gplots - r-rfoc + - r-nloptr run: - bioconductor-flowcore - - r + - r-base - r-car - r-geomap - r-gplots - r-rfoc + - r-nloptr test: commands: - '$R -e "library(''flowDensity'')"' diff --git a/recipes/bioconductor-flowfp/meta.yaml b/recipes/bioconductor-flowfp/meta.yaml index bfd195aa98..ab6c05e8ce 100644 --- a/recipes/bioconductor-flowfp/meta.yaml +++ b/recipes/bioconductor-flowfp/meta.yaml @@ -16,13 +16,13 @@ requirements: - 'bioconductor-biocgenerics >=0.1.6' - bioconductor-flowcore - bioconductor-flowviz - - r + - r-base run: - bioconductor-biobase - 'bioconductor-biocgenerics >=0.1.6' - bioconductor-flowcore - bioconductor-flowviz - - r + - r-base test: commands: - '$R -e "library(''flowFP'')"' diff --git a/recipes/bioconductor-flowviz/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 -# $R CMD INSTALL --build . -# -# # Add more build steps here, if they are necessary. -# -# See -# http://docs.continuum.io/conda/build.html -# for a list of environment variables that are set during the build -# process. # \ No newline at end of file diff --git a/recipes/bioconductor-flowviz/meta.yaml b/recipes/bioconductor-flowviz/meta.yaml index a2be0766ec..8f5258f3e1 100644 --- a/recipes/bioconductor-flowviz/meta.yaml +++ b/recipes/bioconductor-flowviz/meta.yaml @@ -3,8 +3,11 @@ package: version: 1.38.0 source: fn: flowViz_1.38.0.tar.gz - url: https://bioarchive.galaxyproject.org/flowViz_1.38.0.tar.gz - md5: f4305de6bad26e8b906c39cf14a01b2a + url: + - http://bioconductor.org/packages/3.4/bioc/src/contrib/flowViz_1.38.0.tar.gz + - https://bioarchive.galaxyproject.org/flowViz_1.38.0.tar.gz + - https://depot.galaxyproject.org/software/flowViz/flowViz_1.38.0_src_all.tar.gz + md5: ca001789da5bf4d21a63d222d69255c7 build: number: 0 rpaths: @@ -14,23 +17,29 @@ requirements: build: - bioconductor-biobase - bioconductor-flowcore - - r + - r-base - r-hexbin - r-idpmisc + - r-kernsmooth + - r-lattice - r-latticeextra + - r-mass - r-rcolorbrewer run: - bioconductor-biobase - bioconductor-flowcore - - r + - r-base - r-hexbin - r-idpmisc + - r-kernsmooth + - r-lattice - r-latticeextra + - r-mass - r-rcolorbrewer test: commands: - '$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.' 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: - '$R -e "library(''gage'')"' diff --git a/recipes/bioconductor-gagedata/meta.yaml b/recipes/bioconductor-gagedata/meta.yaml index f8970dd94a..c613625115 100644 --- a/recipes/bioconductor-gagedata/meta.yaml +++ b/recipes/bioconductor-gagedata/meta.yaml @@ -1,31 +1,37 @@ package: name: bioconductor-gagedata version: 2.10.0 + source: fn: gageData_2.10.0.tar.gz - url: http://bioconductor.org/packages/release/data/experiment/src/contrib/gageData_2.10.0.tar.gz - md5: a143308c83d08d470695c8449f84490d + url: http://bioconductor.org/packages/3.3/data/experiment/src/contrib/gageData_2.10.0.tar.gz + sha256: 948b38925f573cbd484fd5dd36e4423c8fcdcf8e01487d1a87bf6461dd0cd99e + build: number: 0 rpaths: - lib/R/lib/ - lib/ + requirements: build: - - r + - r-base run: - - r + - r-base + test: commands: - '$R -e "library(''gageData'')"' + 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-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/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 -# $R CMD INSTALL --build . -# -# # Add more build steps here, if they are necessary. -# -# See -# http://docs.continuum.io/conda/build.html -# for a list of environment variables that are set during the build -# process. # \ No newline at end of file diff --git a/recipes/bioconductor-genefilter/meta.yaml b/recipes/bioconductor-genefilter/meta.yaml index b6f0ead6ab..8604abb0c4 100644 --- a/recipes/bioconductor-genefilter/meta.yaml +++ b/recipes/bioconductor-genefilter/meta.yaml @@ -1,10 +1,12 @@ package: name: bioconductor-genefilter - version: 1.56.0 + version: 1.58.1 source: - fn: genefilter_1.56.0.tar.gz - url: http://bioconductor.org/packages/release/bioc/src/contrib/genefilter_1.56.0.tar.gz - md5: 919e4deb451ca4e9dbea1e125e15cf98 + fn: genefilter_1.58.1.tar.gz + url: + - http://bioconductor.org/packages/3.5/bioc/src/contrib/genefilter_1.58.1.tar.gz + - https://depot.galaxyproject.org/software/genefilter/genefilter_1.58.1_src_all.tar.gz + md5: bc1a90bdf93d8db994220545cd80f438 build: number: 0 rpaths: @@ -12,23 +14,25 @@ build: - lib/ requirements: build: - - gcc - bioconductor-annotate - bioconductor-annotationdbi - bioconductor-biobase - 'bioconductor-s4vectors >=0.9.42' - - r + - r-base + - r-survival + - gcc run: - - libgcc - bioconductor-annotate - bioconductor-annotationdbi - bioconductor-biobase - 'bioconductor-s4vectors >=0.9.42' - - r + - r-base + - r-survival + - libgcc # [linux] test: commands: - '$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' 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 -# -$R CMD INSTALL --build . -# -# # Add more build steps here, if they are necessary. -# -# See -# http://docs.continuum.io/conda/build.html -# for a list of environment variables that are set during the build -# process. -# \ No newline at end of file diff --git a/recipes/bioconductor-genelendatabase/1.6.0/meta.yaml b/recipes/bioconductor-genelendatabase/1.6.0/meta.yaml deleted file mode 100644 index 8d8ae00665..0000000000 --- a/recipes/bioconductor-genelendatabase/1.6.0/meta.yaml +++ /dev/null @@ -1,30 +0,0 @@ -package: - name: bioconductor-genelendatabase - version: 1.6.0 -source: - fn: geneLenDataBase_1.6.0.tar.gz - url: http://bioconductor.org/packages/release/data/experiment/src/contrib/geneLenDataBase_1.6.0.tar.gz - md5: 3038e8243c534c06da3108feb952e849 -build: - number: 0 - skip: True # [osx] - rpaths: - - lib/R/lib/ - - lib/ -requirements: - build: - - 'bioconductor-genomicfeatures >=1.3.15' - - bioconductor-rtracklayer - - r - run: - - 'bioconductor-genomicfeatures >=1.3.15' - - bioconductor-rtracklayer - - r -test: - commands: - - '$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' 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: - '$R -e "library(''geneLenDataBase'')"' diff --git a/recipes/bioconductor-geneplotter/meta.yaml b/recipes/bioconductor-geneplotter/meta.yaml index 5ac813412e..25954ca38f 100644 --- a/recipes/bioconductor-geneplotter/meta.yaml +++ b/recipes/bioconductor-geneplotter/meta.yaml @@ -16,15 +16,17 @@ requirements: - bioconductor-annotationdbi - bioconductor-biobase - bioconductor-biocgenerics - - r + - r-base - r-rcolorbrewer + - r-lattice run: - bioconductor-annotate - bioconductor-annotationdbi - bioconductor-biobase - bioconductor-biocgenerics - - r + - r-base - r-rcolorbrewer + - r-lattice test: commands: - '$R -e "library(''geneplotter'')"' diff --git a/recipes/bioconductor-genomation/meta.yaml b/recipes/bioconductor-genomation/meta.yaml index 2ba8f8e5ff..d77816606e 100644 --- a/recipes/bioconductor-genomation/meta.yaml +++ b/recipes/bioconductor-genomation/meta.yaml @@ -4,70 +4,66 @@ 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/ -#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..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: @@ -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-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-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-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-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/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 -# $R CMD INSTALL --build . -# -# # Add more build steps here, if they are necessary. -# -# See -# http://docs.continuum.io/conda/build.html -# for a list of environment variables that are set during the build -# process. -# +# \ No newline at end of file diff --git a/recipes/bioconductor-gostats/meta.yaml b/recipes/bioconductor-gostats/meta.yaml index 726204ba85..fc18dd1c70 100644 --- a/recipes/bioconductor-gostats/meta.yaml +++ b/recipes/bioconductor-gostats/meta.yaml @@ -3,10 +3,12 @@ package: version: 2.38.1 source: fn: GOstats_2.38.1.tar.gz - url: http://bioconductor.org/packages/3.3/bioc/src/contrib/GOstats_2.38.1.tar.gz + url: + - http://bioconductor.org/packages/3.3/bioc/src/contrib/GOstats_2.38.1.tar.gz + - https://depot.galaxyproject.org/software/GOstats/GOstats_2.38.1_src_all.tar.gz md5: 684862c904e7b5f4731bd27d09f9ce43 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -20,7 +22,7 @@ requirements: - 'bioconductor-go.db >=1.13.0' - 'bioconductor-graph >=1.15.15' - bioconductor-rbgl - - r + - r-base run: - 'bioconductor-annotate >=1.13.2' - 'bioconductor-annotationdbi >=0.0.89' @@ -30,12 +32,12 @@ requirements: - 'bioconductor-go.db >=1.13.0' - 'bioconductor-graph >=1.15.15' - bioconductor-rbgl - - r + - r-base test: commands: - '$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.' 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-hilbertvis/meta.yaml b/recipes/bioconductor-hilbertvis/meta.yaml index 71a658fd1e..47ac951205 100644 --- a/recipes/bioconductor-hilbertvis/meta.yaml +++ b/recipes/bioconductor-hilbertvis/meta.yaml @@ -12,9 +12,11 @@ build: - lib/ requirements: build: - - r + - r-base + - r-lattice run: - - r + - r-base + - r-lattice test: commands: - '$R -e "library(''HilbertVis'')"' diff --git a/recipes/bioconductor-hom.hs.inp.db/meta.yaml b/recipes/bioconductor-hom.hs.inp.db/meta.yaml index 82a49ee97f..8648f41817 100644 --- a/recipes/bioconductor-hom.hs.inp.db/meta.yaml +++ b/recipes/bioconductor-hom.hs.inp.db/meta.yaml @@ -13,10 +13,10 @@ build: requirements: build: - 'bioconductor-annotationdbi >=1.29.20' - - r + - r-base run: - 'bioconductor-annotationdbi >=1.29.20' - - r + - r-base test: commands: - '$R -e "library(''hom.Hs.inp.db'')"' diff --git a/recipes/bioconductor-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: - '$R -e "library(''hpar'')"' + about: home: http://bioconductor.org/packages/release/bioc/html/hpar.html license: Artistic-2.0 diff --git a/recipes/bioconductor-ihw/meta.yaml b/recipes/bioconductor-ihw/meta.yaml index 30b13c1e36..0a3defb76a 100644 --- a/recipes/bioconductor-ihw/meta.yaml +++ b/recipes/bioconductor-ihw/meta.yaml @@ -14,13 +14,13 @@ requirements: build: - bioconductor-biocgenerics - bioconductor-lpsymphony - - r + - r-base - r-fdrtool - r-slam run: - bioconductor-biocgenerics - bioconductor-lpsymphony - - r + - r-base - r-fdrtool - r-slam test: diff --git a/recipes/bioconductor-illuminaio/meta.yaml b/recipes/bioconductor-illuminaio/meta.yaml index 12d9996336..0892858415 100644 --- a/recipes/bioconductor-illuminaio/meta.yaml +++ b/recipes/bioconductor-illuminaio/meta.yaml @@ -12,10 +12,10 @@ build: - lib/ requirements: build: - - r + - r-base - r-base64 run: - - r + - r-base - r-base64 test: commands: diff --git a/recipes/bioconductor-illuminamousev2.db/meta.yaml b/recipes/bioconductor-illuminamousev2.db/meta.yaml index 274b51cea4..d2a6d62f9e 100644 --- a/recipes/bioconductor-illuminamousev2.db/meta.yaml +++ b/recipes/bioconductor-illuminamousev2.db/meta.yaml @@ -15,11 +15,11 @@ requirements: build: - 'bioconductor-annotationdbi >=1.29.20' - 'bioconductor-org.mm.eg.db >=3.1.2' - - r + - r-base run: - 'bioconductor-annotationdbi >=1.29.20' - 'bioconductor-org.mm.eg.db >=3.1.2' - - r + - r-base test: commands: - '$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/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 -# -$R CMD INSTALL --build . -# -# # Add more build steps here, if they are necessary. -# -# See -# http://docs.continuum.io/conda/build.html -# for a list of environment variables that are set during the build -# process. -# diff --git a/recipes/bioconductor-iranges/2.4.6/meta.yaml b/recipes/bioconductor-iranges/2.4.6/meta.yaml deleted file mode 100644 index 457ebe3c8d..0000000000 --- a/recipes/bioconductor-iranges/2.4.6/meta.yaml +++ /dev/null @@ -1,36 +0,0 @@ -package: - name: bioconductor-iranges - version: 2.4.6 -source: - fn: IRanges_2.4.6.tar.gz - url: http://bioconductor.org/packages/release/bioc/src/contrib/IRanges_2.4.6.tar.gz - md5: 8a55ec82f777f61a76b6c467af92b4f6 - -build: - skip: False - number: 0 - rpaths: - - lib/R/lib/ - - lib/ -requirements: - build: - - 'bioconductor-biocgenerics >=0.15.10' - - 'bioconductor-s4vectors >=0.8.4' - - r - run: - - 'bioconductor-biocgenerics >=0.15.10' - - 'bioconductor-s4vectors >=0.8.4' - - r -test: - commands: - - '$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.' 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 080891ccdc..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 - run: - - bioconductor-biocgenerics >=0.15.10 - - bioconductor-s4vectors >=0.8.4 - - r -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.' 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..086d4b23bc 100644 --- a/recipes/bioconductor-kcsmart/meta.yaml +++ b/recipes/bioconductor-kcsmart/meta.yaml @@ -15,12 +15,15 @@ requirements: - bioconductor-biocgenerics - bioconductor-multtest - bioconductor-siggenes - - r + - r-base + - r-kernsmooth run: - bioconductor-biocgenerics - bioconductor-multtest - bioconductor-siggenes - - r + - r-base + - r-kernsmooth + 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: - '$R -e "library(''KEGG.db'')"' diff --git a/recipes/bioconductor-kegggraph/meta.yaml b/recipes/bioconductor-kegggraph/meta.yaml index 43876d85df..74d7822acd 100644 --- a/recipes/bioconductor-kegggraph/meta.yaml +++ b/recipes/bioconductor-kegggraph/meta.yaml @@ -13,11 +13,11 @@ build: requirements: build: - bioconductor-graph - - r + - r-base - 'r-xml >=2.3-0' run: - bioconductor-graph - - r + - r-base - 'r-xml >=2.3-0' test: commands: diff --git a/recipes/bioconductor-keggrest/meta.yaml b/recipes/bioconductor-keggrest/meta.yaml index 84e2b55802..330c8dc432 100644 --- a/recipes/bioconductor-keggrest/meta.yaml +++ b/recipes/bioconductor-keggrest/meta.yaml @@ -13,12 +13,12 @@ build: requirements: build: - bioconductor-biostrings - - r + - r-base - r-httr - r-png run: - bioconductor-biostrings - - r + - r-base - r-httr - r-png test: diff --git a/recipes/bioconductor-limma/3.26.7/build.sh b/recipes/bioconductor-limma/3.26.7/build.sh deleted file mode 100644 index 6c7a1726e3..0000000000 --- a/recipes/bioconductor-limma/3.26.7/build.sh +++ /dev/null @@ -1,17 +0,0 @@ - -#!/bin/bash - -# R refuses to build packages that mark themselves as -# "Priority: Recommended" -mv DESCRIPTION DESCRIPTION.old -grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION -# -$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 42990abeac..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 - run: - - r -test: - commands: - - '$R -e "library(''limma'')"' -about: - home: http://bioconductor.org/packages/release/bioc/html/limma.html - license: 'GPL (>=2)' - summary: 'Data analysis, linear models and differential expression for microarray - data.' diff --git a/recipes/bioconductor-camera/1.22.0/build.sh b/recipes/bioconductor-limma/3.28.10/build.sh similarity index 100% rename from recipes/bioconductor-camera/1.22.0/build.sh rename to recipes/bioconductor-limma/3.28.10/build.sh diff --git a/recipes/bioconductor-limma/3.28.10/meta.yaml b/recipes/bioconductor-limma/3.28.10/meta.yaml new file mode 100644 index 0000000000..9eab2136ba --- /dev/null +++ b/recipes/bioconductor-limma/3.28.10/meta.yaml @@ -0,0 +1,30 @@ +package: + name: bioconductor-limma + version: 3.28.10 + +source: + fn: limma_3.28.10_src_all.tar.gz + url: https://depot.galaxyproject.org/software/limma/limma_3.28.10_src_all.tar.gz + sha256: 62c9337a640d4ee31abbec77df37ea3b0d75826cbace3de9914561106e04dfdc + +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + +requirements: + build: + - r-base + run: + - r-base + +test: + commands: + - '$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. diff --git a/recipes/bioconductor-limma/3.28.2/meta.yaml b/recipes/bioconductor-limma/3.28.2/meta.yaml index 610d768419..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 + - r-base run: - - r + - r-base + test: commands: - '$R -e "library(''limma'')"' + about: home: http://bioconductor.org/packages/release/bioc/html/limma.html license: 'GPL (>=2)' - summary: 'Data analysis, linear models and differential expression for microarray - data.' + summary: | + Data analysis, linear models and differential expression for microarray data. diff --git a/recipes/bioconductor-limma/3.28.6/build.sh b/recipes/bioconductor-limma/3.28.6/build.sh deleted file mode 100644 index 6c7a1726e3..0000000000 --- a/recipes/bioconductor-limma/3.28.6/build.sh +++ /dev/null @@ -1,17 +0,0 @@ - -#!/bin/bash - -# R refuses to build packages that mark themselves as -# "Priority: Recommended" -mv DESCRIPTION DESCRIPTION.old -grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION -# -$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. -# \ No newline at end of file diff --git a/recipes/bioconductor-limma/3.28.6/meta.yaml b/recipes/bioconductor-limma/3.28.6/meta.yaml deleted file mode 100644 index 987071ec93..0000000000 --- a/recipes/bioconductor-limma/3.28.6/meta.yaml +++ /dev/null @@ -1,25 +0,0 @@ -package: - name: bioconductor-limma - version: 3.28.6 -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 -build: - number: 0 - rpaths: - - lib/R/lib/ - - lib/ -requirements: - build: - - r - run: - - r -test: - commands: - - '$R -e "library(''limma'')"' -about: - home: http://bioconductor.org/packages/release/bioc/html/limma.html - license: 'GPL (>=2)' - summary: 'Data analysis, linear models and differential expression for microarray - data.' diff --git a/recipes/bioconductor-limma/meta.yaml b/recipes/bioconductor-limma/meta.yaml index 88563a1723..5a92ec503f 100644 --- a/recipes/bioconductor-limma/meta.yaml +++ b/recipes/bioconductor-limma/meta.yaml @@ -1,24 +1,28 @@ package: name: bioconductor-limma version: 3.30.13 + source: - url: https://bioconductor.org/packages/release/bioc/src/contrib/limma_3.30.13.tar.gz - md5: 6505fdccd7ae146652224377cd104e6a + url: https://depot.galaxyproject.org/software/bioconductor-limma/bioconductor-limma_3.30.13_src_all.tar.gz + sha256: a092cf82fe93d5a089dfe8df1a662d67da4cf19f22c65f4011985b95c29a28ca + build: number: 0 rpaths: - lib/R/lib/ - lib/ + requirements: build: - r-base run: - r-base + test: commands: - '$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.' 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..0f0afdb450 100644 --- a/recipes/bioconductor-masigpro/meta.yaml +++ b/recipes/bioconductor-masigpro/meta.yaml @@ -13,14 +13,16 @@ build: requirements: build: - bioconductor-biobase - - r + - r-base - r-mclust - r-venn + - r-mass run: - bioconductor-biobase - - r + - r-base - r-mclust - r-venn + - r-mass test: commands: - '$R -e "library(''maSigPro'')"' 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..d53e62704c 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' @@ -36,6 +36,7 @@ requirements: - r-quadprog - r-rcolorbrewer - r-reshape + - r-nlme run: - 'bioconductor-biobase >=2.17.8' - 'bioconductor-biocgenerics >=0.15.3' @@ -52,7 +53,7 @@ requirements: - bioconductor-s4vectors - bioconductor-siggenes - 'bioconductor-summarizedexperiment >=1.1.6' - - r + - r-base - r-beanplot - r-data.table - 'r-matrixstats >=0.50.0' @@ -61,6 +62,7 @@ requirements: - r-quadprog - r-rcolorbrewer - r-reshape + - r-nlme test: commands: - '$R -e "library(''minfi'')"' 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..83c2fe0092 100644 --- a/recipes/bioconductor-mosaics/meta.yaml +++ b/recipes/bioconductor-mosaics/meta.yaml @@ -21,7 +21,8 @@ requirements: - bioconductor-iranges - bioconductor-rsamtools - bioconductor-s4vectors - - r + - r-mass + - r-base - r-rcpp - gcc # [linux] - llvm # [osx] @@ -32,7 +33,8 @@ requirements: - bioconductor-iranges - bioconductor-rsamtools - bioconductor-s4vectors - - r + - r-base + - r-mass - 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-motifrg/meta.yaml b/recipes/bioconductor-motifrg/meta.yaml index 9451a4b884..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: @@ -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-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/build.sh b/recipes/bioconductor-motiv/build.sh index 31befe9f81..9b821879d2 100644 --- a/recipes/bioconductor-motiv/build.sh +++ b/recipes/bioconductor-motiv/build.sh @@ -1,18 +1,15 @@ + #!/bin/bash -export LDFLAGS="-L${PREFIX}/lib -Wl,-rpath ${PREFIX}/lib" +export CFLAGS="$(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 -# R refuses to build packages that mark themselves as -# "Priority: Recommended" mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION -# $R CMD INSTALL --build . -# -# # Add more build steps here, if they are necessary. -# -# See -# http://docs.continuum.io/conda/build.html -# for a list of environment variables that are set during the build -# process. -# + diff --git a/recipes/bioconductor-motiv/meta.yaml b/recipes/bioconductor-motiv/meta.yaml index 3d169d701d..384e0328b2 100644 --- a/recipes/bioconductor-motiv/meta.yaml +++ b/recipes/bioconductor-motiv/meta.yaml @@ -1,13 +1,18 @@ package: name: bioconductor-motiv version: 1.30.0 + source: fn: MotIV_1.30.0.tar.gz - url: https://bioarchive.galaxyproject.org/MotIV_1.30.0.tar.gz - md5: a5d51105c30360bcade445659e7172c3 + url: + - http://bioconductor.org/packages/3.4/bioc/src/contrib/MotIV_1.30.0.tar.gz + - https://bioarchive.galaxyproject.org/MotIV_1.30.0.tar.gz + - https://depot.galaxyproject.org/software/MotIV/MotIV_1.30.0_src_all.tar.gz + md5: 19da23b2900e7e9b334084a7bd78c17c + build: + string: bioconductor_{{CONDA_R}}_gsl{{CONDA_GSL}}_{{PKG_BUILDNUM}} number: 0 - string: gsl{{CONDA_GSL}}_{{PKG_BUILDNUM}} rpaths: - lib/R/lib/ - lib/ @@ -19,22 +24,29 @@ requirements: - 'bioconductor-iranges >=1.13.5' - bioconductor-rgadem - bioconductor-s4vectors - - r + - r-base - gsl {{CONDA_GSL}}* - + - r-lattice + - gcc # [linux] + - llvm # [osx] + run: - 'bioconductor-biocgenerics >=0.1.0' - 'bioconductor-biostrings >=1.24.0' - 'bioconductor-iranges >=1.13.5' - bioconductor-rgadem - bioconductor-s4vectors - - r + - r-base + - r-lattice - gsl {{CONDA_GSL}}* + - libgcc # [linux] + test: commands: - '$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, 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 -# $R CMD INSTALL --build . -# -# # Add more build steps here, if they are necessary. -# -# See -# http://docs.continuum.io/conda/build.html -# for a list of environment variables that are set during the build -# process. # \ No newline at end of file diff --git a/recipes/bioconductor-multtest/meta.yaml b/recipes/bioconductor-multtest/meta.yaml index f638d96063..984f55f866 100644 --- a/recipes/bioconductor-multtest/meta.yaml +++ b/recipes/bioconductor-multtest/meta.yaml @@ -3,10 +3,13 @@ package: version: 2.28.0 source: fn: multtest_2.28.0.tar.gz - url: https://bioarchive.galaxyproject.org/multtest_2.28.0.tar.gz - md5: 936e0b615f583c7ca6727d6c9c46eaa0 + url: + - http://bioconductor.org/packages/3.3/bioc/src/contrib/multtest_2.28.0.tar.gz + - https://bioarchive.galaxyproject.org/multtest_2.28.0.tar.gz + - https://depot.galaxyproject.org/software/multtest/multtest_2.28.0_src_all.tar.gz + md5: a82a1564e15fdc5afe6efc4c33a33bbc build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -14,16 +17,20 @@ requirements: build: - bioconductor-biobase - bioconductor-biocgenerics - - r + - r-base + - r-mass + - r-survival run: - bioconductor-biobase - bioconductor-biocgenerics - - r + - r-base + - r-mass + - r-survival test: commands: - '$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 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..4fdacfb915 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: @@ -13,10 +13,12 @@ build: requirements: build: - 'bioconductor-biobase >=2.13.11' - - r + - r-base + - r-matrix run: - 'bioconductor-biobase >=2.13.11' - - r + - r-base + - r-matrix 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.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 026208cc6d..ecfedefee2 100644 --- a/recipes/bioconductor-org.dm.eg.db/meta.yaml +++ b/recipes/bioconductor-org.dm.eg.db/meta.yaml @@ -1,32 +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/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: 0 - rpaths: - - lib/R/lib/ - - lib/ + number: 2 + rpaths: + - lib/R/lib/ + - lib/ requirements: - build: - - bioconductor-annotationdbi >=1.35.4 - - r >=2.7.0 - run: - - bioconductor-annotationdbi >=1.35.4 - - r >=2.7.0 + 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.' 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 -# $R CMD INSTALL --build . -# -# # Add more build steps here, if they are necessary. -# -# See -# http://docs.continuum.io/conda/build.html -# for a list of environment variables that are set during the build -# process. # \ No newline at end of file diff --git a/recipes/bioconductor-org.hs.eg.db/meta.yaml b/recipes/bioconductor-org.hs.eg.db/meta.yaml index a02810d3a8..6348199454 100644 --- a/recipes/bioconductor-org.hs.eg.db/meta.yaml +++ b/recipes/bioconductor-org.hs.eg.db/meta.yaml @@ -3,25 +3,27 @@ package: version: 3.3.0 source: fn: org.Hs.eg.db_3.3.0.tar.gz - url: http://bioconductor.org/packages/release/data/annotation/src/contrib/org.Hs.eg.db_3.3.0.tar.gz + url: + - http://bioconductor.org/packages/3.3/data/annotation/src/contrib/org.Hs.eg.db_3.3.0.tar.gz + - https://depot.galaxyproject.org/software/org.Hs.eg.db/org.Hs.eg.db_3.3.0_src_all.tar.gz md5: ef4a05f46e7cdb0ba23fcd898a4a1d57 build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ requirements: build: - 'bioconductor-annotationdbi >=1.33.10' - - r + - r-base run: - 'bioconductor-annotationdbi >=1.33.10' - - r + - r-base test: commands: - '$R -e "library(''org.Hs.eg.db'')"' 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.' 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..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 @@ -13,15 +13,15 @@ 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')" 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-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-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..211a09b946 100644 --- a/recipes/bioconductor-pcamethods/meta.yaml +++ b/recipes/bioconductor-pcamethods/meta.yaml @@ -14,15 +14,17 @@ requirements: build: - bioconductor-biobase - bioconductor-biocgenerics - - r + - r-base - 'r-rcpp >=0.11.3' + - r-mass - gcc # [linux] - llvm # [osx] run: - bioconductor-biobase - bioconductor-biocgenerics - - r + - r-base - 'r-rcpp >=0.11.3' + - r-mass test: commands: - '$R -e "library(''pcaMethods'')"' 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..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 @@ -13,10 +13,10 @@ build: requirements: build: - bioconductor-qdnaseq - - r + - r-base run: - bioconductor-qdnaseq - - r + - r-base test: commands: - '$R -e "library(''QDNAseq.mm10'')"' diff --git a/recipes/bioconductor-qdnaseq/meta.yaml b/recipes/bioconductor-qdnaseq/meta.yaml index 5a3c6bd803..60bf4daab4 100644 --- a/recipes/bioconductor-qdnaseq/meta.yaml +++ b/recipes/bioconductor-qdnaseq/meta.yaml @@ -19,7 +19,7 @@ requirements: - 'bioconductor-genomicranges >=1.20' - 'bioconductor-iranges >=2.2' - 'bioconductor-rsamtools >=1.20' - - r + - r-base - 'r-matrixstats >=0.50.2' - 'r-r.utils >=2.3.0' run: @@ -30,7 +30,7 @@ requirements: - 'bioconductor-genomicranges >=1.20' - 'bioconductor-iranges >=2.2' - 'bioconductor-rsamtools >=1.20' - - r + - r-base - 'r-matrixstats >=0.50.2' - 'r-r.utils >=2.3.0' test: diff --git a/recipes/bioconductor-qvalue/meta.yaml b/recipes/bioconductor-qvalue/meta.yaml index a1b87fd4f0..e4c5232035 100644 --- a/recipes/bioconductor-qvalue/meta.yaml +++ b/recipes/bioconductor-qvalue/meta.yaml @@ -2,8 +2,8 @@ package: name: bioconductor-qvalue version: 2.6.0 source: - url: https://bioconductor.org/packages/release/bioc/src/contrib/qvalue_2.6.0.tar.gz - md5: be8b7972cb37667edd96948c9b56ce89 + url: https://depot.galaxyproject.org/software/bioconductor-qvalue/bioconductor-qvalue_2.6.0_src_all.tar.gz + sha256: d8690a917dd548425387ca00a2c2ad1c8fbadbbc09e019ed4b22cfb0438032b6 build: number: 0 rpaths: diff --git a/recipes/bioconductor-rbgl/meta.yaml b/recipes/bioconductor-rbgl/meta.yaml index 0ddc936bcd..6ae1aef7d5 100644 --- a/recipes/bioconductor-rbgl/meta.yaml +++ b/recipes/bioconductor-rbgl/meta.yaml @@ -13,10 +13,10 @@ build: requirements: build: - bioconductor-graph - - r + - r-base run: - bioconductor-graph - - r + - r-base test: commands: - '$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..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 @@ -17,7 +20,7 @@ requirements: - bioconductor-genomicranges - bioconductor-iranges - bioconductor-rtracklayer - - r + - r-base - r-memoise run: - bioconductor-bsgenome @@ -25,11 +28,13 @@ requirements: - bioconductor-genomicranges - bioconductor-iranges - bioconductor-rtracklayer - - r + - r-base - r-memoise + test: commands: - '$R -e "library(''regioneR'')"' + about: home: http://bioconductor.org/packages/release/bioc/html/regioneR.html license: Artistic-2.0 diff --git a/recipes/bioconductor-repitools/meta.yaml b/recipes/bioconductor-repitools/meta.yaml index f25129300f..cdc86de134 100644 --- a/recipes/bioconductor-repitools/meta.yaml +++ b/recipes/bioconductor-repitools/meta.yaml @@ -3,7 +3,7 @@ package: version: 1.20.0 source: fn: Repitools_1.20.0.tar.gz - url: http://bioconductor.org/packages/release/bioc/src/contrib/Repitools_1.20.0.tar.gz + url: https://depot.galaxyproject.org/software/bioconductor-repitools/bioconductor-repitools_1.20.0_src_all.tar.gz md5: 3f27f4e075425ed0b3a9bb47bcaf8aaf build: number: 0 @@ -25,11 +25,12 @@ requirements: - bioconductor-rsamtools - bioconductor-rtracklayer - 'bioconductor-s4vectors >=0.9.25' - - r + - r-base - r-aroma.affymetrix - r-gplots - r-gsmoothr - r-rsolnp + - r-cluster run: - 'bioconductor-biocgenerics >=0.8.0' - bioconductor-biostrings @@ -44,11 +45,12 @@ requirements: - bioconductor-rsamtools - bioconductor-rtracklayer - 'bioconductor-s4vectors >=0.9.25' - - r + - r-base - r-aroma.affymetrix - r-gplots - r-gsmoothr - r-rsolnp + - r-cluster test: commands: - '$R -e "library(''Repitools'')"' 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 -# $R CMD INSTALL --build . -# -# # Add more build steps here, if they are necessary. -# -# See -# http://docs.continuum.io/conda/build.html -# for a list of environment variables that are set during the build -# process. # \ No newline at end of file diff --git a/recipes/bioconductor-rgadem/meta.yaml b/recipes/bioconductor-rgadem/meta.yaml index 1e284e3ed2..c221e78387 100644 --- a/recipes/bioconductor-rgadem/meta.yaml +++ b/recipes/bioconductor-rgadem/meta.yaml @@ -3,8 +3,11 @@ package: version: 2.22.0 source: fn: rGADEM_2.22.0.tar.gz - url: https://bioarchive.galaxyproject.org/rGADEM_2.22.0.tar.gz - md5: 3b4449b9ddf478cd77ce515d9d2d80d9 + url: + - http://bioconductor.org/packages/3.4/bioc/src/contrib/rGADEM_2.22.0.tar.gz + - https://bioarchive.galaxyproject.org/rGADEM_2.22.0.tar.gz + - https://depot.galaxyproject.org/software/rGADEM/rGADEM_2.22.0_src_all.tar.gz + md5: 68855b9cecf4cb029027b6df0a0b6b2d build: number: 0 rpaths: @@ -16,18 +19,18 @@ requirements: - bioconductor-bsgenome - bioconductor-iranges - bioconductor-seqlogo - - r + - r-base run: - bioconductor-biostrings - bioconductor-bsgenome - bioconductor-iranges - bioconductor-seqlogo - - r + - r-base test: commands: - '$R -e "library(''rGADEM'')"' 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.' 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/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 -# $R CMD INSTALL --build . -# -# # Add more build steps here, if they are necessary. -# -# See -# http://docs.continuum.io/conda/build.html -# for a list of environment variables that are set during the build -# process. # \ No newline at end of file diff --git a/recipes/bioconductor-ringo/meta.yaml b/recipes/bioconductor-ringo/meta.yaml index 6b02ff5ed4..fdb0976383 100644 --- a/recipes/bioconductor-ringo/meta.yaml +++ b/recipes/bioconductor-ringo/meta.yaml @@ -3,10 +3,13 @@ package: version: 1.38.0 source: fn: Ringo_1.38.0.tar.gz - url: https://bioarchive.galaxyproject.org/Ringo_1.38.0.tar.gz - md5: 6189371605ced5ce1f2922a66954a5ae + url: + - http://bioconductor.org/packages/3.4/bioc/src/contrib/Ringo_1.38.0.tar.gz + - https://bioarchive.galaxyproject.org/Ringo_1.38.0.tar.gz + - https://depot.galaxyproject.org/software/Ringo/Ringo_1.38.0_src_all.tar.gz + md5: 17a1b47d16f09dd4525f26b272c48539 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -17,7 +20,9 @@ requirements: - bioconductor-genefilter - bioconductor-limma - bioconductor-vsn - - r + - r-base + - r-lattice + - r-matrix - r-rcolorbrewer run: - 'bioconductor-biobase >=1.14.1' @@ -25,13 +30,15 @@ requirements: - bioconductor-genefilter - bioconductor-limma - bioconductor-vsn - - r + - r-base + - r-lattice + - r-matrix - r-rcolorbrewer test: commands: - '$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, 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..6d40accb58 100644 --- a/recipes/bioconductor-ropls/meta.yaml +++ b/recipes/bioconductor-ropls/meta.yaml @@ -1,27 +1,35 @@ package: name: bioconductor-ropls - version: 1.4.4 + version: 1.6.0 + 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 + 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 + - r-base + - bioconductor-biobase run: - - r + - r-base + - bioconductor-biobase + 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 +44,4 @@ 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/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..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: @@ -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 - - r - - r-bitops 1.0_6 + - bioconductor-biocgenerics + - bioconductor-biocparallel + - bioconductor-biostrings + - bioconductor-genomeinfodb + - bioconductor-genomicranges + - bioconductor-iranges + - bioconductor-s4vectors + - bioconductor-xvector + - bioconductor-zlibbioc + - r-base + - 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 - - r - - r-bitops 1.0_6 + - bioconductor-biocgenerics + - bioconductor-biocparallel + - bioconductor-biostrings + - bioconductor-genomeinfodb + - bioconductor-genomicranges + - bioconductor-iranges + - bioconductor-s4vectors + - bioconductor-xvector + - bioconductor-zlibbioc + - r-base + - r-bitops test: commands: 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: - '$R -e "library(''S4Vectors'')"' diff --git a/recipes/bioconductor-scan.upc/meta.yaml b/recipes/bioconductor-scan.upc/meta.yaml index 9172b545ce..d4df440ff5 100644 --- a/recipes/bioconductor-scan.upc/meta.yaml +++ b/recipes/bioconductor-scan.upc/meta.yaml @@ -24,6 +24,7 @@ requirements: - bioconductor-affyio - r-dbi - r-rsqlite + - r-mass run: - r-base - r-foreach @@ -36,6 +37,7 @@ requirements: - bioconductor-affyio - r-dbi - r-rsqlite + - r-mass test: commands: - '$R -e "library(''SCAN.UPC'')"' diff --git a/recipes/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-seqpattern/meta.yaml b/recipes/bioconductor-seqpattern/meta.yaml index 454aa2622d..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: @@ -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-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/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 -# -$R CMD INSTALL --build . -# -# # Add more build steps here, if they are necessary. -# -# See -# http://docs.continuum.io/conda/build.html -# for a list of environment variables that are set during the build -# process. -# \ No newline at end of file diff --git a/recipes/bioconductor-summarizedexperiment/1.0.2/meta.yaml b/recipes/bioconductor-summarizedexperiment/1.0.2/meta.yaml deleted file mode 100644 index 194bd7c6aa..0000000000 --- a/recipes/bioconductor-summarizedexperiment/1.0.2/meta.yaml +++ /dev/null @@ -1,38 +0,0 @@ -package: - name: bioconductor-summarizedexperiment - version: 1.0.2 -source: - fn: SummarizedExperiment_1.0.2.tar.gz - url: https://bioc.ism.ac.jp/packages/3.2/bioc/src/contrib/SummarizedExperiment_1.0.2.tar.gz - md5: ce5b5d0aa2868f754bc8d136ebd2e6cd -build: - number: 1 - rpaths: - - lib/R/lib/ - - lib/ -requirements: - build: - - bioconductor-biobase - - 'bioconductor-biocgenerics >=0.15.3' - - bioconductor-genomeinfodb - - 'bioconductor-genomicranges >=1.22.1' - - bioconductor-iranges - - 'bioconductor-s4vectors >=0.7.11' - - r - run: - - bioconductor-biobase - - 'bioconductor-biocgenerics >=0.15.3' - - bioconductor-genomeinfodb - - 'bioconductor-genomicranges >=1.22.1' - - bioconductor-iranges - - 'bioconductor-s4vectors >=0.7.11' - - r -test: - commands: - - '$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.' 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 025897f812..95bfa74706 100644 --- a/recipes/bioconductor-summarizedexperiment/meta.yaml +++ b/recipes/bioconductor-summarizedexperiment/meta.yaml @@ -1,51 +1,42 @@ 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: 2 rpaths: - 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 - - r-matrix 1.2_6 + - bioconductor-biobase + - 'bioconductor-biocgenerics >=0.15.3' + - bioconductor-genomeinfodb + - 'bioconductor-genomicranges >=1.23.15' + - 'bioconductor-iranges >=2.7.2' + - 'bioconductor-s4vectors >=0.11.7' + - r-base + - r-matrix 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 - - r-matrix 1.2_6 - + - bioconductor-biobase + - 'bioconductor-biocgenerics >=0.15.3' + - bioconductor-genomeinfodb + - 'bioconductor-genomicranges >=1.23.15' + - 'bioconductor-iranges >=2.7.2' + - 'bioconductor-s4vectors >=0.11.7' + - r-base + - r-matrix 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 diff --git a/recipes/bioconductor-sva/meta.yaml b/recipes/bioconductor-sva/meta.yaml index ef3da3c9c5..b44a27cc52 100644 --- a/recipes/bioconductor-sva/meta.yaml +++ b/recipes/bioconductor-sva/meta.yaml @@ -15,18 +15,21 @@ requirements: - gcc # [linux] - llvm # [osx] - bioconductor-genefilter - - r + - r-base + - r-mgcv run: - libgcc # [linux] - bioconductor-genefilter - - r + - r-base + - r-mgcv test: commands: - '$R -e "library(''sva'')"' about: home: http://bioconductor.org/packages/release/bioc/html/sva.html license: Artistic-2.0 - summary: 'The sva package contains functions for removing batch effects and other + summary: | + The sva package contains functions for removing batch effects and other unwanted variation in high-throughput experiment. Specifically, the sva package contains functions for the identifying and building surrogate variables for high-dimensional data sets. Surrogate variables are covariates constructed directly from high-dimensional @@ -40,4 +43,4 @@ about: Removing batch effects and using surrogate variables in differential expression analysis have been shown to reduce dependence, stabilize error rate estimates, and improve reproducibility, see (Leek and Storey 2007 PLoS Genetics, 2008 PNAS - or Leek et al. 2011 Nat. Reviews Genetics).' + or Leek et al. 2011 Nat. Reviews Genetics). diff --git a/recipes/bioconductor-synergyfinder/meta.yaml b/recipes/bioconductor-synergyfinder/meta.yaml index 62f7ff3797..793cc78d83 100644 --- a/recipes/bioconductor-synergyfinder/meta.yaml +++ b/recipes/bioconductor-synergyfinder/meta.yaml @@ -20,6 +20,7 @@ requirements: - 'r-kriging >=1.1' - 'r-nleqslv >=3.0' - 'r-reshape2 >=1.4.1' + - r-nloptr run: - r-base - 'r-drc >=2.5-12' @@ -29,6 +30,7 @@ requirements: - 'r-kriging >=1.1' - 'r-nleqslv >=3.0' - 'r-reshape2 >=1.4.1' + - r-nloptr test: commands: - '$R -e "library(''synergyfinder'')"' 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..aa3977e543 100644 --- a/recipes/bioconductor-topgo/meta.yaml +++ b/recipes/bioconductor-topgo/meta.yaml @@ -17,20 +17,22 @@ 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' + - r-lattice run: - 'bioconductor-annotationdbi >=1.7.19' - 'bioconductor-biobase >=2.0.0' - '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' + - r-lattice test: commands: - '$R -e "library(''topGO'')"' diff --git a/recipes/bioconductor-txdb.dmelanogaster.ucsc.dm3.ensgene/meta.yaml b/recipes/bioconductor-txdb.dmelanogaster.ucsc.dm3.ensgene/meta.yaml index aa2ce82a10..0f3c981dee 100644 --- a/recipes/bioconductor-txdb.dmelanogaster.ucsc.dm3.ensgene/meta.yaml +++ b/recipes/bioconductor-txdb.dmelanogaster.ucsc.dm3.ensgene/meta.yaml @@ -15,11 +15,11 @@ requirements: build: - bioconductor-annotationdbi - 'bioconductor-genomicfeatures >=1.21.30' - - r + - r-base run: - bioconductor-annotationdbi - 'bioconductor-genomicfeatures >=1.21.30' - - r + - r-base test: commands: - '$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/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 -# $R CMD INSTALL --build . -# -# # Add more build steps here, if they are necessary. -# -# See -# http://docs.continuum.io/conda/build.html -# for a list of environment variables that are set during the build -# process. # \ No newline at end of file diff --git a/recipes/bioconductor-tximport/meta.yaml b/recipes/bioconductor-tximport/meta.yaml index 58166f91ff..8584349e0d 100644 --- a/recipes/bioconductor-tximport/meta.yaml +++ b/recipes/bioconductor-tximport/meta.yaml @@ -3,23 +3,25 @@ package: version: 1.0.3 source: fn: tximport_1.0.3.tar.gz - url: http://bioconductor.org/packages/release/bioc/src/contrib/tximport_1.0.3.tar.gz + url: + - http://bioconductor.org/packages/3.3/bioc/src/contrib/tximport_1.0.3.tar.gz + - https://depot.galaxyproject.org/software/tximport/tximport_1.0.3_src_all.tar.gz md5: c6e0a617f255af19fae34fe8e8096204 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ requirements: build: - - r + - r-base run: - - r + - r-base test: commands: - '$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/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..65dbaa230f 100644 --- a/recipes/bioconductor-xcms/1.44.0/meta.yaml +++ b/recipes/bioconductor-xcms/1.44.0/meta.yaml @@ -17,15 +17,17 @@ requirements: - bioconductor-biocgenerics - 'bioconductor-mzr >=1.1.6' - bioconductor-protgenerics - - r + - r-base - r-rcolorbrewer + - r-lattice run: - bioconductor-biobase - bioconductor-biocgenerics - 'bioconductor-mzr >=1.1.6' - bioconductor-protgenerics - - r + - r-base - r-rcolorbrewer + - r-lattice test: commands: - '$R -e "library(''xcms'')"' diff --git a/recipes/bioconductor-xcms/1.46.0/meta.yaml b/recipes/bioconductor-xcms/1.46.0/meta.yaml index 3080a48f44..33cb4488a7 100644 --- a/recipes/bioconductor-xcms/1.46.0/meta.yaml +++ b/recipes/bioconductor-xcms/1.46.0/meta.yaml @@ -17,15 +17,17 @@ requirements: - bioconductor-biocgenerics - 'bioconductor-mzr >=1.1.6' - bioconductor-protgenerics - - r + - r-base - r-rcolorbrewer + - r-lattice run: - bioconductor-biobase - bioconductor-biocgenerics - 'bioconductor-mzr >=1.1.6' - bioconductor-protgenerics - - r + - r-base - r-rcolorbrewer + - r-lattice test: commands: - '$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 40aee104da..c74d5e8a9c 100644 --- a/recipes/bioconductor-xcms/1.48.0/meta.yaml +++ b/recipes/bioconductor-xcms/1.48.0/meta.yaml @@ -17,15 +17,17 @@ requirements: - bioconductor-biocgenerics - 'bioconductor-mzr >=1.1.6' - bioconductor-protgenerics - - r + - r-base - r-rcolorbrewer + - r-lattice run: - bioconductor-biobase - bioconductor-biocgenerics - 'bioconductor-mzr >=1.1.6' - bioconductor-protgenerics - - r + - r-base - r-rcolorbrewer + - r-lattice test: commands: - '$R -e "library(''xcms'')"' diff --git a/recipes/bioconductor-xcms/meta.yaml b/recipes/bioconductor-xcms/meta.yaml index 9e192260bc..495cc333a2 100644 --- a/recipes/bioconductor-xcms/meta.yaml +++ b/recipes/bioconductor-xcms/meta.yaml @@ -1,23 +1,26 @@ package: name: bioconductor-xcms version: 1.50.1 + source: fn: 205a104fcf75b3726436c2bb9686b50255cb44bf.zip url: https://github.com/Bioconductor-mirror/xcms/archive/205a104fcf75b3726436c2bb9686b50255cb44bf.zip md5: f8125671e0c991b7eff606d9df4258d0 + build: number: 0 skip: True # [osx] rpaths: - lib/R/lib/ - lib/ + requirements: build: - bioconductor-biobase - bioconductor-biocgenerics - 'bioconductor-mzr >=1.1.6' - bioconductor-protgenerics - - r + - r-base - r-rcolorbrewer - r-plyr - r-rann @@ -25,12 +28,13 @@ requirements: - bioconductor-biocparallel - bioconductor-s4vectors - bioconductor-massspecwavelet + - r-lattice run: - bioconductor-biobase - bioconductor-biocgenerics - 'bioconductor-mzr >=1.1.6' - bioconductor-protgenerics - - r + - r-base - r-rcolorbrewer - r-plyr - r-rann @@ -38,9 +42,12 @@ requirements: - bioconductor-biocparallel - bioconductor-s4vectors - bioconductor-massspecwavelet + - r-lattice + test: commands: - '$R -e "library(''xcms'')"' + about: home: http://bioconductor.org/packages/release/bioc/html/xcms.html license: 'GPL (>= 2) + file LICENSE' diff --git a/recipes/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 -# $R CMD INSTALL --build . -# -# # Add more build steps here, if they are necessary. -# -# See -# http://docs.continuum.io/conda/build.html -# for a list of environment variables that are set during the build -# process. # \ No newline at end of file diff --git a/recipes/bioconductor-zlibbioc/meta.yaml b/recipes/bioconductor-zlibbioc/meta.yaml index 511be7fdc0..d09d543834 100644 --- a/recipes/bioconductor-zlibbioc/meta.yaml +++ b/recipes/bioconductor-zlibbioc/meta.yaml @@ -3,23 +3,26 @@ package: version: 1.20.0 source: fn: zlibbioc_1.20.0.tar.gz - url: https://bioarchive.galaxyproject.org/zlibbioc_1.20.0.tar.gz - md5: efdf012f000323d1e284123907f0007a + url: + - http://bioconductor.org/packages/3.4/bioc/src/contrib/zlibbioc_1.20.0.tar.gz + - https://bioarchive.galaxyproject.org/zlibbioc_1.20.0.tar.gz + - https://depot.galaxyproject.org/software/zlibbioc/zlibbioc_1.20.0_src_all.tar.gz + md5: f68b45fca70f39c7958fb43c0504c546 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ requirements: build: - - r + - r-base run: - - r + - r-base test: commands: - '$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 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/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' 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..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 @@ -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/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/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/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: diff --git a/recipes/kobas/meta.yaml b/recipes/kobas/meta.yaml index 7077751752..488f7484be 100644 --- a/recipes/kobas/meta.yaml +++ b/recipes/kobas/meta.yaml @@ -25,8 +25,8 @@ requirements: - pandas - biopython - sqlite - - r - - rpy2 + - r-base + - rpy2 >=2.8.5 test: imports: diff --git a/recipes/lefse/meta.yaml b/recipes/lefse/meta.yaml index da047ce66d..22c98b8bb5 100644 --- a/recipes/lefse/meta.yaml +++ b/recipes/lefse/meta.yaml @@ -15,13 +15,13 @@ requirements: - python run: - python - - r + - r-base - r-survival - r-mvtnorm - r-modeltools - r-coin - r-mass - - rpy2 >=2.1 + - rpy2 >=2.8.5 - numpy - matplotlib >=1.0 - argparse [py26] 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 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/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}') 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/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..dcd6b4055d 100644 --- a/recipes/mgkit/meta.yaml +++ b/recipes/mgkit/meta.yaml @@ -40,9 +40,9 @@ requirements: - scipy >=0.15.1 - semidbm >=0.5.1 - pymongo >=3.1.1 - - r + - r-base - htseq >=0.6.0 - - rpy2 >=2.3.8 + - rpy2 >=2.8.5 - enum34 run: @@ -55,9 +55,9 @@ requirements: - scipy >=0.15.1 - semidbm >=0.5.1 - pymongo >=3.1.1 - - r + - r-base - htseq >=0.6.0 - - rpy2 >=2.3.8 + - rpy2 >=2.8.5 - enum34 test: 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 ee36d3a74b..1872bce337 100644 --- a/recipes/multigps/0.72/meta.yaml +++ b/recipes/multigps/0.72/meta.yaml @@ -14,9 +14,9 @@ source: requirements: run: - - r + - 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 aa7a285db6..3f366226ff 100644 --- a/recipes/multigps/0.73/meta.yaml +++ b/recipes/multigps/0.73/meta.yaml @@ -14,9 +14,9 @@ source: requirements: run: - - r + - 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 9ef0292333..082852de89 100644 --- a/recipes/multigps/0.74/meta.yaml +++ b/recipes/multigps/0.74/meta.yaml @@ -16,9 +16,9 @@ source: requirements: run: - - r + - r-base - bioconductor-edger - - java-jdk >=8 + - openjdk >=8 - meme >=4.11.2 test: 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 3f0769b44d..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 - - numpy - - scipy - - r - - r-ggplot2 - - run: - - python - - h5py - - rpy2 - - numpy - - scipy - - r - - 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 - diff --git a/recipes/nanoraw/meta.yaml b/recipes/nanoraw/meta.yaml index b51b6b2e8b..47c537b3b0 100644 --- a/recipes/nanoraw/meta.yaml +++ b/recipes/nanoraw/meta.yaml @@ -14,26 +14,26 @@ build: entry_points: - nanoraw = nanoraw.__main__:main number: 0 - skip: True # [not py27] + skip: True # [not py27] requirements: build: - python - setuptools - h5py - - rpy2 + - rpy2 >=2.4.2 - numpy - scipy - - r + - r-base - r-ggplot2 run: - python - h5py - - rpy2 + - rpy2 >=2.4.2 - numpy - scipy - - r + - r-base - r-ggplot2 test: @@ -41,7 +41,7 @@ test: - nanoraw commands: - - nanoraw --help + - nanoraw --help | grep significant_fasta about: home: https://github.com/marcus1487/nanoraw 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/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 e4a2d47bbc..0000000000 --- a/recipes/poretools/0.5.0/meta.yaml +++ /dev/null @@ -1,35 +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 - -requirements: - build: - - python - - rpy2 >=2.4.2 - - h5py >=2.0 - - watchdog >=0.8.3 - - run: - - python - - hdf5 >=1.8.7 - - r >=3.0.0 - - rpy2 >=2.4.2 - - h5py >=2.0 - - watchdog >=0.8.3 - - qcli >=0.1.1 - - r-ggplot2 -build: - skip: True # [not py27] - -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 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/r-abind/meta.yaml b/recipes/r-abind/meta.yaml index b0cc4a90de..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: @@ -18,10 +17,10 @@ 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..59de764fc2 100644 --- a/recipes/r-ade4/meta.yaml +++ b/recipes/r-ade4/meta.yaml @@ -1,40 +1,26 @@ 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: 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. # 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 - + - r-base run: - - r + - r-base test: commands: @@ -42,41 +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-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-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-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..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 @@ -22,14 +21,14 @@ 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..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 @@ -18,10 +17,9 @@ 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 + - r-base - r-mass - r-r.cache >=0.12.0 - r-r.devices >=2.13.2 @@ -34,9 +32,8 @@ requirements: - r-future - r-listenv - r-matrixstats >=0.50.1 - run: - - r + - r-base - r-mass - r-r.cache >=0.12.0 - r-r.devices >=2.13.2 @@ -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-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..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 @@ -21,7 +20,7 @@ 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 +35,7 @@ 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-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-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-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-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-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..e16afa2cd8 100644 --- a/recipes/r-bio3d/meta.yaml +++ b/recipes/r-bio3d/meta.yaml @@ -1,41 +1,26 @@ 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 - + - r-base run: - - r + - r-base test: commands: @@ -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 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-bma/meta.yaml b/recipes/r-bma/meta.yaml index aa427e07d5..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: @@ -16,10 +12,9 @@ build: - lib/R/lib/ - lib/ -# Suggests: MASS, forward requirements: build: - - r + - r-base - r-inline - r-leaps - r-robustbase @@ -28,7 +23,7 @@ requirements: - gcc run: - - r + - r-base - r-inline - r-leaps - r-robustbase @@ -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-boutroslabplottinggeneral/meta.yaml b/recipes/r-boutroslabplottinggeneral/meta.yaml index 1be7f03fe9..c26648e457 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 @@ -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-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-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-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..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 @@ -31,13 +30,13 @@ 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-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-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-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-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..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: @@ -15,13 +14,13 @@ build: requirements: build: - - r + - r-base - r-rcpp - gcc # [linux] - llvm # [osx] run: - - r + - r-base - r-rcpp test: diff --git a/recipes/r-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-dendextend/meta.yaml b/recipes/r-dendextend/meta.yaml index 0b11fffdc5..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 @@ -31,12 +30,12 @@ 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..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 + - r-base run: - - r + - 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-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-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-dorng/meta.yaml b/recipes/r-dorng/meta.yaml index 5cd58dfcae..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 @@ -31,14 +30,14 @@ 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-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-dunn.test/meta.yaml b/recipes/r-dunn.test/meta.yaml index 151d1d8d28..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 @@ -29,13 +28,12 @@ build: - lib/R/lib/ - lib/ - requirements: build: - - r + - r-base run: - - r + - r-base test: commands: @@ -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-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..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 @@ -32,11 +31,11 @@ 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..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: @@ -17,12 +16,12 @@ build: requirements: build: - - r + - r-base - fftw - gcc # [not win] run: - - r + - r-base - fftw - libgcc # [not win] 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 7ed24eed9c..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. @@ -31,12 +22,12 @@ 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] @@ -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-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-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-futile.logger/meta.yaml b/recipes/r-futile.logger/meta.yaml index 3f1e2b986f..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 @@ -31,12 +28,12 @@ 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 @@ -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-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-future/0.9.0/meta.yaml b/recipes/r-future/0.9.0/meta.yaml index 14dea31e52..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 @@ -19,12 +18,12 @@ 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..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 @@ -22,13 +21,13 @@ 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..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' @@ -17,12 +16,12 @@ 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..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 @@ -18,7 +17,7 @@ build: requirements: build: - - r + - r-base - r-mass - r-gamlss.data >=5.0_0 - r-gamlss.dist >=4.3.1 @@ -28,7 +27,7 @@ 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-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-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..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: @@ -16,7 +15,7 @@ build: - lib/ requirements: build: - - r + - r-base - r-mba - r-rpmg - r-fields @@ -25,7 +24,7 @@ requirements: - {{native}}toolchain # [win] - gcc # [not win] run: - - r + - r-base - r-mba - r-rpmg - r-fields @@ -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-getoptlong/meta.yaml b/recipes/r-getoptlong/meta.yaml index 50c3564868..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. @@ -31,12 +20,12 @@ 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 @@ -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-ggally/0.5.0/meta.yaml b/recipes/r-ggally/0.5.0/meta.yaml index e6ae0de5c9..9b58624280 100644 --- a/recipes/r-ggally/0.5.0/meta.yaml +++ b/recipes/r-ggally/0.5.0/meta.yaml @@ -1,50 +1,37 @@ 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: fn: GGally_0.5.0.tar.gz url: - - http://cran.r-project.org/src/contrib/GGally_0.5.0.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 + 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 + - 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 + - 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: @@ -52,41 +39,9 @@ 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) 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-ggally/meta.yaml b/recipes/r-ggally/meta.yaml index 37a0a0af85..2a049dc2c1 100644 --- a/recipes/r-ggally/meta.yaml +++ b/recipes/r-ggally/meta.yaml @@ -7,32 +7,21 @@ 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 + - https://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 + - r-base - r-rcolorbrewer - r-ggplot2 >=2.2.0 - r-gtable >=0.2.0 @@ -41,7 +30,7 @@ requirements: - r-reshape >=0.8.5 run: - - r + - r-base - r-rcolorbrewer - r-ggplot2 >=2.2.0 - r-gtable >=0.2.0 @@ -55,11 +44,6 @@ 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 @@ -71,32 +55,3 @@ 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 diff --git a/recipes/r-ggalt/meta.yaml b/recipes/r-ggalt/meta.yaml index 6b0e9e20d1..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: @@ -19,7 +18,7 @@ build: # Suggests: testthat, gridExtra, knitr, rmarkdown, ggthemes requirements: build: - - r + - r-base - r-kernsmooth # [not win] - r-mass # [not win] - r-rcolorbrewer @@ -32,7 +31,7 @@ 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..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 @@ -31,12 +30,12 @@ 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-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-globals/0.6.0/meta.yaml b/recipes/r-globals/0.6.0/meta.yaml index a6991fadb6..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 @@ -17,11 +16,11 @@ build: requirements: build: - - r + - r-base - r-codetools # [not win] run: - - r + - r-base - r-codetools # [not win] test: @@ -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-globals/meta.yaml b/recipes/r-globals/meta.yaml index ef188e74be..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 @@ -21,11 +20,11 @@ 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..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 @@ -31,11 +30,11 @@ 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..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 @@ -32,14 +31,14 @@ 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 @@ -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-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..91357332d7 100644 --- a/recipes/r-htmltools/meta.yaml +++ b/recipes/r-htmltools/meta.yaml @@ -1,43 +1,24 @@ 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 + - r-base - r-digest run: - - r + - r-base - r-digest + - readline test: commands: @@ -45,40 +26,7 @@ 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 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 deleted file mode 100644 index e925b4a780..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 - - bioconductor-xcms - - r-rsm - - bioconductor-camera - #- libnetcdf 4.2.1.1 - - run: - - r - - 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 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..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 @@ -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-ks/meta.yaml b/recipes/r-ks/meta.yaml index b327030afb..b09c0739da 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 +37,8 @@ requirements: - r-multicool - r-mvtnorm >=1.0_0 - r-rgl >=0.66 + - libglu # [linux] + - readline test: commands: @@ -48,3 +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-lambda.r/meta.yaml b/recipes/r-lambda.r/meta.yaml index 45ee61b99a..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 @@ -31,10 +30,10 @@ build: # Suggests: RUnit requirements: build: - - r + - r-base run: - - r + - r-base test: commands: diff --git a/recipes/r-leaps/meta.yaml b/recipes/r-leaps/meta.yaml index 06a444c5ef..6a8a40e955 100644 --- a/recipes/r-leaps/meta.yaml +++ b/recipes/r-leaps/meta.yaml @@ -3,30 +3,15 @@ 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. # number: 1 - - # This is required to make R link correctly on Linux. rpaths: - lib/R/lib/ - lib/ @@ -34,9 +19,7 @@ build: requirements: build: - r-base - - gcc # [linux] - - llvm # [osx] - + - gcc run: - r-base - libgcc # [linux] 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..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 @@ -19,10 +18,10 @@ 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..375164b492 100644 --- a/recipes/r-listenv/meta.yaml +++ b/recipes/r-listenv/meta.yaml @@ -8,7 +8,7 @@ package: source: fn: listenv_0.6.0.tar.gz url: - - http://cran.r-project.org/src/contrib/listenv_0.6.0.tar.gz + - 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 @@ -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-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..2d28ab8403 100644 --- a/recipes/r-maldiquantforeign/meta.yaml +++ b/recipes/r-maldiquantforeign/meta.yaml @@ -5,7 +5,7 @@ package: source: fn: MALDIquantForeign_0.10.tar.gz url: - - http://cran.r-project.org/src/contrib/MALDIquantForeign_0.10.tar.gz + - 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 @@ -22,7 +22,7 @@ build: # Suggests: knitr, testthat (>= 0.8), RNetCDF (>= 1.6.1) requirements: build: - - r + - r-base - r-maldiquant >=1.11.7 - r-xml - r-base64enc @@ -31,13 +31,14 @@ requirements: - r-readmzxmldata >=2.7 run: - - r + - r-base - r-maldiquant >=1.11.7 - r-xml - r-base64enc - r-digest - r-readbrukerflexdata >=1.7 - r-readmzxmldata >=2.7 + - readline test: commands: @@ -58,30 +59,3 @@ 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 diff --git a/recipes/r-matrixeqtl/meta.yaml b/recipes/r-matrixeqtl/meta.yaml index ebaf380f5f..31c5531e55 100644 --- a/recipes/r-matrixeqtl/meta.yaml +++ b/recipes/r-matrixeqtl/meta.yaml @@ -21,10 +21,9 @@ build: requirements: build: - - r - + - r-base run: - - r + - r-base test: commands: @@ -41,26 +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-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-mba/meta.yaml b/recipes/r-mba/meta.yaml index 9153406a27..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: @@ -16,14 +15,14 @@ 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: @@ -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-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-microseq/build.sh b/recipes/r-microseq/build.sh new file mode 100644 index 0000000000..81250b8ff4 --- /dev/null +++ b/recipes/r-microseq/build.sh @@ -0,0 +1,7 @@ +#!/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 . diff --git a/recipes/r-microseq/meta.yaml b/recipes/r-microseq/meta.yaml new file mode 100644 index 0000000000..202c6b27ee --- /dev/null +++ b/recipes/r-microseq/meta.yaml @@ -0,0 +1,42 @@ +{% 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 + rpaths: + - lib/R/lib/ + - lib/ + +requirements: + build: + - r-base + - r-rcpp >=0.11.1 + - gcc + + run: + - r-base + - r-rcpp >=0.11.1 + - 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 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-mixomics/meta.yaml b/recipes/r-mixomics/meta.yaml index 294fdd0009..135e3e182c 100644 --- a/recipes/r-mixomics/meta.yaml +++ b/recipes/r-mixomics/meta.yaml @@ -3,25 +3,22 @@ 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 + sha256: 0a0b5cc2cb7ffcadcf2a5eab35c0f2d8cc9d1a60e7c83086a3909742c02bb471 build: number: 0 - - # This is required to make R link correctly on Linux. + # rgl not available on OSX for conda-forge + skip: True # [osx] rpaths: - lib/R/lib/ - lib/ - requirements: build: - r-base @@ -38,7 +35,6 @@ requirements: - r-rgl - r-tidyr - libglu # [linux] - run: - r-base - r-mass @@ -61,16 +57,11 @@ test: - $R -e "library('mixOmics')" # [not win] - "\"%R%\" -e \"library('mixOmics')\"" # [win] - # You can also put a file called run_test.py, run_test.sh, or run_test.bat - # in the recipe that will be run at test time. - - # requires: - # Put any additional test requirements here. - about: home: http://www.mixOmics.org license: GPL (>= 2) - summary: 'Multivariate methods are well suited to large omics data sets where the number of + summary: | + Multivariate methods are well suited to large omics data sets where the number of variables (e.g. genes, proteins, metabolites) is much larger than the number of samples (patients, cells, mice). They have the appealing properties of reducing the dimension of the data by using instrumental variables (components), which are @@ -89,6 +80,9 @@ about: Correlation Analysis, sparse Partial Least Squares and sparse Discriminant Analysis. Recently we implemented integrative methods to combine multiple data sets: horizontal integration with regularised Generalised Canonical Correlation Analysis and vertical - integration with multi-group Partial Least Squares.' - + integration with multi-group Partial Least Squares. license_family: GPL3 + +extra: + container: + extended-base: true diff --git a/recipes/r-mmgenome/meta.yaml b/recipes/r-mmgenome/meta.yaml index 4b9b5d32b7..e2c0fc6124 100644 --- a/recipes/r-mmgenome/meta.yaml +++ b/recipes/r-mmgenome/meta.yaml @@ -20,7 +20,7 @@ build: requirements: build: - - r + - r-base - r-sp >=1.0.15 - r-gridextra >=0.9.1 - r-ggplot2 >=1.0.0 @@ -32,7 +32,7 @@ requirements: - r-dplyr >=0.4.0 run: - - r + - r-base - r-sp >=1.0.15 - r-gridextra >=0.9.1 - r-ggplot2 >=1.0.0 diff --git a/recipes/r-multicool/build.sh b/recipes/r-multicool/build.sh index 0c37df6e8e..a30e93faef 100644 --- a/recipes/r-multicool/build.sh +++ b/recipes/r-multicool/build.sh @@ -1,13 +1,11 @@ #!/bin/bash -# R refuses to build packages that mark themselves as Priority: Recommended +if [ "$(uname)" == "Darwin" ]; then + CXXFLAGS="$CXXFLAGS -fno-common" +fi + + 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-multicool/meta.yaml b/recipes/r-multicool/meta.yaml index 7b0741fb2c..a4348018b6 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" + 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/multicool_0.1-9.tar.gz - - 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 - # This is required to make R link correctly on Linux. rpaths: - lib/R/lib/ - lib/ @@ -22,31 +18,25 @@ build: requirements: build: - - r + - r-base - r-rcpp >=0.11.2 - - gcc + - gcc # [not osx] + - llvm # [osx] 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: 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 @@ -57,28 +47,4 @@ 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 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 + The C++ code and Python code are distributed without conditions. 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-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-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-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-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-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-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-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-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-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..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: @@ -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..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. @@ -34,13 +25,13 @@ build: requirements: build: - - r + - r-base - r-deldir - r-plotrix - r-splancs run: - - r + - r-base - r-deldir - r-plotrix - r-splancs @@ -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-plasmidprofiler/meta.yaml b/recipes/r-plasmidprofiler/meta.yaml index cad508f5f9..ecbb8a3dea 100644 --- a/recipes/r-plasmidprofiler/meta.yaml +++ b/recipes/r-plasmidprofiler/meta.yaml @@ -17,40 +17,40 @@ build: requirements: build: - - r 3.3.1 - - 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-base + - 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 3.3.1 - - 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-base + - 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: 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-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-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-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-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..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 @@ -20,10 +19,10 @@ 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..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 @@ -31,13 +30,13 @@ 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..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 @@ -34,12 +31,12 @@ build: # Suggests: testthat requirements: build: - - r + - r-base - r-r6 - r-prettyunits run: - - r + - r-base - r-r6 - r-prettyunits @@ -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-proj4/meta.yaml b/recipes/r-proj4/meta.yaml index ffae5983e5..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 + - r-base - gcc # [not win] - - proj4 + - proj4 4.9.3 run: - - r + - 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 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 7d3b8587d8..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 @@ -21,10 +20,10 @@ 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..b1d364803d 100644 --- a/recipes/r-pscbs/meta.yaml +++ b/recipes/r-pscbs/meta.yaml @@ -1,37 +1,22 @@ 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 + - r-base - bioconductor-dnacopy - r-r.cache >=0.12.0 - r-r.methodss3 >=1.7.0 @@ -42,7 +27,7 @@ requirements: - r-matrixstats >=0.15.0 run: - - r + - r-base - bioconductor-dnacopy - r-r.cache >=0.12.0 - r-r.methodss3 >=1.7.0 @@ -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-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..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 @@ -31,11 +30,11 @@ 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-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-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-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.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..b512eb3703 100644 --- a/recipes/r-r.filesets/meta.yaml +++ b/recipes/r-r.filesets/meta.yaml @@ -8,20 +8,17 @@ 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 + - r-base - r-r.cache >=0.12.0 - r-r.methodss3 >=1.7.0 - r-r.oo >=1.19.0 @@ -31,7 +28,7 @@ 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 @@ -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.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.rsp/meta.yaml b/recipes/r-r.rsp/meta.yaml index c03e717d7a..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 @@ -18,17 +17,16 @@ 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 + - 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 @@ -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-rBLAST/meta.yaml b/recipes/r-rBLAST/meta.yaml index ba16408a2c..7618851450 100644 --- a/recipes/r-rBLAST/meta.yaml +++ b/recipes/r-rBLAST/meta.yaml @@ -2,20 +2,20 @@ 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/ - 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-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-rcircos/1.1.3/meta.yaml b/recipes/r-rcircos/1.1.3/meta.yaml index b8b85d0262..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 @@ -32,10 +31,10 @@ 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-rcppgsl/meta.yaml b/recipes/r-rcppgsl/meta.yaml index 1888c41b1d..0e9d49e95e 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 + sha256: 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 >=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: - 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-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..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 @@ -21,10 +20,10 @@ build: requirements: build: - - r + - r-base run: - - r + - r-base test: commands: @@ -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 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..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: @@ -15,14 +14,14 @@ 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 @@ -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-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..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: @@ -18,14 +17,14 @@ 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 @@ -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. 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-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..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: @@ -16,7 +15,7 @@ build: - lib/ requirements: build: - - r + - r-base - r-cluster - r-lattice - r-mvtnorm @@ -26,7 +25,7 @@ requirements: - {{native}}toolchain # [win] - gcc # [not win] run: - - r + - r-base - r-cluster - r-lattice - r-mvtnorm @@ -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 diff --git a/recipes/r-rseis/meta.yaml b/recipes/r-rseis/meta.yaml index 9aed07dab5..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: @@ -16,14 +15,14 @@ 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..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 @@ -31,10 +30,10 @@ 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..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: @@ -16,12 +15,12 @@ build: - lib/ requirements: build: - - r + - r-base - posix # [win] - {{native}}toolchain # [win] - gcc # [not win] run: - - r + - r-base test: commands: - $R -e "library('Rwave')" # [not win] diff --git a/recipes/r-sartools/1.2.0/build.sh b/recipes/r-sartools/1.2.0/build.sh deleted file mode 100644 index 7fe0351a83..0000000000 --- a/recipes/r-sartools/1.2.0/build.sh +++ /dev/null @@ -1,14 +0,0 @@ -#!/bin/bash - -# R refuses to build packages that mark themselves as Priority: Recommended -mv DESCRIPTION DESCRIPTION.old -grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION - -$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 9ed158cce7..0000000000 --- a/recipes/r-sartools/1.2.0/meta.yaml +++ /dev/null @@ -1,70 +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: - # 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 - - r-knitr - - bioconductor-deseq2 - - bioconductor-edger - - run: - - r - - r-knitr - - bioconductor-deseq2 - - bioconductor-edger - -test: - commands: - # You can put additional test commands to be run here. - - $R -e "library('SARTools')" # [not win] - #- "\"%R%\" -e \"library('SARTools')\"" # [win] - - # You can also put a file called run_test.py, run_test.sh, or run_test.bat - # in the recipe that will be run at test time. - - # requires: - # Put any additional test requirements here. - -about: - home: https://github.com/PF2-pasteur-fr/SARTools - license: GPL-2 - summary: SARTools provides R tools and an environment for the statistical analysis of RNA-Seq projects load and clean data, produce figures, perform statistical analysis/testing with DESeq2 or edgeR, export results and create final report. - - -# The original GitHub metadata for this package was: -# https://github.com/PF2-pasteur-fr/SARTools/blob/master/DESCRIPTION - -#Package: SARTools -#Type: Package -#Title: Statistical Analysis of RNA-Seq Tools -#Version: 1.2.0 -#Date: 2015-12-03 -#Author: Marie-Agnes Dillies and Hugo Varet -#Maintainer: Hugo Varet -#Depends: R (>= 3.2.2), DESeq2 (>= 1.10.0), edgeR (>= 3.12.0), xtable -#Imports: knitr, GenomicRanges, S4Vectors, limma, genefilter (>= 1.44.0) -#VignetteBuilder: knitr -#Encoding: latin1 -#Description: SARTools provides R tools and an environment for the statistical analysis of RNA-Seq projects: load and clean data, produce figures, perform statistical analysis/testing with DESeq2 or edgeR, export results and create final report. -#License: GPL-2 - -# See -# http://docs.continuum.io/conda/build.html for -# more information about meta.yaml diff --git a/recipes/r-sartools/1.3.2/build.sh b/recipes/r-sartools/1.3.2/build.sh deleted file mode 100644 index 7fe0351a83..0000000000 --- a/recipes/r-sartools/1.3.2/build.sh +++ /dev/null @@ -1,14 +0,0 @@ -#!/bin/bash - -# R refuses to build packages that mark themselves as Priority: Recommended -mv DESCRIPTION DESCRIPTION.old -grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION - -$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 6d31e61727..0000000000 --- a/recipes/r-sartools/1.3.2/meta.yaml +++ /dev/null @@ -1,70 +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 - -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: parallel -requirements: - build: - - r - - r-knitr - - bioconductor-deseq2 - - bioconductor-edger - - run: - - r - - r-knitr - - 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-ipo/build.sh b/recipes/r-sartools/build.sh similarity index 100% rename from recipes/r-ipo/build.sh rename to recipes/r-sartools/build.sh 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. 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-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-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 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..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 @@ -31,11 +30,11 @@ build: # Suggests: segmented requirements: build: - - r + - r-base - r-ade4 run: - - r + - r-base - r-ade4 test: 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-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..bdcd70eb3c 100644 --- a/recipes/r-sleuth/meta.yaml +++ b/recipes/r-sleuth/meta.yaml @@ -10,21 +10,23 @@ build: - lib/ requirements: build: - - r + - r-base - bioconductor-rhdf5 - r-ggplot2 - r-dplyr - r-tidyr - r-shiny - r-data.table + - r-matrixstats run: - - r + - r-base - bioconductor-rhdf5 - r-ggplot2 - r-dplyr - r-tidyr - r-shiny - r-data.table + - r-matrixstats test: commands: - '$R -e "library(''sleuth'')"' diff --git a/recipes/r-snow/meta.yaml b/recipes/r-snow/meta.yaml index 20488a0ed4..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 @@ -32,10 +31,10 @@ 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..302c65f141 100644 --- a/recipes/r-soap-nmr/meta.yaml +++ b/recipes/r-soap-nmr/meta.yaml @@ -1,18 +1,21 @@ 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 + - r-base - r-matrix - r-ptw - r-ggplot2 @@ -20,16 +23,18 @@ requirements: - r-matrixstats - r-reshape2 run: - - r + - r-base - r-matrix - r-ptw - r-ggplot2 - r-gridextra - r-matrixstats - r-reshape2 + test: commands: - '$R -e "require(''SOAP'')"' + about: home: https://github.com/ManonMartin/SOAP-NMR license: 'GPL2' 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..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 @@ -18,7 +17,7 @@ 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 +31,7 @@ requirements: - llvm # [osx] run: - - r + - r-base - r-learnbayes - r-mass - r-matrix >=1.0.12 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 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. 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 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..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: @@ -21,13 +20,13 @@ 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..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 @@ -31,7 +30,7 @@ build: # Suggests: parallel, tcltk requirements: build: - - r + - r-base - r-mass # [not win] - r-cluster # [not win] - r-lattice # [not win] @@ -40,7 +39,7 @@ 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_4/meta.yaml b/recipes/r-vegan/2.3_4/meta.yaml index b9a08c36d3..592cddeafc 100644 --- a/recipes/r-vegan/2.3_4/meta.yaml +++ b/recipes/r-vegan/2.3_4/meta.yaml @@ -1,49 +1,40 @@ 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: 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 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 diff --git a/recipes/r-venndiagram/meta.yaml b/recipes/r-venndiagram/meta.yaml index 80d1f3d3a5..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 @@ -30,11 +21,11 @@ build: # Suggests: testthat requirements: build: - - r + - r-base - r-futile.logger run: - - r + - r-base - r-futile.logger test: @@ -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 diff --git a/recipes/r-viridis/meta.yaml b/recipes/r-viridis/meta.yaml index 8936630439..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: @@ -17,12 +16,12 @@ 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: 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 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 5aeca78e77..0000000000 --- a/recipes/rpy2/meta.yaml +++ /dev/null @@ -1,54 +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 -# patches: - # List any patch files here - # - fix.patch - -build: - rpaths: - - lib/R/lib/ - - lib/ - skip: False - number: 1 - -requirements: - build: - - python - - r - - setuptools - - argparse # [py26] - - singledispatch # [not (py34 or py35)] - - six - - readline - - run: - - python - - r - - argparse # [py26] - - singledispatch # [not (py34 or py35)] - - six - - readline - -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)' - -# See -# http://docs.continuum.io/conda/build.html for -# more information about meta.yaml 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/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 diff --git a/recipes/triform2/meta.yaml b/recipes/triform2/meta.yaml index 0a922bd4ed..f6d4f52d43 100644 --- a/recipes/triform2/meta.yaml +++ b/recipes/triform2/meta.yaml @@ -20,11 +20,11 @@ requirements: - numpy - natsort - joblib - - rpy2 + - rpy2 >=2.4.2 - bioconductor-iranges - bioconductor-biocgenerics - bioconductor-genomicranges - - r + - r-base - bx-python run: @@ -35,11 +35,11 @@ requirements: - numpy - natsort - joblib - - rpy2 + - rpy2 >=2.4.2 - 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 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 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 ] 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']) 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" diff --git a/sorted-r-blacklist b/sorted-r-blacklist index 1c2ff29346..9fb8cdddbc 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 +46,33 @@ 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 + + -# TODO: r-phonr seems to loop indefinitely when trying to build. -recipes/r-phonr +########################################## +recipes/r-maldiquantforeign -recipes/bioconductor-mmdiff +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 -# try disabling to avoid osx timeouts -recipes/triform2