diff --git a/build-fail-blacklist b/build-fail-blacklist index f99ccdf8a3c19..2a16e199742b7 100644 --- a/build-fail-blacklist +++ b/build-fail-blacklist @@ -891,6 +891,8 @@ recipes/bioconductor-rcpi recipes/r-dartr recipes/bioconductor-dsimer recipes/bioconductor-pga +recipes/bioconductor-linc +recipes/bioconductor-fourcseq # r-dagitity missing -> missing of V8 in cf recipes/r-pcalg @@ -898,6 +900,7 @@ recipes/bioconductor-epinem # R clusterr GCC7 builds missing recipes/r-jackstraw +recipes/bioconductor-biocancer # r-feature missing/broken recipes/bioconductor-flowmerge @@ -932,9 +935,7 @@ recipes/bioconductor-r3cpet recipes/bioconductor-omicspca recipes/bioconductor-madseq recipes/bioconductor-doqtl - -# Waiting on gcc7 builds of deps -# recipes/bioconductor-biocancer +recipes/bioconductor-debrowser # Not enough memory on circleci recipes/bioconductor-conumee diff --git a/recipes/bioconductor-eegc/meta.yaml b/recipes/bioconductor-eegc/meta.yaml index 6b32ea092ad88..4e9949f3c26aa 100644 --- a/recipes/bioconductor-eegc/meta.yaml +++ b/recipes/bioconductor-eegc/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.8.0" %} +{% set version = "1.8.1" %} {% set name = "eegc" %} {% set bioc = "3.8" %} @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 80ae17a861a02b93bac38afb632948b1 + md5: acac7f97fcfcc9641aab15beda10c60c build: number: 0 rpaths: diff --git a/recipes/bioconductor-mageckflute/meta.yaml b/recipes/bioconductor-mageckflute/meta.yaml index 751f8509aaa73..85f02cfbb3983 100644 --- a/recipes/bioconductor-mageckflute/meta.yaml +++ b/recipes/bioconductor-mageckflute/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.2.1" %} +{% set version = "1.2.2" %} {% set name = "MAGeCKFlute" %} {% set bioc = "3.8" %} @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 80c61e7aae7789fcd50e2f08b97e1d35 + md5: 50c6209facdbb9a7b9f33cd7b4b6867c build: number: 0 rpaths: diff --git a/recipes/r-diffcorr/meta.yaml b/recipes/r-diffcorr/meta.yaml index 827d2801c4ac7..a207f73aa9116 100644 --- a/recipes/r-diffcorr/meta.yaml +++ b/recipes/r-diffcorr/meta.yaml @@ -27,14 +27,14 @@ requirements: - r-base - r-fdrtool - r-igraph - - r-multtest - - r-pcamethods + - bioconductor-multtest + - bioconductor-pcamethods run: - r-base - r-fdrtool - r-igraph - - r-multtest - - r-pcamethods + - bioconductor-multtest + - bioconductor-pcamethods test: commands: diff --git a/recipes/r-isva/build.sh b/recipes/r-isva/build.sh new file mode 100644 index 0000000000000..1314b1f953cfe --- /dev/null +++ b/recipes/r-isva/build.sh @@ -0,0 +1,33 @@ +if [[ $target_platform =~ linux.* ]] || [[ $target_platform == win-32 ]] || [[ $target_platform == win-64 ]] || [[ $target_platform == osx-64 ]]; then + export DISABLE_AUTOBREW=1 + $R CMD INSTALL --build . +else + mkdir -p $PREFIX/lib/R/library/isva + mv * $PREFIX/lib/R/library/isva + if [[ $target_platform == osx-64 ]]; then + pushd $PREFIX + for libdir in lib/R/lib lib/R/modules lib/R/library lib/R/bin/exec sysroot/usr/lib; do + pushd $libdir || exit 1 + for SHARED_LIB in $(find . -type f -iname "*.dylib" -or -iname "*.so" -or -iname "R"); do + echo "fixing SHARED_LIB $SHARED_LIB" + install_name_tool -change /Library/Frameworks/R.framework/Versions/3.5.0-MRO/Resources/lib/libR.dylib "$PREFIX"/lib/R/lib/libR.dylib $SHARED_LIB || true + install_name_tool -change /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libR.dylib "$PREFIX"/lib/R/lib/libR.dylib $SHARED_LIB || true + install_name_tool -change /usr/local/clang4/lib/libomp.dylib "$PREFIX"/lib/libomp.dylib $SHARED_LIB || true + install_name_tool -change /usr/local/gfortran/lib/libgfortran.3.dylib "$PREFIX"/lib/libgfortran.3.dylib $SHARED_LIB || true + install_name_tool -change /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libquadmath.0.dylib "$PREFIX"/lib/libquadmath.0.dylib $SHARED_LIB || true + install_name_tool -change /usr/local/gfortran/lib/libquadmath.0.dylib "$PREFIX"/lib/libquadmath.0.dylib $SHARED_LIB || true + install_name_tool -change /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libgfortran.3.dylib "$PREFIX"/lib/libgfortran.3.dylib $SHARED_LIB || true + install_name_tool -change /usr/lib/libgcc_s.1.dylib "$PREFIX"/lib/libgcc_s.1.dylib $SHARED_LIB || true + install_name_tool -change /usr/lib/libiconv.2.dylib "$PREFIX"/sysroot/usr/lib/libiconv.2.dylib $SHARED_LIB || true + install_name_tool -change /usr/lib/libncurses.5.4.dylib "$PREFIX"/sysroot/usr/lib/libncurses.5.4.dylib $SHARED_LIB || true + install_name_tool -change /usr/lib/libicucore.A.dylib "$PREFIX"/sysroot/usr/lib/libicucore.A.dylib $SHARED_LIB || true + install_name_tool -change /usr/lib/libexpat.1.dylib "$PREFIX"/lib/libexpat.1.dylib $SHARED_LIB || true + install_name_tool -change /usr/lib/libcurl.4.dylib "$PREFIX"/lib/libcurl.4.dylib $SHARED_LIB || true + install_name_tool -change /usr/lib/libc++.1.dylib "$PREFIX"/lib/libc++.1.dylib $SHARED_LIB || true + install_name_tool -change /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libc++.1.dylib "$PREFIX"/lib/libc++.1.dylib $SHARED_LIB || true + done + popd + done + popd + fi +fi diff --git a/recipes/r-isva/meta.yaml b/recipes/r-isva/meta.yaml new file mode 100644 index 0000000000000..cdaea0074dd2c --- /dev/null +++ b/recipes/r-isva/meta.yaml @@ -0,0 +1,65 @@ +{% set version = '1.9' %} +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} + +package: + name: r-isva + version: {{ version|replace("-", "_") }} + +source: + url: + - {{ cran_mirror }}/src/contrib/isva_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/isva/isva_{{ version }}.tar.gz + sha256: 9fd016e0b34034d271d45f8a0d0db62780bf0187112e45f610aa9237014e1d17 + +build: + merge_build_host: True # [win] + number: 0 + skip: true # [win32] + noarch: generic + rpaths: + - lib/R/lib/ + - lib/ + +requirements: + build: + + host: + - r-base + - r-jade + - r-fastica + - bioconductor-qvalue + run: + - r-base + - r-jade + - r-fastica + - bioconductor-qvalue + +test: + commands: + - $R -e "library('isva')" # [not win] + - "\"%R%\" -e \"library('isva')\"" # [win] + +about: + home: https://CRAN.R-project.org/package=isva + license: GPL-2 + summary: 'Independent Surrogate Variable Analysis is an algorithm for feature selection in + the presence of potential confounding factors (see Teschendorff AE et al 2011, ).' + license_family: GPL2 + license_file: '{{ environ["PREFIX"] }}\/lib\/R\/share\/licenses\/GPL-2' # [unix] + license_file: '{{ environ["PREFIX"] }}\R\share\licenses\GPL-2' # [win] + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + +extra: + recipe-maintainers: + - conda-forge/r +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-smartsva/build.sh b/recipes/r-smartsva/build.sh new file mode 100644 index 0000000000000..78d2e25928514 --- /dev/null +++ b/recipes/r-smartsva/build.sh @@ -0,0 +1,33 @@ +if [[ $target_platform =~ linux.* ]] || [[ $target_platform == win-32 ]] || [[ $target_platform == win-64 ]] || [[ $target_platform == osx-64 ]]; then + export DISABLE_AUTOBREW=1 + $R CMD INSTALL --build . +else + mkdir -p $PREFIX/lib/R/library/SmartSVA + mv * $PREFIX/lib/R/library/SmartSVA + if [[ $target_platform == osx-64 ]]; then + pushd $PREFIX + for libdir in lib/R/lib lib/R/modules lib/R/library lib/R/bin/exec sysroot/usr/lib; do + pushd $libdir || exit 1 + for SHARED_LIB in $(find . -type f -iname "*.dylib" -or -iname "*.so" -or -iname "R"); do + echo "fixing SHARED_LIB $SHARED_LIB" + install_name_tool -change /Library/Frameworks/R.framework/Versions/3.5.0-MRO/Resources/lib/libR.dylib "$PREFIX"/lib/R/lib/libR.dylib $SHARED_LIB || true + install_name_tool -change /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libR.dylib "$PREFIX"/lib/R/lib/libR.dylib $SHARED_LIB || true + install_name_tool -change /usr/local/clang4/lib/libomp.dylib "$PREFIX"/lib/libomp.dylib $SHARED_LIB || true + install_name_tool -change /usr/local/gfortran/lib/libgfortran.3.dylib "$PREFIX"/lib/libgfortran.3.dylib $SHARED_LIB || true + install_name_tool -change /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libquadmath.0.dylib "$PREFIX"/lib/libquadmath.0.dylib $SHARED_LIB || true + install_name_tool -change /usr/local/gfortran/lib/libquadmath.0.dylib "$PREFIX"/lib/libquadmath.0.dylib $SHARED_LIB || true + install_name_tool -change /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libgfortran.3.dylib "$PREFIX"/lib/libgfortran.3.dylib $SHARED_LIB || true + install_name_tool -change /usr/lib/libgcc_s.1.dylib "$PREFIX"/lib/libgcc_s.1.dylib $SHARED_LIB || true + install_name_tool -change /usr/lib/libiconv.2.dylib "$PREFIX"/sysroot/usr/lib/libiconv.2.dylib $SHARED_LIB || true + install_name_tool -change /usr/lib/libncurses.5.4.dylib "$PREFIX"/sysroot/usr/lib/libncurses.5.4.dylib $SHARED_LIB || true + install_name_tool -change /usr/lib/libicucore.A.dylib "$PREFIX"/sysroot/usr/lib/libicucore.A.dylib $SHARED_LIB || true + install_name_tool -change /usr/lib/libexpat.1.dylib "$PREFIX"/lib/libexpat.1.dylib $SHARED_LIB || true + install_name_tool -change /usr/lib/libcurl.4.dylib "$PREFIX"/lib/libcurl.4.dylib $SHARED_LIB || true + install_name_tool -change /usr/lib/libc++.1.dylib "$PREFIX"/lib/libc++.1.dylib $SHARED_LIB || true + install_name_tool -change /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libc++.1.dylib "$PREFIX"/lib/libc++.1.dylib $SHARED_LIB || true + done + popd + done + popd + fi +fi diff --git a/recipes/r-smartsva/meta.yaml b/recipes/r-smartsva/meta.yaml new file mode 100644 index 0000000000000..13f0a74536215 --- /dev/null +++ b/recipes/r-smartsva/meta.yaml @@ -0,0 +1,78 @@ +{% set version = '0.1.3' %} +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} + +package: + name: r-smartsva + version: {{ version|replace("-", "_") }} + +source: + url: + - {{ cran_mirror }}/src/contrib/SmartSVA_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/SmartSVA/SmartSVA_{{ version }}.tar.gz + sha256: d7925743d04bd52dee575a477cc7e8395fedb08f5dbb8427e61e3d6dbfd04881 + +build: + merge_build_host: True # [win] + number: 0 + skip: true # [win32] + rpaths: + - lib/R/lib/ + - lib/ + +requirements: + build: + - {{ compiler('c') }} # [not win] + - {{ compiler('cxx') }} # [not win] + - {{native}}toolchain # [win] + - {{posix}}filesystem # [win] + - {{posix}}make + - {{posix}}sed # [win] + - {{posix}}coreutils # [win] + - {{posix}}zip # [win] + host: + - r-base + - r-rspectra + - r-rcpp + - r-rcppeigen + - r-isva + - bioconductor-sva + run: + - r-base + - {{native}}gcc-libs # [win] + - r-rspectra + - r-rcpp + - r-rcppeigen + - r-isva + - bioconductor-sva + +test: + commands: + - $R -e "library('SmartSVA')" # [not win] + - "\"%R%\" -e \"library('SmartSVA')\"" # [win] + +about: + home: https://CRAN.R-project.org/package=SmartSVA + license: GPL-3 + summary: Introduces a fast and efficient Surrogate Variable Analysis algorithm that captures + variation of unknown sources (batch effects) for high-dimensional data sets. The + algorithm is built on the 'irwsva.build' function of the 'sva' package and proposes + a revision on it that achieves an order of magnitude faster running time while trading + no accuracy loss in return. + license_family: GPL3 + license_file: '{{ environ["PREFIX"] }}\/lib\/R\/share\/licenses\/GPL-3' # [unix] + license_file: '{{ environ["PREFIX"] }}\R\share\licenses\GPL-3' # [win] + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + +extra: + recipe-maintainers: + - conda-forge/r +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak