diff --git a/build-fail-blacklist b/build-fail-blacklist index 2a16e199742b7..71b727b980673 100644 --- a/build-fail-blacklist +++ b/build-fail-blacklist @@ -803,7 +803,7 @@ recipes/r-dbchip recipes/r-asics recipes/r-biom -# Deprecated in Bioconductor +# Deprecated/build fail in Bioconductor recipes/bioconductor-atlasrdf recipes/bioconductor-jmosaics recipes/bioconductor-meshsim @@ -813,6 +813,7 @@ recipes/bioconductor-rcytoscape recipes/bioconductor-browservizdemo recipes/bioconductor-pannbuilder recipes/bioconductor-splicer +recipes/bioconductor-flowq # Old bioconductor version that's no longer available recipes/bioconductor-edger/3.12.1 diff --git a/recipes/bioconductor-outrider/meta.yaml b/recipes/bioconductor-outrider/meta.yaml index 6202c450c8b5a..0affe5dc69e80 100644 --- a/recipes/bioconductor-outrider/meta.yaml +++ b/recipes/bioconductor-outrider/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.0.0" %} +{% set version = "1.0.1" %} {% set name = "OUTRIDER" %} {% 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: 589f062de187f5b31a2ab045181d9f34 + md5: 89fbc10855ad4fb905ad705dc3002f53 build: number: 0 rpaths: diff --git a/recipes/r-htscluster/build.sh b/recipes/r-htscluster/build.sh new file mode 100644 index 0000000000000..771cd2a639a8f --- /dev/null +++ b/recipes/r-htscluster/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/HTSCluster + mv * $PREFIX/lib/R/library/HTSCluster + 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-htscluster/meta.yaml b/recipes/r-htscluster/meta.yaml new file mode 100644 index 0000000000000..d6d94b32ef7c4 --- /dev/null +++ b/recipes/r-htscluster/meta.yaml @@ -0,0 +1,49 @@ +{% set version = '2.0.8' %} +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} + +package: + name: r-htscluster + version: {{ version|replace("-", "_") }} + +source: + url: + - {{ cran_mirror }}/src/contrib/HTSCluster_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/HTSCluster/HTSCluster_{{ version }}.tar.gz + sha256: 6f82fa50bd95620fe5dea7c66a1876a6fea0bd46bb3e1aa54806f5060d74cb72 + +build: + number: 0 + noarch: generic + rpaths: + - lib/R/lib/ + - lib/ + +requirements: + build: + + host: + - r-base + - r-capushe + - bioconductobioconductor-edger + - r-plotrix + run: + - r-base + - r-capushe + - bioconductobioconductor-edger + - r-plotrix + +test: + commands: + - $R -e "library('HTSCluster')" # [not win] + - "\"%R%\" -e \"library('HTSCluster')\"" # [win] + +about: + home: https://CRAN.R-project.org/package=HTSCluster + license: GPL (>= 3) + summary: A Poisson mixture model is implemented to cluster genes from high- throughput transcriptome + sequencing (RNA-seq) data. Parameter estimation is performed using either the EM + or CEM algorithm, and the slope heuristics are used for model selection (i.e., to + choose the number of clusters). + license_family: GPL3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' diff --git a/recipes/r-nbpseq/build.sh b/recipes/r-nbpseq/build.sh new file mode 100644 index 0000000000000..950a2bc1ebcf8 --- /dev/null +++ b/recipes/r-nbpseq/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/NBPSeq + mv * $PREFIX/lib/R/library/NBPSeq + 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-nbpseq/meta.yaml b/recipes/r-nbpseq/meta.yaml new file mode 100644 index 0000000000000..6444394f61301 --- /dev/null +++ b/recipes/r-nbpseq/meta.yaml @@ -0,0 +1,49 @@ +{% set version = '0.3.0' %} +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} + +package: + name: r-nbpseq + version: {{ version|replace("-", "_") }} + +source: + url: + - {{ cran_mirror }}/src/contrib/NBPSeq_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/NBPSeq/NBPSeq_{{ version }}.tar.gz + sha256: 7e251fa017d91ffa7b0c5e740859db4aa4f9bc3b46632983e03c4da161a79e50 + +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + +requirements: + build: + - {{ compiler('c') }} # [not win] + - {{native}}toolchain # [win] + - {{posix}}filesystem # [win] + - {{posix}}make + - {{posix}}sed # [win] + - {{posix}}coreutils # [win] + - {{posix}}zip # [win] + host: + - r-base + - bioconductor-qvalue + run: + - r-base + - {{native}}gcc-libs # [win] + - bioconductor-qvalue + +test: + commands: + - $R -e "library('NBPSeq')" # [not win] + - "\"%R%\" -e \"library('NBPSeq')\"" # [win] + +about: + home: https://CRAN.R-project.org/package=NBPSeq + license: GPL-2 + summary: Negative Binomial (NB) models for two-group comparisons and regression inferences + from RNA-Sequencing Data. + license_family: GPL2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2'