diff --git a/build-fail-blacklist b/build-fail-blacklist index cf67a5f2a3e68..15969d4663e4a 100644 --- a/build-fail-blacklist +++ b/build-fail-blacklist @@ -810,6 +810,7 @@ recipes/bioconductor-meshsim recipes/bioconductor-mmdiff recipes/bioconductor-mmnet recipes/bioconductor-rcytoscape +recipes/bioconductor-browservizdemo # Old bioconductor version that's no longer available recipes/bioconductor-edger/3.12.1 @@ -873,22 +874,33 @@ recipes/bioconductor-ncigraph recipes/bioconductor-lymphoseq recipes/bioconductor-universalmotif recipes/bioconductor-phantasus +recipes/bioconductor-degraph +recipes/bioconductor-biggr # r-feature missing/broken recipes/bioconductor-flowmerge recipes/bioconductor-flowmeans +recipes/bioconductor-confess +recipes/bioconductor-flowtype -# some wired test error with the Docker tests +# some weird test error in Docker (and downstream dependent packages) +recipes/bioconductor-rqt +recipes/bioconductor-fccac +recipes/bioconductor-funchip recipes/bioconductor-flowstats recipes/bioconductor-nethet recipes/bioconductor-iterativebma recipes/bioconductor-narrowpeaks recipes/bioconductor-iwtomics +recipes/bioconductor-flowvs +recipes/bioconductor-opencyto +recipes/bioconductor-cytoml +recipes/bioconductor-platecore # missing r-* deps recipes/bioconductor-mcagui recipes/bioconductor-rexposome - # JVM errors recipes/bioconductor-rgmql +recipes/bioconductor-camthc diff --git a/recipes/r-gap/build.sh b/recipes/r-gap/build.sh new file mode 100644 index 0000000000000..148fdeaf11b55 --- /dev/null +++ b/recipes/r-gap/build.sh @@ -0,0 +1,34 @@ +#!/bin/bash +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/gap + mv * $PREFIX/lib/R/library/gap + 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-gap/meta.yaml b/recipes/r-gap/meta.yaml new file mode 100644 index 0000000000000..e8bfce038288c --- /dev/null +++ b/recipes/r-gap/meta.yaml @@ -0,0 +1,46 @@ +{% set version = '1.1-22' %} +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} + +package: + name: r-gap + version: {{ version|replace("-", "_") }} + +source: + url: + - {{ cran_mirror }}/src/contrib/gap_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/gap/gap_{{ version }}.tar.gz + sha256: 71a691aac9ce29bfcf1159eacba1866c8571b781f68fb32a3e52fb8584f03ef7 + +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + +requirements: + build: + - {{ compiler('c') }} + - {{ compiler('fortran') }} + - {{posix}}make + host: + - r-base + run: + - r-base + +test: + commands: + - $R -e "library('gap')" # [not win] + - "\"%R%\" -e \"library('gap')\"" # [win] + +about: + home: https://jinghuazhao.github.io + license: GPL (>= 2) + summary: It is designed as an integrated package for genetic data analysis of both population + and family data. Currently, it contains functions for sample size calculations of + both population-based and family-based designs, probability of familial disease + aggregation, kinship calculation, statistics in linkage analysis, and association + analysis involving genetic markers including haplotype analysis with or without + environmental covariates. + license_family: GPL3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' diff --git a/recipes/r-grain/bld.bat b/recipes/r-grain/bld.bat deleted file mode 100644 index b7e1203063141..0000000000000 --- a/recipes/r-grain/bld.bat +++ /dev/null @@ -1,2 +0,0 @@ -"%R%" CMD INSTALL --build . -IF %ERRORLEVEL% NEQ 0 exit 1 diff --git a/recipes/r-isogene/bld.bat b/recipes/r-isogene/bld.bat deleted file mode 100644 index b7e1203063141..0000000000000 --- a/recipes/r-isogene/bld.bat +++ /dev/null @@ -1,2 +0,0 @@ -"%R%" CMD INSTALL --build . -IF %ERRORLEVEL% NEQ 0 exit 1 diff --git a/recipes/r-jackstraw/bld.bat b/recipes/r-jackstraw/bld.bat deleted file mode 100644 index b7e1203063141..0000000000000 --- a/recipes/r-jackstraw/bld.bat +++ /dev/null @@ -1,2 +0,0 @@ -"%R%" CMD INSTALL --build . -IF %ERRORLEVEL% NEQ 0 exit 1 diff --git a/recipes/r-orqa/bld.bat b/recipes/r-orqa/bld.bat deleted file mode 100644 index b7e1203063141..0000000000000 --- a/recipes/r-orqa/bld.bat +++ /dev/null @@ -1,2 +0,0 @@ -"%R%" CMD INSTALL --build . -IF %ERRORLEVEL% NEQ 0 exit 1 diff --git a/recipes/r-pcalg/bld.bat b/recipes/r-pcalg/bld.bat deleted file mode 100644 index b7e1203063141..0000000000000 --- a/recipes/r-pcalg/bld.bat +++ /dev/null @@ -1,2 +0,0 @@ -"%R%" CMD INSTALL --build . -IF %ERRORLEVEL% NEQ 0 exit 1 diff --git a/recipes/r-rapidr/meta.yaml b/recipes/r-rapidr/meta.yaml index c114b3590903c..4944888a2f785 100644 --- a/recipes/r-rapidr/meta.yaml +++ b/recipes/r-rapidr/meta.yaml @@ -25,24 +25,23 @@ requirements: - {{posix}}zip # [win] host: - r-base - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - bioconductor-biostrings + - bioconductor-genomicalignments + - bioconductor-genomicranges - r-propcis - - 'bioconductor-rsamtools >=1.32.0,<1.34.0' + - bioconductor-rsamtools - r-data.table run: - r-base - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - bioconductor-biostrings + - bioconductor-genomicalignments + - bioconductor-genomicranges - r-propcis - - 'bioconductor-rsamtools >=1.32.0,<1.34.0' + - bioconductor-rsamtools - r-data.table test: commands: - - $R -e "library('RAPIDR')" # [not win] - "\"%R%\" -e \"library('RAPIDR')\"" # [win]