diff --git a/build-fail-blacklist b/build-fail-blacklist index 5afd92cf50adb..87a5406a94404 100644 --- a/build-fail-blacklist +++ b/build-fail-blacklist @@ -890,7 +890,6 @@ recipes/bioconductor-phantasus recipes/bioconductor-degraph recipes/bioconductor-biggr recipes/r-coloc -recipes/r-rcdk recipes/bioconductor-chic recipes/bioconductor-rcellminer recipes/bioconductor-goprofiles @@ -974,6 +973,14 @@ recipes/bioconductor-esatac recipes/bioconductor-arrayexpresshts recipes/bioconductor-rdavidwebservice recipes/bioconductor-compgo +recipes/bioconductor-idmappingretrieval +recipes/bioconductor-mirlab +recipes/bioconductor-mirsm +recipes/bioconductor-damirseq +recipes/r-rcdk # Missing root dependency recipes/bioconductor-xps + +# Build never completes +recipes/bioconductor-cancer diff --git a/recipes/bioconductor-champ/meta.yaml b/recipes/bioconductor-champ/meta.yaml index 24ea2b612444f..18818562707ac 100644 --- a/recipes/bioconductor-champ/meta.yaml +++ b/recipes/bioconductor-champ/meta.yaml @@ -48,6 +48,7 @@ requirements: - r-doparallel - r-hmisc - r-isva + - r-kpmt - r-matrixstats - 'r-plotly >=4.5.6' - r-plyr @@ -87,6 +88,7 @@ requirements: - r-doparallel - r-hmisc - r-isva + - r-kpmt - r-matrixstats - 'r-plotly >=4.5.6' - r-plyr diff --git a/recipes/r-bc3net/bld.bat b/recipes/r-bc3net/bld.bat deleted file mode 100644 index b7e1203063141..0000000000000 --- a/recipes/r-bc3net/bld.bat +++ /dev/null @@ -1,2 +0,0 @@ -"%R%" CMD INSTALL --build . -IF %ERRORLEVEL% NEQ 0 exit 1 diff --git a/recipes/r-cp4p/bld.bat b/recipes/r-cp4p/bld.bat deleted file mode 100644 index b7e1203063141..0000000000000 --- a/recipes/r-cp4p/bld.bat +++ /dev/null @@ -1,2 +0,0 @@ -"%R%" CMD INSTALL --build . -IF %ERRORLEVEL% NEQ 0 exit 1 diff --git a/recipes/r-enrichr/bld.bat b/recipes/r-enrichr/bld.bat deleted file mode 100644 index b7e1203063141..0000000000000 --- a/recipes/r-enrichr/bld.bat +++ /dev/null @@ -1,2 +0,0 @@ -"%R%" CMD INSTALL --build . -IF %ERRORLEVEL% NEQ 0 exit 1 diff --git a/recipes/r-imp4p/bld.bat b/recipes/r-imp4p/bld.bat deleted file mode 100644 index b7e1203063141..0000000000000 --- a/recipes/r-imp4p/bld.bat +++ /dev/null @@ -1,2 +0,0 @@ -"%R%" CMD INSTALL --build . -IF %ERRORLEVEL% NEQ 0 exit 1 diff --git a/recipes/r-mess/build.sh b/recipes/r-mess/build.sh new file mode 100644 index 0000000000000..519537a2e336f --- /dev/null +++ b/recipes/r-mess/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/MESS + mv * $PREFIX/lib/R/library/MESS + 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-mess/meta.yaml b/recipes/r-mess/meta.yaml new file mode 100644 index 0000000000000..1e6f7d5244000 --- /dev/null +++ b/recipes/r-mess/meta.yaml @@ -0,0 +1,59 @@ +{% set version = '0.5.4' %} +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} + +package: + name: r-mess + version: {{ version|replace("-", "_") }} + +source: + url: + - {{ cran_mirror }}/src/contrib/MESS_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/MESS/MESS_{{ version }}.tar.gz + sha256: f49f870729030945ff672f7fac4a0b2e7d71e9c61537dd1d732449cead160984 + +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + +requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - {{posix}}make + host: + - r-base + - r-mass + - r-matrix + - r-rcpp + - r-rcpparmadillo + - r-geem + - r-geepack + - r-glmnet + - r-kinship2 + - r-mvtnorm + run: + - r-base + - r-mass + - r-matrix + - r-rcpp + - r-rcpparmadillo + - r-geem + - r-geepack + - r-glmnet + - r-kinship2 + - r-mvtnorm + +test: + commands: + - $R -e "library('MESS')" + +about: + home: https://github.com/ekstroem/MESS + license: GPL-2 + summary: A mixed collection of useful and semi-useful diverse statistical functions, some of + which may even be referenced in The R Primer book. + license_family: GPL2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' diff --git a/recipes/r-plsgenomics/bld.bat b/recipes/r-plsgenomics/bld.bat deleted file mode 100644 index b7e1203063141..0000000000000 --- a/recipes/r-plsgenomics/bld.bat +++ /dev/null @@ -1,2 +0,0 @@ -"%R%" CMD INSTALL --build . -IF %ERRORLEVEL% NEQ 0 exit 1 diff --git a/recipes/r-rismed/bld.bat b/recipes/r-rismed/bld.bat deleted file mode 100644 index b7e1203063141..0000000000000 --- a/recipes/r-rismed/bld.bat +++ /dev/null @@ -1,2 +0,0 @@ -"%R%" CMD INSTALL --build . -IF %ERRORLEVEL% NEQ 0 exit 1 diff --git a/recipes/r-tcr/bld.bat b/recipes/r-tcr/bld.bat deleted file mode 100644 index b7e1203063141..0000000000000 --- a/recipes/r-tcr/bld.bat +++ /dev/null @@ -1,2 +0,0 @@ -"%R%" CMD INSTALL --build . -IF %ERRORLEVEL% NEQ 0 exit 1