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#!/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/NAM | ||
mv * $PREFIX/lib/R/library/NAM | ||
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 |
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{% set version = '1.6.4' %} | ||
{% set posix = 'm2-' if win else '' %} | ||
{% set native = 'm2w64-' if win else '' %} | ||
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||
package: | ||
name: r-nam | ||
version: {{ version|replace("-", "_") }} | ||
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||
source: | ||
url: | ||
- {{ cran_mirror }}/src/contrib/NAM_{{ version }}.tar.gz | ||
- {{ cran_mirror }}/src/contrib/Archive/NAM/NAM_{{ version }}.tar.gz | ||
sha256: a45ecf3286f7c17028d38a8389b7173b1ec38047768cec64a5e961649964ad2c | ||
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||
build: | ||
merge_build_host: True # [win] | ||
number: 0 | ||
|
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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-rcpp | ||
- r-randomforest | ||
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||
run: | ||
- r-base | ||
- {{native}}gcc-libs # [win] | ||
- r-rcpp | ||
- r-randomforest | ||
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test: | ||
commands: | ||
- $R -e "library('NAM')" # [not win] | ||
- "\"%R%\" -e \"library('NAM')\"" # [win] | ||
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||
about: | ||
home: https://CRAN.R-project.org/package=NAM | ||
license: GPL-3 | ||
summary: Designed for association studies in nested association mapping (NAM) panels, experimental | ||
and random panels. The method is described by Xavier et al. (2015) <doi:10.1093/bioinformatics/btv448>. | ||
It includes tools for genome-wide associations of multiple populations, marker quality | ||
control, population genetics analysis, genome-wide prediction, solving mixed models | ||
and finding variance components through likelihood and Bayesian methods. | ||
license_family: GPL3 | ||
license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' | ||
|
||
extra: | ||
recipe-maintainers: | ||
- johanneskoester | ||
- bgruening | ||
- daler | ||
- jdblischak | ||
- cbrueffer | ||
- dbast | ||
- Chris-Lowe-Integrity |