r-corbi (#12325)

bioconda · Nov 24, 2018 · 8d6f86b · 8d6f86b
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diff --git a/recipes/r-corbi/build.sh b/recipes/r-corbi/build.sh
@@ -0,0 +1,38 @@
+#!/bin/bash
+
+if [[ $target_platform =~ linux.* ]] || [[ $target_platform == win-32 ]] || [[ $target_platform == win-64 ]] || [[ $target_platform == osx-64 ]]; then
+  export DISABLE_AUTOBREW=1
+  mv DESCRIPTION DESCRIPTION.old
+  grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION
+  $R CMD INSTALL --build .
+else
+  mkdir -p $PREFIX/lib/R/library/Corbi
+  mv * $PREFIX/lib/R/library/Corbi
+
+  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-corbi/meta.yaml b/recipes/r-corbi/meta.yaml
@@ -0,0 +1,64 @@
+{% set version = '0.4-2' %}
+
+{% set posix = 'm2-' if win else '' %}
+{% set native = 'm2w64-' if win else '' %}
+
+package:
+  name: r-corbi
+  version: {{ version|replace("-", "_") }}
+
+source:
+  url:
+    - {{ cran_mirror }}/src/contrib/Corbi_{{ version }}.tar.gz
+    - {{ cran_mirror }}/src/contrib/Archive/Corbi/Corbi_{{ version }}.tar.gz
+  sha256: fc7adee4866c5fbcdc0b051bb3e910df0400651b7c6b749dbd51f94c6f440840
+
+build:
+  merge_build_host: True  # [win]
+
+  number: 0
+
+
+  rpaths:
+    - lib/R/lib/
+    - lib/
+
+
+requirements:
+  build:
+    - {{ compiler('c') }}        # [not win]
+    - {{ compiler('cxx') }}      # [not win]
+    - {{ compiler('fortran') }}
+    - {{native}}toolchain        # [win]
+    - {{posix}}filesystem        # [win]
+    - {{posix}}make
+    - {{posix}}sed               # [win]
+    - {{posix}}coreutils         # [win]
+    - {{posix}}zip               # [win]
+
+  host:
+    - r-base
+    - r-crf
+    - r-matrix
+    - r-mpmi
+
+  run:
+    - r-base
+    - {{native}}gcc-libs         # [win]
+    - r-crf
+    - r-matrix
+    - r-mpmi
+
+test:
+  commands:
+    - $R -e "library('Corbi')"           # [not win]
+    - "\"%R%\" -e \"library('Corbi')\""  # [win]
+
+about:
+  home: https://github.com/wulingyun/Corbi
+  license: GPL (>= 2)
+  summary: Provides a bundle of basic and fundamental bioinformatics tools, such as network querying
+    and alignment, subnetwork extraction and search, network biomarker identification.
+  license_family: GPL3
+
+