From 4e0eccc34384cdf8e1d3bd549b66b45acf22f627 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gildas=20Le=20Corguill=C3=A9?=
 <lecorguille@users.noreply.github.com>
Date: Tue, 19 Feb 2019 14:30:31 +0100
Subject: [PATCH] r-momr (#13703)

---
 recipes/r-momr/build.sh  | 38 +++++++++++++++++++++++++++++++++
 recipes/r-momr/meta.yaml | 46 ++++++++++++++++++++++++++++++++++++++++
 2 files changed, 84 insertions(+)
 create mode 100644 recipes/r-momr/build.sh
 create mode 100644 recipes/r-momr/meta.yaml

diff --git a/recipes/r-momr/build.sh b/recipes/r-momr/build.sh
new file mode 100644
index 0000000000000..18ef739ab577b
--- /dev/null
+++ b/recipes/r-momr/build.sh
@@ -0,0 +1,38 @@
+#!/bin/bash
+
+if [[ $target_platform =~ linux.* ]] || [[ $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/momr
+  mv * $PREFIX/lib/R/library/momr
+
+  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-momr/meta.yaml b/recipes/r-momr/meta.yaml
new file mode 100644
index 0000000000000..aca822d4fef39
--- /dev/null
+++ b/recipes/r-momr/meta.yaml
@@ -0,0 +1,46 @@
+{% set version = '1.1' %}
+
+package:
+  name: r-momr
+  version: {{ version|replace("-", "_") }}
+
+source:
+  url:
+    - {{ cran_mirror }}/src/contrib/momr_{{ version }}.tar.gz
+    - {{ cran_mirror }}/src/contrib/Archive/momr/momr_{{ version }}.tar.gz
+  sha256: b9249b5b7fd6a201ba015327db1ed54abc958bd03e8a4713c249d486b8fa3b24
+
+build:
+  number: 0
+  rpaths:
+    - lib/R/lib/
+    - lib/
+
+requirements:
+  host:
+    - r-base
+    - r-hmisc
+    - r-gplots
+    - r-nortest
+
+  run:
+    - r-base
+    - r-hmisc
+    - r-gplots
+    - r-nortest
+
+test:
+  commands:
+    - $R -e "library('momr')"
+
+about:
+  home: https://CRAN.R-project.org/package=momr
+  license: Artistic-2.0 (Restricts use)
+  summary: '''MetaOMineR'' suite is a set of R packages that offers many functions and modules
+    needed for the analyses  of quantitative metagenomics data. ''momr'' is the core
+    package and contains routines for biomarker identification and exploration. Developed
+    since the beginning of field, ''momr'' has evolved and is structured around the
+    different modules  such as preprocessing, analysis, vizualisation, etc. See package
+    help for more information.'
+  license_family: OTHER
+  license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/Artistic-2.0'