From 0b3caddb203a9ecb7fb0fdbeb12847cd05455d02 Mon Sep 17 00:00:00 2001
From: Christopher Lowe <lowechris1991@gmail.com>
Date: Sat, 24 Nov 2018 20:45:19 -0500
Subject: [PATCH] r-nam (#12327)

---
 recipes/r-nam/build.sh  | 34 ++++++++++++++++++++
 recipes/r-nam/meta.yaml | 69 +++++++++++++++++++++++++++++++++++++++++
 2 files changed, 103 insertions(+)
 create mode 100644 recipes/r-nam/build.sh
 create mode 100644 recipes/r-nam/meta.yaml

diff --git a/recipes/r-nam/build.sh b/recipes/r-nam/build.sh
new file mode 100644
index 0000000000000..f98a41ea93092
--- /dev/null
+++ b/recipes/r-nam/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/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
diff --git a/recipes/r-nam/meta.yaml b/recipes/r-nam/meta.yaml
new file mode 100644
index 0000000000000..ac8f3537750eb
--- /dev/null
+++ b/recipes/r-nam/meta.yaml
@@ -0,0 +1,69 @@
+{% set version = '1.6.4' %}
+{% set posix = 'm2-' if win else '' %}
+{% set native = 'm2w64-' if win else '' %}
+
+package:
+  name: r-nam
+  version: {{ version|replace("-", "_") }}
+
+source:
+  url:
+    - {{ cran_mirror }}/src/contrib/NAM_{{ version }}.tar.gz
+    - {{ cran_mirror }}/src/contrib/Archive/NAM/NAM_{{ version }}.tar.gz
+  sha256: a45ecf3286f7c17028d38a8389b7173b1ec38047768cec64a5e961649964ad2c
+
+build:
+  merge_build_host: True  # [win]
+  number: 0
+
+  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
+
+  run:
+    - r-base
+    - {{native}}gcc-libs         # [win]
+    - r-rcpp
+    - r-randomforest
+
+test:
+  commands:
+    - $R -e "library('NAM')"           # [not win]
+    - "\"%R%\" -e \"library('NAM')\""  # [win]
+
+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