Bulk updates for 040119 (#12910)

bioconda · Jan 4, 2019 · 363a330 · 363a330
1 parent 6b0bdda
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diff --git a/build-fail-blacklist b/build-fail-blacklist
@@ -906,6 +906,8 @@ recipes/r-qpcr
 recipes/bioconductor-normqpcr
 recipes/bioconductor-post
 recipes/bioconductor-interactivedisplay
+recipes/bioconductor-icheck
+recipes/bioconductor-bgx
 
 # r-dagitity missing -> missing of V8 in cf
 recipes/r-pcalg

diff --git a/recipes/r-bc3net/bld.bat b/recipes/r-bc3net/bld.bat
@@ -0,0 +1,2 @@
+"%R%" CMD INSTALL --build .
+IF %ERRORLEVEL% NEQ 0 exit 1
diff --git a/recipes/r-bc3net/build.sh b/recipes/r-bc3net/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/bc3net
+  mv * $PREFIX/lib/R/library/bc3net
+  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-bc3net/meta.yaml b/recipes/r-bc3net/meta.yaml
@@ -0,0 +1,73 @@
+{% set version = '1.0.4' %}
+{% set posix = 'm2-' if win else '' %}
+{% set native = 'm2w64-' if win else '' %}
+
+package:
+  name: r-bc3net
+  version: {{ version|replace("-", "_") }}
+
+source:
+  url:
+    - {{ cran_mirror }}/src/contrib/bc3net_{{ version }}.tar.gz
+    - {{ cran_mirror }}/src/contrib/Archive/bc3net/bc3net_{{ version }}.tar.gz
+  sha256: 506ca8d5bab1e915bda38014b26a518df103cb4e64211ecf81e1e8b04183af95
+
+build:
+  merge_build_host: True  # [win]
+  number: 0
+  noarch: generic
+  rpaths:
+    - lib/R/lib/
+    - lib/
+
+requirements:
+  build:
+
+  host:
+    - r-base
+    - r-matrix
+    - r-c3net
+    - r-igraph
+    - r-infotheo
+    - r-lattice
+  run:
+    - r-base
+    - r-matrix
+    - r-c3net
+    - r-igraph
+    - r-infotheo
+    - r-lattice
+
+test:
+  commands:
+    - $R -e "library('bc3net')"           # [not win]
+    - "\"%R%\" -e \"library('bc3net')\""  # [win]
+
+about:
+  home: https://CRAN.R-project.org/package=bc3net
+  license: GPL (>= 2)
+  summary: 'Implementation of the BC3NET algorithm for gene regulatory network inference (de
+    Matos Simoes and Frank Emmert-Streib, Bagging Statistical Network Inference from
+    Large-Scale Gene Expression Data, PLoS ONE 7(3): e33624, <doi:10.1371/journal.pone.0033624>).'
+  license_family: GPL3
+  license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2'
+
+extra:
+  recipe-maintainers:
+    - conda-forge/r
+
+# Package: bc3net
+# Version: 1.0.4
+# Date: 2016-11-26
+# Title: Gene Regulatory Network Inference with Bc3net
+# Authors@R: c(person("Ricardo", "de Matos Simoes", role=c("aut","cre"), email="[email protected]"), person("Frank", "Emmert-Streib", role=c("aut"), email="[email protected]"))
+# Author: Ricardo de Matos Simoes [aut, cre], Frank Emmert-Streib [aut]
+# Maintainer: Ricardo de Matos Simoes <[email protected]>
+# Depends: R (>= 3.0.0), c3net, infotheo, igraph, Matrix, lattice
+# Suggests:
+# Description: Implementation of the BC3NET algorithm for gene regulatory network inference (de Matos Simoes and Frank Emmert-Streib, Bagging Statistical Network Inference from Large-Scale Gene Expression Data, PLoS ONE 7(3): e33624, <doi:10.1371/journal.pone.0033624>).
+# License: GPL (>= 2)
+# Repository: CRAN
+# NeedsCompilation: no
+# Packaged: 2016-11-27 21:32:12 UTC; ricardo
+# Date/Publication: 2016-11-28 08:21:04
diff --git a/recipes/r-cp4p/bld.bat b/recipes/r-cp4p/bld.bat
@@ -0,0 +1,2 @@
+"%R%" CMD INSTALL --build .
+IF %ERRORLEVEL% NEQ 0 exit 1
diff --git a/recipes/r-cp4p/build.sh b/recipes/r-cp4p/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/cp4p
+  mv * $PREFIX/lib/R/library/cp4p
+  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-cp4p/meta.yaml b/recipes/r-cp4p/meta.yaml
@@ -0,0 +1,70 @@
+{% set version = '0.3.5' %}
+{% set posix = 'm2-' if win else '' %}
+{% set native = 'm2w64-' if win else '' %}
+
+package:
+  name: r-cp4p
+  version: {{ version|replace("-", "_") }}
+
+source:
+  url:
+    - {{ cran_mirror }}/src/contrib/cp4p_{{ version }}.tar.gz
+    - {{ cran_mirror }}/src/contrib/Archive/cp4p/cp4p_{{ version }}.tar.gz
+  sha256: 8cce7deeae654fe7344d64202f412457bb11bcb781583a4ad825909a17a0f39a
+
+build:
+  merge_build_host: True  # [win]
+  number: 0
+  noarch: generic
+  rpaths:
+    - lib/R/lib/
+    - lib/
+
+requirements:
+  build:
+
+  host:
+    - r-base
+    - r-mess
+    - bioconductor-limma
+    - bioconductor-multtest
+    - bioconductor-qvalue
+  run:
+    - r-base
+    - r-mess
+    - bioconductor-limma
+    - bioconductor-multtest
+    - bioconductor-qvalue
+
+test:
+  commands:
+    - $R -e "library('cp4p')"           # [not win]
+    - "\"%R%\" -e \"library('cp4p')\""  # [win]
+
+about:
+  home: https://CRAN.R-project.org/package=cp4p
+  license: GPL-3
+  summary: Functions to check whether a vector of p-values respects the assumptions of FDR (false
+    discovery rate) control procedures and to compute adjusted p-values.
+  license_family: GPL3
+  license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3'
+
+extra:
+  recipe-maintainers:
+    - conda-forge/r
+
+# Package: cp4p
+# Type: Package
+# Title: Calibration Plot for Proteomics
+# Version: 0.3.5
+# Date: 2016-05-11
+# Author: Quentin Giai Gianetto, Florence Combes, Claire Ramus, Christophe Bruley, Yohann CoutA, Thomas Burger
+# Maintainer: Quentin Giai Gianetto <[email protected]>
+# Description: Functions to check whether a vector of p-values respects the assumptions of FDR (false discovery rate) control procedures and to compute adjusted p-values.
+# License: GPL-3
+# Depends: R (>= 3.2.0), MESS, graphics, stats, multtest, qvalue, limma
+# Encoding: UTF-8
+# NeedsCompilation: no
+# Packaged: 2016-05-16 15:21:26 UTC; ligges
+# Repository: CRAN
+# Date/Publication: 2016-05-16 16:21:27
diff --git a/recipes/r-enrichr/bld.bat b/recipes/r-enrichr/bld.bat
@@ -0,0 +1,2 @@
+"%R%" CMD INSTALL --build .
+IF %ERRORLEVEL% NEQ 0 exit 1
diff --git a/recipes/r-enrichr/build.sh b/recipes/r-enrichr/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/enrichR
+  mv * $PREFIX/lib/R/library/enrichR
+  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-enrichr/meta.yaml b/recipes/r-enrichr/meta.yaml
@@ -0,0 +1,70 @@
+{% set version = '1.0' %}
+{% set posix = 'm2-' if win else '' %}
+{% set native = 'm2w64-' if win else '' %}
+
+package:
+  name: r-enrichr
+  version: {{ version|replace("-", "_") }}
+
+source:
+  url:
+    - {{ cran_mirror }}/src/contrib/enrichR_{{ version }}.tar.gz
+    - {{ cran_mirror }}/src/contrib/Archive/enrichR/enrichR_{{ version }}.tar.gz
+  sha256: b6baf724ca8f6aa50c9ec598164d3368df2ac25c0d138cfedb10fba60bc9cd51
+
+build:
+  merge_build_host: True  # [win]
+  number: 0
+  noarch: generic
+  rpaths:
+    - lib/R/lib/
+    - lib/
+
+requirements:
+  build:
+
+  host:
+    - r-base
+    - r-httr
+    - r-rjson
+  run:
+    - r-base
+    - r-httr
+    - r-rjson
+
+test:
+  commands:
+    - $R -e "library('enrichR')"           # [not win]
+    - "\"%R%\" -e \"library('enrichR')\""  # [win]
+
+about:
+  home: https://CRAN.R-project.org/package=enrichR
+  license: GPL (>= 2)
+  summary: Provides an R interface to all 'Enrichr' databases, a web-based tool for analysing
+    gene sets and returns any enrichment of common annotated biological functions. <http://amp.pharm.mssm.edu/Enrichr/>.
+  license_family: GPL3
+  license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2'
+
+extra:
+  recipe-maintainers:
+    - conda-forge/r
+
+# Package: enrichR
+# Title: Provides an R Interface to 'Enrichr'
+# Version: 1.0
+# Authors@R: person("Wajid", "Jawaid", email = "[email protected]", role = c("aut", "cre"))
+# Description: Provides an R interface to all 'Enrichr' databases, a web-based tool for analysing gene sets and returns any enrichment of common annotated biological functions. <http://amp.pharm.mssm.edu/Enrichr/>.
+# Depends: R (>= 3.0.0)
+# License: GPL (>= 2)
+# Encoding: UTF-8
+# LazyData: true
+# Imports: httr, rjson
+# RoxygenNote: 6.0.1
+# Suggests: knitr, rmarkdown
+# VignetteBuilder: knitr
+# NeedsCompilation: no
+# Packaged: 2017-04-02 15:35:12 UTC; wajid
+# Author: Wajid Jawaid [aut, cre]
+# Maintainer: Wajid Jawaid <[email protected]>
+# Repository: CRAN
+# Date/Publication: 2017-04-02 17:26:32 UTC
diff --git a/recipes/r-imp4p/bld.bat b/recipes/r-imp4p/bld.bat
@@ -0,0 +1,2 @@
+"%R%" CMD INSTALL --build .
+IF %ERRORLEVEL% NEQ 0 exit 1
diff --git a/recipes/r-imp4p/build.sh b/recipes/r-imp4p/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/imp4p
+  mv * $PREFIX/lib/R/library/imp4p
+  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