updates for bulk (#12884)

bioconda · Jan 1, 2019 · 8fc94fe · 8fc94fe
1 parent 00e9976
commit 8fc94fe
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Showing 8 changed files with 221 additions and 11 deletions.
diff --git a/build-fail-blacklist b/build-fail-blacklist
@@ -891,13 +891,16 @@ recipes/bioconductor-rcpi
 recipes/r-dartr
 recipes/bioconductor-dsimer
 recipes/bioconductor-pga
+recipes/bioconductor-linc
+recipes/bioconductor-fourcseq
 
 # r-dagitity missing -> missing of V8 in cf
 recipes/r-pcalg
 recipes/bioconductor-epinem
 
 # R clusterr GCC7 builds missing
 recipes/r-jackstraw
+recipes/bioconductor-biocancer
 
 # r-feature missing/broken
 recipes/bioconductor-flowmerge
@@ -932,9 +935,7 @@ recipes/bioconductor-r3cpet
 recipes/bioconductor-omicspca
 recipes/bioconductor-madseq
 recipes/bioconductor-doqtl
-
-# Waiting on gcc7 builds of deps
-# recipes/bioconductor-biocancer
+recipes/bioconductor-debrowser
 
 # Not enough memory on circleci
 recipes/bioconductor-conumee

diff --git a/recipes/bioconductor-eegc/meta.yaml b/recipes/bioconductor-eegc/meta.yaml
@@ -1,4 +1,4 @@
-{% set version = "1.8.0" %}
+{% set version = "1.8.1" %}
 {% set name = "eegc" %}
 {% set bioc = "3.8" %}
 
@@ -10,7 +10,7 @@ source:
     - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz'
     - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz'
     - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz'
-  md5: 80ae17a861a02b93bac38afb632948b1
+  md5: acac7f97fcfcc9641aab15beda10c60c
 build:
   number: 0
   rpaths:

diff --git a/recipes/bioconductor-mageckflute/meta.yaml b/recipes/bioconductor-mageckflute/meta.yaml
@@ -1,4 +1,4 @@
-{% set version = "1.2.1" %}
+{% set version = "1.2.2" %}
 {% set name = "MAGeCKFlute" %}
 {% set bioc = "3.8" %}
 
@@ -10,7 +10,7 @@ source:
     - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz'
     - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz'
     - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz'
-  md5: 80c61e7aae7789fcd50e2f08b97e1d35
+  md5: 50c6209facdbb9a7b9f33cd7b4b6867c
 build:
   number: 0
   rpaths:

diff --git a/recipes/r-diffcorr/meta.yaml b/recipes/r-diffcorr/meta.yaml
@@ -27,14 +27,14 @@ requirements:
     - r-base
     - r-fdrtool
     - r-igraph
-    - r-multtest
-    - r-pcamethods
+    - bioconductor-multtest
+    - bioconductor-pcamethods
   run:
     - r-base
     - r-fdrtool
     - r-igraph
-    - r-multtest
-    - r-pcamethods
+    - bioconductor-multtest
+    - bioconductor-pcamethods
 
 test:
   commands:

diff --git a/recipes/r-isva/build.sh b/recipes/r-isva/build.sh
@@ -0,0 +1,33 @@
+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/isva
+  mv * $PREFIX/lib/R/library/isva
+  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-isva/meta.yaml b/recipes/r-isva/meta.yaml
@@ -0,0 +1,65 @@
+{% set version = '1.9' %}
+{% set posix = 'm2-' if win else '' %}
+{% set native = 'm2w64-' if win else '' %}
+
+package:
+  name: r-isva
+  version: {{ version|replace("-", "_") }}
+
+source:
+  url:
+    - {{ cran_mirror }}/src/contrib/isva_{{ version }}.tar.gz
+    - {{ cran_mirror }}/src/contrib/Archive/isva/isva_{{ version }}.tar.gz
+  sha256: 9fd016e0b34034d271d45f8a0d0db62780bf0187112e45f610aa9237014e1d17
+
+build:
+  merge_build_host: True  # [win]
+  number: 0
+  skip: true  # [win32]
+  noarch: generic
+  rpaths:
+    - lib/R/lib/
+    - lib/
+
+requirements:
+  build:
+
+  host:
+    - r-base
+    - r-jade
+    - r-fastica
+    - bioconductor-qvalue
+  run:
+    - r-base
+    - r-jade
+    - r-fastica
+    - bioconductor-qvalue
+
+test:
+  commands:
+    - $R -e "library('isva')"           # [not win]
+    - "\"%R%\" -e \"library('isva')\""  # [win]
+
+about:
+  home: https://CRAN.R-project.org/package=isva
+  license: GPL-2
+  summary: 'Independent Surrogate Variable Analysis is an algorithm for feature selection in
+    the presence of potential confounding factors (see Teschendorff AE et al 2011, <doi:
+    10.1093/bioinformatics/btr171>).'
+  license_family: GPL2
+  license_file: '{{ environ["PREFIX"] }}\/lib\/R\/share\/licenses\/GPL-2'  # [unix]
+  license_file: '{{ environ["PREFIX"] }}\R\share\licenses\GPL-2'  # [win]
+  license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2'
+
+extra:
+  recipe-maintainers:
+    - conda-forge/r
+extra:
+  recipe-maintainers:
+    - MathiasHaudgaard
+    - FrodePedersen
+    - ArneKr
+    - johanneskoester
+    - bgruening
+    - daler
+    - jdblischak
diff --git a/recipes/r-smartsva/build.sh b/recipes/r-smartsva/build.sh
@@ -0,0 +1,33 @@
+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/SmartSVA
+  mv * $PREFIX/lib/R/library/SmartSVA
+  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-smartsva/meta.yaml b/recipes/r-smartsva/meta.yaml
@@ -0,0 +1,78 @@
+{% set version = '0.1.3' %}
+{% set posix = 'm2-' if win else '' %}
+{% set native = 'm2w64-' if win else '' %}
+
+package:
+  name: r-smartsva
+  version: {{ version|replace("-", "_") }}
+
+source:
+  url:
+    - {{ cran_mirror }}/src/contrib/SmartSVA_{{ version }}.tar.gz
+    - {{ cran_mirror }}/src/contrib/Archive/SmartSVA/SmartSVA_{{ version }}.tar.gz
+  sha256: d7925743d04bd52dee575a477cc7e8395fedb08f5dbb8427e61e3d6dbfd04881
+
+build:
+  merge_build_host: True  # [win]
+  number: 0
+  skip: true  # [win32]
+  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-rspectra
+    - r-rcpp
+    - r-rcppeigen
+    - r-isva
+    - bioconductor-sva
+  run:
+    - r-base
+    - {{native}}gcc-libs         # [win]
+    - r-rspectra
+    - r-rcpp
+    - r-rcppeigen
+    - r-isva
+    - bioconductor-sva
+
+test:
+  commands:
+    - $R -e "library('SmartSVA')"           # [not win]
+    - "\"%R%\" -e \"library('SmartSVA')\""  # [win]
+
+about:
+  home: https://CRAN.R-project.org/package=SmartSVA
+  license: GPL-3
+  summary: Introduces a fast and efficient Surrogate Variable Analysis algorithm that captures
+    variation of unknown sources (batch effects) for high-dimensional data sets. The
+    algorithm is built on the 'irwsva.build' function of the 'sva' package and proposes
+    a revision on it that achieves an order of magnitude faster running time while trading
+    no accuracy loss in return.
+  license_family: GPL3
+  license_file: '{{ environ["PREFIX"] }}\/lib\/R\/share\/licenses\/GPL-3'  # [unix]
+  license_file: '{{ environ["PREFIX"] }}\R\share\licenses\GPL-3'  # [win]
+  license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3'
+
+extra:
+  recipe-maintainers:
+    - conda-forge/r
+extra:
+  recipe-maintainers:
+    - MathiasHaudgaard
+    - FrodePedersen
+    - ArneKr
+    - johanneskoester
+    - bgruening
+    - daler
+    - jdblischak