[BULK] A few fixes

build-fail-blacklist

@@ -810,6 +810,7 @@ recipes/bioconductor-meshsim
 recipes/bioconductor-mmdiff
 recipes/bioconductor-mmnet
 recipes/bioconductor-rcytoscape
+recipes/bioconductor-browservizdemo
 
 # Old bioconductor version that's no longer available
 recipes/bioconductor-edger/3.12.1
@@ -873,22 +874,33 @@ recipes/bioconductor-ncigraph
 recipes/bioconductor-lymphoseq
 recipes/bioconductor-universalmotif
 recipes/bioconductor-phantasus
+recipes/bioconductor-degraph
+recipes/bioconductor-biggr
 
 # r-feature missing/broken
 recipes/bioconductor-flowmerge
 recipes/bioconductor-flowmeans
+recipes/bioconductor-confess
+recipes/bioconductor-flowtype
 
-# some wired test error with the Docker tests
+# some weird test error in Docker (and downstream dependent packages)
+recipes/bioconductor-rqt
+recipes/bioconductor-fccac
+recipes/bioconductor-funchip
 recipes/bioconductor-flowstats
 recipes/bioconductor-nethet
 recipes/bioconductor-iterativebma
 recipes/bioconductor-narrowpeaks
 recipes/bioconductor-iwtomics
+recipes/bioconductor-flowvs
+recipes/bioconductor-opencyto
+recipes/bioconductor-cytoml
+recipes/bioconductor-platecore
 
 # missing r-* deps
 recipes/bioconductor-mcagui
 recipes/bioconductor-rexposome
 
-
 # JVM errors
 recipes/bioconductor-rgmql
+recipes/bioconductor-camthc

recipes/r-gap/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/gap
+  mv * $PREFIX/lib/R/library/gap
+  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

recipes/r-gap/meta.yaml

@@ -0,0 +1,46 @@
+{% set version = '1.1-22' %}
+{% set posix = 'm2-' if win else '' %}
+{% set native = 'm2w64-' if win else '' %}
+
+package:
+  name: r-gap
+  version: {{ version|replace("-", "_") }}
+
+source:
+  url:
+    - {{ cran_mirror }}/src/contrib/gap_{{ version }}.tar.gz
+    - {{ cran_mirror }}/src/contrib/Archive/gap/gap_{{ version }}.tar.gz
+  sha256: 71a691aac9ce29bfcf1159eacba1866c8571b781f68fb32a3e52fb8584f03ef7
+
+build:
+  number: 0
+  rpaths:
+    - lib/R/lib/
+    - lib/
+
+requirements:
+  build:
+    - {{ compiler('c') }}
+    - {{ compiler('fortran') }}
+    - {{posix}}make
+  host:
+    - r-base
+  run:
+    - r-base
+
+test:
+  commands:
+    - $R -e "library('gap')"           # [not win]
+    - "\"%R%\" -e \"library('gap')\""  # [win]
+
+about:
+  home: https://jinghuazhao.github.io
+  license: GPL (>= 2)
+  summary: It is designed as an integrated package for genetic data analysis of both population
+    and family data. Currently, it contains functions for sample size calculations of
+    both population-based and family-based designs, probability of familial disease
+    aggregation, kinship calculation, statistics in linkage analysis, and association
+    analysis involving genetic markers including haplotype analysis with or without
+    environmental covariates.
+  license_family: GPL3
+  license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2'

recipes/r-rapidr/meta.yaml

@@ -25,24 +25,23 @@ requirements:
     - {{posix}}zip               # [win]
   host:
     - r-base
-    - 'bioconductor-biostrings >=2.48.0,<2.50.0'
-    - 'bioconductor-genomicalignments >=1.16.0,<1.18.0'
-    - 'bioconductor-genomicranges >=1.32.7,<1.34.0'
+    - bioconductor-biostrings
+    - bioconductor-genomicalignments
+    - bioconductor-genomicranges
     - r-propcis
-    - 'bioconductor-rsamtools >=1.32.0,<1.34.0'
+    - bioconductor-rsamtools
     - r-data.table
   run:
     - r-base
-    - 'bioconductor-biostrings >=2.48.0,<2.50.0'
-    - 'bioconductor-genomicalignments >=1.16.0,<1.18.0'
-    - 'bioconductor-genomicranges >=1.32.7,<1.34.0'
+    - bioconductor-biostrings
+    - bioconductor-genomicalignments
+    - bioconductor-genomicranges
     - r-propcis
-    - 'bioconductor-rsamtools >=1.32.0,<1.34.0'
+    - bioconductor-rsamtools
     - r-data.table
 
 test:
   commands:
-
     - $R -e "library('RAPIDR')"           # [not win]
     - "\"%R%\" -e \"library('RAPIDR')\""  # [win]