work on some bioconductor packages (bioconda#15400)

* trial building some packages * bioc-cancer should be blacklisted still, update rbowtie2 * skip lpsymphony on OSX
kpalin · Aug 7, 2019 · 6d7d333 · 6d7d333
1 parent 0e07104
commit 6d7d333
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Showing 3 changed files with 3 additions and 10 deletions.
diff --git a/build-fail-blacklist b/build-fail-blacklist
@@ -720,9 +720,6 @@ recipes/bioconductor-s4vectors/0.8.11
 # r-bibitr missing -> missing V8 in conda-forge
 recipes/bioconductor-mirsm
 
-# Build never completes
-recipes/bioconductor-cancer
-
 # Marked as build fails in bioconductor release 3.9
 recipes/bioconductor-birte
 recipes/bioconductor-dsimer
@@ -763,15 +760,9 @@ recipes/bioconductor-biocgenerics
 # Source seems to have moved
 recipes/discovar
 
-# ld: unknown option: -T
-recipes/bioconductor-lpsymphony
-
 # Requires GTK+
 recipes/bioconductor-hilbertvisgui
 
-# fatal error: zlib.h: No such file or directory
-recipes/bioconductor-rbowtie2
-
 # cannot find -llapack
 recipes/bioconductor-tofsims
 
@@ -1120,6 +1111,7 @@ recipes/bioconductor-cagefightr
 recipes/bioconductor-cager
 recipes/bioconductor-camera
 recipes/bioconductor-camthc
+recipes/bioconductor-cancer
 recipes/bioconductor-cancerclass
 recipes/bioconductor-cancerdata
 recipes/bioconductor-cancermutationanalysis

diff --git a/recipes/bioconductor-lpsymphony/meta.yaml b/recipes/bioconductor-lpsymphony/meta.yaml
@@ -13,6 +13,7 @@ source:
   md5: acce764137f7f9a82443decd693b5efb
 build:
   number: 0
+  skip: True  # [osx]
   rpaths:
     - lib/R/lib/
     - lib/

diff --git a/recipes/bioconductor-rbowtie2/build.sh b/recipes/bioconductor-rbowtie2/build.sh
@@ -6,7 +6,7 @@ echo -e "CC=$CC
 FC=$FC
 CFLAGS=$CFLAGS
 CXXFLAGS=$CXXFLAGS
-CXX=$CXX
+CXX=$CXX -I${PREFIX}/include -L${PREFIX}/lib
 CXX98=$CXX
 CXX11=$CXX
 CXX14=$CXX" > ~/.R/Makevars