From 8fb1ca2bbba75dd33dd23b5d65c005fcb2b802e2 Mon Sep 17 00:00:00 2001
From: Devon Ryan <dpryan79@gmail.com>
Date: Mon, 6 Aug 2018 01:14:48 +0200
Subject: [PATCH 1/2] Remove various packages from the blacklist

---
 build-fail-blacklist          | 9 ---------
 recipes/graphmap/build.sh     | 7 ++++---
 recipes/graphmap/meta.yaml    | 4 ++--
 recipes/hera/build.sh         | 1 +
 recipes/htseq/0.6.1/meta.yaml | 1 +
 5 files changed, 8 insertions(+), 14 deletions(-)

diff --git a/build-fail-blacklist b/build-fail-blacklist
index a530855dd664c..9f7e38d72524f 100644
--- a/build-fail-blacklist
+++ b/build-fail-blacklist
@@ -1586,18 +1586,9 @@ recipes/ms
 # GL missing, needs the extended base image
 recipes/emperor
 
-recipes/graphmap
-# /opt/rh/devtoolset-2/root/usr/libexec/gcc/x86_64-redhat-linux/4.8.2/ld: cannot find -lz
-recipes/hera
-
-
 # RuntimeError: Setuptools downloading is disabled in conda build. Be sure to add all dependencies in the meta.yaml  url=https://pypi.org/simple/HyPhy/
 recipes/hivtrace
 
-
-# [Jun 26 23:28:29] SERR ImportError: libstdc++.so.6: cannot open shared object file: No such file or directory
-recipes/htseq/0.6.1
-
 # sed: can't read /opt/conda/conda-bld/idba_1530055808563/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/bin/aclocal: No such file or directory
 recipes/idba
 # socket.timeout: timed out
diff --git a/recipes/graphmap/build.sh b/recipes/graphmap/build.sh
index f8299953f8ad2..76d0c033cdec1 100644
--- a/recipes/graphmap/build.sh
+++ b/recipes/graphmap/build.sh
@@ -1,8 +1,9 @@
 #!/bin/bash
 
-export CFLAGS="-I$PREFIX/include"
-export LDFLAGS="-L$PREFIX/lib"
-export CPATH=${PREFIX}/include
+export CPP_INCLUDE_PATH=${PREFIX}/include
+export CPLUS_INCLUDE_PATH=${PREFIX}/include
+export CXX_INCLUDE_PATH=${PREFIX}/include
+export LIBRARY_PATH=${PREFIX}/lib
 
 mkdir -p $PREFIX/bin
 
diff --git a/recipes/graphmap/meta.yaml b/recipes/graphmap/meta.yaml
index b431ced175890..6703fd981a9f4 100644
--- a/recipes/graphmap/meta.yaml
+++ b/recipes/graphmap/meta.yaml
@@ -18,12 +18,12 @@ source:
 
 requirements:
   build:
-    - {{ compiler('c') }}
+    - {{ compiler('cxx') }}
   host:
     - wget
     - zlib
   run:
-  - zlib
+    - zlib
 
 test:
   commands:
diff --git a/recipes/hera/build.sh b/recipes/hera/build.sh
index 1dda83016fc47..38a355459ef73 100644
--- a/recipes/hera/build.sh
+++ b/recipes/hera/build.sh
@@ -2,6 +2,7 @@
 
 mkdir -p $PREFIX/bin
 
+export LIBRARY_PATH=${PREFIX}/lib
 if [ `uname` == Darwin ]; then
   export CFLAGS="-I$PREFIX/include -fgnu89-inline -O2 -D USE_JEMALLOC  -w -lz -Wl,-rpath,${PREFIX}/lib"
 else
diff --git a/recipes/htseq/0.6.1/meta.yaml b/recipes/htseq/0.6.1/meta.yaml
index 0b591e6ea82fc..92214d99ba9af 100644
--- a/recipes/htseq/0.6.1/meta.yaml
+++ b/recipes/htseq/0.6.1/meta.yaml
@@ -14,6 +14,7 @@ package:
 requirements:
   host:
   - python
+  - cython
   - numpy ==1.7.1
   - matplotlib ==1.2.1
   run:

From 427631ef17445f7cbd942bda8d942852aee72163 Mon Sep 17 00:00:00 2001
From: Devon Ryan <dpryan79@gmail.com>
Date: Mon, 6 Aug 2018 01:33:59 +0200
Subject: [PATCH 2/2] graphmap uses openmp, which is problematic with clang

---
 recipes/graphmap/meta.yaml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/recipes/graphmap/meta.yaml b/recipes/graphmap/meta.yaml
index 6703fd981a9f4..4e67de98d501b 100644
--- a/recipes/graphmap/meta.yaml
+++ b/recipes/graphmap/meta.yaml
@@ -8,6 +8,7 @@ package:
 
 build:
   number: 2
+  skip: True  # [osx]
 
 source:
   url: https://github.com/isovic/{{ name|lower }}/archive/eb8c75d68b03be95464318afa69b645a59f8f6b7.tar.gz