bioconda · dpryan79 · Aug 10, 2018 · Aug 10, 2018 · Aug 10, 2018 · Aug 10, 2018
diff --git a/build-fail-blacklist b/build-fail-blacklist
@@ -1470,10 +1470,11 @@ recipes/searchgui/3.2.20
 # something wrong with the test
 recipes/remurna
 
-# ./Histogram.h:315:14: error: 'swap<Histogram>' is missing exception specification 'noexcept(is_nothrow_move_constructible<Histogram>::value && is_nothrow_move_assignable<Histogram>::value)'
+# https://github.com/bcgsc/abyss/issues/130 and https://github.com/bioconda/bioconda-recipes/pull/6131
 recipes/abyss/1.9.0
 recipes/abyss/1.5.2
 
+# Test uses a program that makes incorrect assumptions about shebangs (you can't reliably use "#!/usr/bin/env program --arguments")
 recipes/amos
 
 # aclocal error, but also downloads mauve tarballs, but there is now a mauve pkgs, is it still needed?
@@ -1598,8 +1599,6 @@ recipes/openbabel/2.3.2
 
 recipes/parafly
 
-recipes/agg
-
 # RuntimeError: Setuptools downloading is disabled in conda build. Be sure to add all dependencies in the meta.yaml  url=https://files.pythonhosted.org/packages/source/c/certifi/certifi-2016.9.26.tar.gz#md5=baa81e951a29958563689d868ef1064d
 recipes/imfusion/0.3.0
 recipes/imfusion/0.3.2
@@ -1721,9 +1720,6 @@ recipes/trimmomatic/0.35
 recipes/rdkit/2015.09.2
 recipes/rdkit/2016.03.3
 
-# patching fails
-recipes/allegro
-
 # broken pipe
 recipes/antarna
 
@@ -1759,10 +1755,6 @@ recipes/frogs
 # post-link error
 recipes/antismash
 
-# libgfortran
-recipes/apoc
-recipes/maaslin
-
 # zlib
 recipes/megahit
 

diff --git a/recipes/abyss/1.5.2/meta.yaml b/recipes/abyss/1.5.2/meta.yaml
@@ -15,7 +15,7 @@ source:
 
 requirements:
   build:
-    - {{ compiler('c') }}
+    - {{ compiler('cxx') }}
   host:
     - boost
     - sparsehash

diff --git a/recipes/abyss/1.9.0/meta.yaml b/recipes/abyss/1.9.0/meta.yaml
@@ -16,7 +16,7 @@ source:
 
 requirements:
   build:
-    - {{ compiler('c') }}
+    - {{ compiler('cxx') }}
   host:
     - boost
     - sparsehash

diff --git a/recipes/agg/build.sh b/recipes/agg/build.sh
@@ -1,5 +1,10 @@
 #!/bin/bash
 
 mkdir -p $PREFIX/bin
+export C_INCLUDE_PATH=${PREFIX}/include
+export CPP_INCLUDE_PATH=${PREFIX}/include
+export CXX_INCLUDE_PATH=${PREFIX}/include
+export CPLUS_INCLUDE_PATH=${PREFIX}/include
+export LIBRARY_PATH=${PREFIX}/lib
 make
 mv agg $PREFIX/bin
diff --git a/recipes/agg/meta.yaml b/recipes/agg/meta.yaml
@@ -1,19 +1,21 @@
-{% set version = "0.3.5" %}
-{% set sha256 = "4736abd5af428e2ea07895f2d441a921a47f919fbf5fd4f84c77f5d8357375aa" %}
+{% set version = "0.3.6" %}
+{% set sha256 = "921054d8f7a249df303d14438879b181b35ed682eb4754ab88667c4c44eed29b" %}
 
 package:
   name: agg
   version: {{ version }}
 
 build:
-  number: 2
+  number: 0
+  skip: True  # [osx]
 
 source:
   url: https://github.com/Illumina/agg/archive/v{{ version }}.tar.gz
   sha256: {{ sha256 }}
 
 requirements:
   build:
+    - {{ compiler('cxx') }}
     - {{ compiler('c') }}
   host:
     - zlib

diff --git a/recipes/allegro/build.sh b/recipes/allegro/build.sh
@@ -1,3 +1,8 @@
+#!/bin/bash
+export CPP_INCLUDE_PATH=${PREFIX}/include
+export CXX_INCLUDE_PATH=${PREFIX}/include
+export CPLUS_INCLUDE_PATH=${PREFIX}/include
+export LIBRARY_PATH=${PREFIX}/lib
 
 ./configure
 make

diff --git a/recipes/allegro/meta.yaml b/recipes/allegro/meta.yaml
@@ -5,7 +5,7 @@ package:
   version: 3
 
 source:
-  url: https://github.com/BioTools-Tek/packages/blob/d16884a20a64e74df9021d8af9b9ed5c312ba306/allegro2/allegro2-2017-10-11.tar.gz?raw=true
+  url: https://github.com/BioTools-Tek/packages/raw/master/allegro2/allegro2-2017-10-11.tar.gz
   sha256: {{ sha256 }}
   patches:
     - patches/calcassoc.patch
@@ -21,7 +21,7 @@ build:
 
 requirements:
   build:
-    - {{ compiler('c') }}
+    - {{ compiler('cxx') }}
   host:
     - zlib
     - patch

diff --git a/recipes/amos/build.sh b/recipes/amos/build.sh
@@ -1,7 +1,6 @@
 #!/bin/bash
 
-rm -r test tutorial
-./bootstrap
+rm -rf test tutorial
 ./configure \
     --prefix=$PREFIX
 make

diff --git a/recipes/amos/meta.yaml b/recipes/amos/meta.yaml
@@ -3,8 +3,10 @@ package:
   version: "3.1.0"
 
 source:
-  git_url: http://git.code.sf.net/p/amos/code
-  git_rev: 9bd658
+  url: https://sourceforge.net/projects/amos/files/amos/3.1.0/amos-3.1.0.tar.gz
+  sha256: 2d9f50e39186ad3dde3d3b28cc265e8d632430657f40fc3978ce34ab1b3db43b
+  patches:
+    - patch
 
 build:
   number: 4

diff --git a/recipes/amos/patch b/recipes/amos/patch
@@ -0,0 +1,10 @@
+--- src/Align/find-tandem.cc	2011-07-25 01:27:26.000000000 +0200
++++ src/Align/find-tandem.cc	2011-07-25 01:27:26.000000000 +0200
+@@ -6,6 +6,7 @@
+ #include <string>
+ #include <vector>
+ #include <ctime>
++#include <unistd.h>
+ #include <sys/time.h>
+ using namespace std;
+
diff --git a/recipes/antarna/build.sh b/recipes/antarna/build.sh
@@ -0,0 +1,3 @@
+#!/bin/bash
+
+$PYTHON setup.py install --single-version-externally-managed --record=record.txt
diff --git a/recipes/antarna/meta.yaml b/recipes/antarna/meta.yaml
@@ -12,7 +12,6 @@ source:
 build:
   number: 1
   skip: True  # [osx or py3k]
-  script: python -m pip install --no-deps --ignore-installed .
 
 requirements:
   host:
@@ -39,5 +38,7 @@ about:
   summary: antaRNA is a python based implementation of ant-colony optimization of the RNA inverse folding problem.
 
 extra:
+  container:
+    extended-base: True
   identifiers:
     - biotools:antarna
diff --git a/recipes/apoc/meta.yaml b/recipes/apoc/meta.yaml
@@ -14,6 +14,7 @@ build:
 requirements:
   build:
     - {{ compiler('c') }}
+    - {{ compiler('fortran') }}
   run:
 
 test: