From 0b73fdfdb7a1c13799ae1950ebc7b6cab5b6b3fb Mon Sep 17 00:00:00 2001 From: dpryan79 Date: Fri, 10 Aug 2018 14:35:53 +0200 Subject: [PATCH 1/3] Remove various recipes from the black list --- build-fail-blacklist | 12 ++---------- recipes/abyss/1.5.2/meta.yaml | 2 +- recipes/abyss/1.9.0/meta.yaml | 2 +- recipes/agg/build.sh | 5 +++++ recipes/agg/meta.yaml | 7 ++++--- recipes/allegro/build.sh | 5 +++++ recipes/allegro/meta.yaml | 4 ++-- recipes/amos/build.sh | 3 +-- recipes/amos/meta.yaml | 6 ++++-- recipes/amos/patch | 10 ++++++++++ recipes/antarna/build.sh | 3 +++ recipes/antarna/meta.yaml | 3 ++- 12 files changed, 40 insertions(+), 22 deletions(-) create mode 100644 recipes/amos/patch create mode 100644 recipes/antarna/build.sh diff --git a/build-fail-blacklist b/build-fail-blacklist index ca85d2c2eb580..e1cfa2a566eb9 100644 --- a/build-fail-blacklist +++ b/build-fail-blacklist @@ -1474,13 +1474,14 @@ recipes/remurna # Can't locate Text/Soundex.pm in @INC recipes/repeatmasker -# ./Histogram.h:315:14: error: 'swap' is missing exception specification 'noexcept(is_nothrow_move_constructible::value && is_nothrow_move_assignable::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 # missing URL recipes/augustus +# 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? @@ -1605,8 +1606,6 @@ 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 @@ -1728,9 +1727,6 @@ recipes/trimmomatic/0.35 recipes/rdkit/2015.09.2 recipes/rdkit/2016.03.3 -# patching fails -recipes/allegro - # broken pipe recipes/antarna @@ -1766,10 +1762,6 @@ 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 index 167debb8b5815..6afde6f0e7c98 100644 --- 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 index 5357eba2e36cb..44e351a3085ac 100644 --- 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 index 014012818c2a8..f6ef6c8977361 100644 --- 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 $PREFIX/bin diff --git a/recipes/agg/meta.yaml b/recipes/agg/meta.yaml index af87d7c99f667..6b3fa999f3bd0 100644 --- a/recipes/agg/meta.yaml +++ b/recipes/agg/meta.yaml @@ -1,12 +1,12 @@ -{% set version = "0.3.5" %} -{% set sha256 = "4736abd5af428e2ea07895f2d441a921a47f919fbf5fd4f84c77f5d8357375aa" %} +{% set version = "0.3.6" %} +{% set sha256 = "921054d8f7a249df303d14438879b181b35ed682eb4754ab88667c4c44eed29b" %} package: name: agg version: {{ version }} build: - number: 2 + number: 0 source: url: https://github.com/Illumina/agg/archive/v{{ version }}.tar.gz @@ -14,6 +14,7 @@ source: requirements: build: + - {{ compiler('cxx') }} - {{ compiler('c') }} host: - zlib diff --git a/recipes/allegro/build.sh b/recipes/allegro/build.sh index 6889e8fc1a07d..5b425a05d3a3b 100644 --- a/recipes/allegro/build.sh +++ b/recipes/allegro/build.sh @@ -1,3 +1,8 @@ +#!/bin/bash +export CPP_INCLUDE_PATH=${PREFIX}/include +export CXX_INCLUDE_PATH=${PREFIX}/include +export CPLUS_INCLUDE_PATH=${PREFIX}/include +export LIBRARY_PATH=${PREFIX}/lib ./configure make diff --git a/recipes/allegro/meta.yaml b/recipes/allegro/meta.yaml index 558baa3dd317e..075ff4612d3ed 100644 --- a/recipes/allegro/meta.yaml +++ b/recipes/allegro/meta.yaml @@ -5,7 +5,7 @@ package: version: 3 source: - url: https://github.com/BioTools-Tek/packages/blob/d16884a20a64e74df9021d8af9b9ed5c312ba306/allegro2/allegro2-2017-10-11.tar.gz?raw=true + url: https://github.com/BioTools-Tek/packages/raw/master/allegro2/allegro2-2017-10-11.tar.gz sha256: {{ sha256 }} patches: - patches/calcassoc.patch @@ -21,7 +21,7 @@ build: requirements: build: - - {{ compiler('c') }} + - {{ compiler('cxx') }} host: - zlib - patch diff --git a/recipes/amos/build.sh b/recipes/amos/build.sh index 1fc55277b13f9..ded3ac091684b 100644 --- a/recipes/amos/build.sh +++ b/recipes/amos/build.sh @@ -1,7 +1,6 @@ #!/bin/bash -rm -r test tutorial -./bootstrap +rm -rf test tutorial ./configure \ --prefix=$PREFIX make diff --git a/recipes/amos/meta.yaml b/recipes/amos/meta.yaml index a0178bc6f17f2..d0ef0b14219c1 100644 --- 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 new file mode 100644 index 0000000000000..16e7cd13f9f10 --- /dev/null +++ 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 + #include + #include ++#include + #include + using namespace std; + diff --git a/recipes/antarna/build.sh b/recipes/antarna/build.sh new file mode 100644 index 0000000000000..3786386a73c83 --- /dev/null +++ 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 index 76d7569408b90..7bf97e1705546 100644 --- 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 From ddcc1d8e83bb5972ed2d66642033a388191117dc Mon Sep 17 00:00:00 2001 From: dpryan79 Date: Fri, 10 Aug 2018 16:54:08 +0200 Subject: [PATCH 2/3] apoc needs fortran --- recipes/apoc/meta.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/recipes/apoc/meta.yaml b/recipes/apoc/meta.yaml index 63cc54e7b60bf..d3cce0fc4a44b 100644 --- a/recipes/apoc/meta.yaml +++ b/recipes/apoc/meta.yaml @@ -14,6 +14,7 @@ build: requirements: build: - {{ compiler('c') }} + - {{ compiler('fortran') }} run: test: From 48abeae3307c4e80c8be0435563a784d99dbef31 Mon Sep 17 00:00:00 2001 From: dpryan79 Date: Fri, 10 Aug 2018 20:27:48 +0200 Subject: [PATCH 3/3] skip OSX with agg --- recipes/agg/meta.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/recipes/agg/meta.yaml b/recipes/agg/meta.yaml index 6b3fa999f3bd0..c8e0547c0f740 100644 --- a/recipes/agg/meta.yaml +++ b/recipes/agg/meta.yaml @@ -7,6 +7,7 @@ package: build: number: 0 + skip: True # [osx] source: url: https://github.com/Illumina/agg/archive/v{{ version }}.tar.gz