From 99b972ab6478d058fd80b5ff198b59249f5f8198 Mon Sep 17 00:00:00 2001 From: Milad Miladi Date: Fri, 10 Aug 2018 12:02:16 +0200 Subject: [PATCH 1/8] nanopolish outof blacklist --- build-fail-blacklist | 2 +- recipes/nanopolish/meta.yaml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/build-fail-blacklist b/build-fail-blacklist index ca85d2c2eb580..b7c888a093477 100644 --- a/build-fail-blacklist +++ b/build-fail-blacklist @@ -2191,6 +2191,6 @@ recipes/abricate/0.7 recipes/abricate # clang -recipes/nanopolish +# recipes/nanopolish ####################### OSX errors above ############### diff --git a/recipes/nanopolish/meta.yaml b/recipes/nanopolish/meta.yaml index 5ed7783d7ccbb..33bf2f09fd2cf 100644 --- a/recipes/nanopolish/meta.yaml +++ b/recipes/nanopolish/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version }} build: - number: 0 + number: 1 source: url: https://github.com/jts/nanopolish/archive/v{{ version }}.tar.gz From 4846f82f92a09fe264d690235c4883192c73a9d7 Mon Sep 17 00:00:00 2001 From: Milad Miladi Date: Fri, 10 Aug 2018 12:43:06 +0200 Subject: [PATCH 2/8] openmp --- recipes/nanopolish/meta.yaml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/recipes/nanopolish/meta.yaml b/recipes/nanopolish/meta.yaml index 33bf2f09fd2cf..80a77802322d4 100644 --- a/recipes/nanopolish/meta.yaml +++ b/recipes/nanopolish/meta.yaml @@ -24,6 +24,7 @@ requirements: - eigen - ncurses - bzip2 + - openmp run: - python @@ -33,6 +34,7 @@ requirements: - eigen - ncurses - libdeflate + - openmp test: commands: From 6ce5b56e736d8007e6088e539da4a2891f5e1e65 Mon Sep 17 00:00:00 2001 From: Milad Miladi Date: Fri, 10 Aug 2018 13:14:30 +0200 Subject: [PATCH 3/8] cxx compiler --- build-fail-blacklist | 1 - recipes/nanopolish/meta.yaml | 2 ++ 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/build-fail-blacklist b/build-fail-blacklist index b7c888a093477..46755de5a50a4 100644 --- a/build-fail-blacklist +++ b/build-fail-blacklist @@ -2191,6 +2191,5 @@ recipes/abricate/0.7 recipes/abricate # clang -# recipes/nanopolish ####################### OSX errors above ############### diff --git a/recipes/nanopolish/meta.yaml b/recipes/nanopolish/meta.yaml index 80a77802322d4..18c1ca7a0e967 100644 --- a/recipes/nanopolish/meta.yaml +++ b/recipes/nanopolish/meta.yaml @@ -16,7 +16,9 @@ source: requirements: build: + - {{ compiler('cxx') }} - {{ compiler('c') }} + host: - fast5 ==0.6.5 - htslib >1.4 From 73b23392eb3f80be76008617bcc23786e0a5f557 Mon Sep 17 00:00:00 2001 From: Milad Miladi Date: Fri, 10 Aug 2018 16:37:39 +0200 Subject: [PATCH 4/8] config for build --- recipes/nanopolish/conda_build_config.yaml | 6 ++++++ 1 file changed, 6 insertions(+) create mode 100644 recipes/nanopolish/conda_build_config.yaml diff --git a/recipes/nanopolish/conda_build_config.yaml b/recipes/nanopolish/conda_build_config.yaml new file mode 100644 index 0000000000000..a864705eed8d4 --- /dev/null +++ b/recipes/nanopolish/conda_build_config.yaml @@ -0,0 +1,6 @@ +c_compiler: + - gcc # [linux] + - clang # [osx] +cxx_compiler: + - gxx # [linux] + - clangxx # [osx] From 4ac5b0b0daf83f6067d611b3cd60e2aa7bd496a9 Mon Sep 17 00:00:00 2001 From: Bjoern Gruening Date: Fri, 10 Aug 2018 19:49:40 +0200 Subject: [PATCH 5/8] compiler mess --- recipes/nanopolish/conda_build_config.yaml | 6 ------ recipes/nanopolish/meta.yaml | 4 +--- 2 files changed, 1 insertion(+), 9 deletions(-) delete mode 100644 recipes/nanopolish/conda_build_config.yaml diff --git a/recipes/nanopolish/conda_build_config.yaml b/recipes/nanopolish/conda_build_config.yaml deleted file mode 100644 index a864705eed8d4..0000000000000 --- a/recipes/nanopolish/conda_build_config.yaml +++ /dev/null @@ -1,6 +0,0 @@ -c_compiler: - - gcc # [linux] - - clang # [osx] -cxx_compiler: - - gxx # [linux] - - clangxx # [osx] diff --git a/recipes/nanopolish/meta.yaml b/recipes/nanopolish/meta.yaml index 18c1ca7a0e967..dadc8824adcaa 100644 --- a/recipes/nanopolish/meta.yaml +++ b/recipes/nanopolish/meta.yaml @@ -16,9 +16,7 @@ source: requirements: build: - - {{ compiler('cxx') }} - - {{ compiler('c') }} - + - gcc host: - fast5 ==0.6.5 - htslib >1.4 From 12eb50b12dee3cbbcc9ac63262405c82f21c048d Mon Sep 17 00:00:00 2001 From: Bjoern Gruening Date: Fri, 10 Aug 2018 19:55:12 +0200 Subject: [PATCH 6/8] skip linting for compilers to accept the hack --- recipes/nanopolish/meta.yaml | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/recipes/nanopolish/meta.yaml b/recipes/nanopolish/meta.yaml index dadc8824adcaa..206135a9f0f33 100644 --- a/recipes/nanopolish/meta.yaml +++ b/recipes/nanopolish/meta.yaml @@ -46,3 +46,7 @@ about: license: MIT license_file: LICENSE summary: 'Signal-level algorithms for MinION data.' + +extra: + skip-lints: + - should_use_compilers From e0526946d4ac6b2ebd4b6f1c6d0b9420948e4030 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= Date: Fri, 10 Aug 2018 20:08:16 +0200 Subject: [PATCH 7/8] Update meta.yaml --- recipes/nanopolish/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/nanopolish/meta.yaml b/recipes/nanopolish/meta.yaml index 206135a9f0f33..7d5805f261959 100644 --- a/recipes/nanopolish/meta.yaml +++ b/recipes/nanopolish/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version }} build: - number: 1 + number: 0 source: url: https://github.com/jts/nanopolish/archive/v{{ version }}.tar.gz From 8ef996dce5ecc8735333d1cc9a8512e31abce1cf Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= Date: Fri, 10 Aug 2018 21:05:53 +0200 Subject: [PATCH 8/8] of course old style needs libgcc --- recipes/nanopolish/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/nanopolish/meta.yaml b/recipes/nanopolish/meta.yaml index 7d5805f261959..3b86746df020d 100644 --- a/recipes/nanopolish/meta.yaml +++ b/recipes/nanopolish/meta.yaml @@ -25,7 +25,6 @@ requirements: - ncurses - bzip2 - openmp - run: - python - hdf5 @@ -35,6 +34,7 @@ requirements: - ncurses - libdeflate - openmp + - libgcc test: commands: