From a0c8abd60151d608e5326b9ed2f783889d657fed Mon Sep 17 00:00:00 2001 From: David Laehnemann Date: Thu, 26 Oct 2023 13:55:18 +0200 Subject: [PATCH 1/9] fix: [bioconductor-rhdf5] explicitly include libcurl dependency I think that this will fix an issue with `libcrypto.so` not being found that I reported over at `rhdf5`: https://github.com/grimbough/rhdf5/issues/131 --- recipes/bioconductor-rhdf5/meta.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/recipes/bioconductor-rhdf5/meta.yaml b/recipes/bioconductor-rhdf5/meta.yaml index 77ff1c59b2fd9..c1d88b01228de 100644 --- a/recipes/bioconductor-rhdf5/meta.yaml +++ b/recipes/bioconductor-rhdf5/meta.yaml @@ -26,6 +26,7 @@ requirements: - r-base - libblas - liblapack + - libcurl run: - 'bioconductor-rhdf5filters >=1.12.0,<1.13.0' - 'bioconductor-rhdf5lib >=1.22.0,<1.23.0' From 37bf42e474db8a8ce44a6ffb6083b7fb19bcf16d Mon Sep 17 00:00:00 2001 From: David Laehnemann Date: Thu, 26 Oct 2023 15:31:48 +0200 Subject: [PATCH 2/9] bump version number --- recipes/bioconductor-rhdf5/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/bioconductor-rhdf5/meta.yaml b/recipes/bioconductor-rhdf5/meta.yaml index c1d88b01228de..2a8707e5c5761 100644 --- a/recipes/bioconductor-rhdf5/meta.yaml +++ b/recipes/bioconductor-rhdf5/meta.yaml @@ -13,7 +13,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 19c8340a70f1ce28043ba56bb9da1238 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ From 381f64b7df080c6ebd3cc745c81e70a0d7348951 Mon Sep 17 00:00:00 2001 From: David Laehnemann Date: Thu, 26 Oct 2023 17:40:32 +0200 Subject: [PATCH 3/9] Update bioconductor-rhdf5: include `run_exports` with `pin_subpackage` --- recipes/bioconductor-rhdf5/meta.yaml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/recipes/bioconductor-rhdf5/meta.yaml b/recipes/bioconductor-rhdf5/meta.yaml index 2a8707e5c5761..de345d6e572e9 100644 --- a/recipes/bioconductor-rhdf5/meta.yaml +++ b/recipes/bioconductor-rhdf5/meta.yaml @@ -17,6 +17,8 @@ build: rpaths: - lib/R/lib/ - lib/ + run_exports: + - {{ pin_subpackage(name, max_pin="x.x") }} # Suggests: bit64, BiocStyle, knitr, rmarkdown, testthat, bench, dplyr, ggplot2, mockery, BiocParallel # SystemRequirements: GNU make requirements: From bc26c458fdca78cd90eb12b9dcc4b46cdb9066d1 Mon Sep 17 00:00:00 2001 From: David Laehnemann Date: Thu, 26 Oct 2023 22:15:19 +0200 Subject: [PATCH 4/9] introduce full_name variable to include `bioconductor-` prefix --- recipes/bioconductor-rhdf5/meta.yaml | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/recipes/bioconductor-rhdf5/meta.yaml b/recipes/bioconductor-rhdf5/meta.yaml index de345d6e572e9..8437eaf55f365 100644 --- a/recipes/bioconductor-rhdf5/meta.yaml +++ b/recipes/bioconductor-rhdf5/meta.yaml @@ -1,16 +1,17 @@ {% set version = "2.44.0" %} {% set name = "rhdf5" %} +{% set full_name = "bioconductor-" ~ name %} {% set bioc = "3.17" %} package: - name: 'bioconductor-{{ name|lower }}' + name: '{{ full_name|lower }}' version: '{{ version }}' source: url: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + - 'https://depot.galaxyproject.org/software/{{ full_name }}/{{ full_name }}_{{ version }}_src_all.tar.gz' md5: 19c8340a70f1ce28043ba56bb9da1238 build: number: 1 @@ -18,7 +19,7 @@ build: - lib/R/lib/ - lib/ run_exports: - - {{ pin_subpackage(name, max_pin="x.x") }} + - {{ pin_subpackage(full_name, max_pin="x.x") }} # Suggests: bit64, BiocStyle, knitr, rmarkdown, testthat, bench, dplyr, ggplot2, mockery, BiocParallel # SystemRequirements: GNU make requirements: @@ -50,7 +51,7 @@ extra: identifiers: - biotools:rhdf5 parent_recipe: - name: bioconductor-rhdf5 + name: '{{ full_name|lower }}' path: recipes/bioconductor-rhdf5 version: 2.24.0 From 837378fd79dc5111e723ab1beb19d1e6aed1c030 Mon Sep 17 00:00:00 2001 From: David Laehnemann Date: Fri, 27 Oct 2023 13:40:35 +0200 Subject: [PATCH 5/9] remove libcurl again, as this is handled downstream in bioconductor-rhd5flib This is the PR that handles this: https://github.com/bioconda/bioconda-recipes/pull/43930 And here's the discussion that pinpoints where the libcurl dependency belongs: https://github.com/grimbough/rhdf5/issues/131#issuecomment-1782502851 --- recipes/bioconductor-rhdf5/meta.yaml | 1 - 1 file changed, 1 deletion(-) diff --git a/recipes/bioconductor-rhdf5/meta.yaml b/recipes/bioconductor-rhdf5/meta.yaml index 8437eaf55f365..c8c355cf98299 100644 --- a/recipes/bioconductor-rhdf5/meta.yaml +++ b/recipes/bioconductor-rhdf5/meta.yaml @@ -29,7 +29,6 @@ requirements: - r-base - libblas - liblapack - - libcurl run: - 'bioconductor-rhdf5filters >=1.12.0,<1.13.0' - 'bioconductor-rhdf5lib >=1.22.0,<1.23.0' From cba49013d5ccd378f0576dfbe81ad9a3b9d4c0af Mon Sep 17 00:00:00 2001 From: David Laehnemann Date: Fri, 27 Oct 2023 13:43:33 +0200 Subject: [PATCH 6/9] clean up full_name usage --- recipes/bioconductor-rhdf5/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/bioconductor-rhdf5/meta.yaml b/recipes/bioconductor-rhdf5/meta.yaml index c8c355cf98299..ec3fbde4200d2 100644 --- a/recipes/bioconductor-rhdf5/meta.yaml +++ b/recipes/bioconductor-rhdf5/meta.yaml @@ -1,10 +1,10 @@ {% set version = "2.44.0" %} {% set name = "rhdf5" %} -{% set full_name = "bioconductor-" ~ name %} +{% set full_name = "bioconductor-" ~ name|lower %} {% set bioc = "3.17" %} package: - name: '{{ full_name|lower }}' + name: '{{ full_name }}' version: '{{ version }}' source: url: @@ -50,7 +50,7 @@ extra: identifiers: - biotools:rhdf5 parent_recipe: - name: '{{ full_name|lower }}' - path: recipes/bioconductor-rhdf5 + name: '{{ full_name }}' + path: `recipes/{{ full_name }}' version: 2.24.0 From d8bf84766a93ad6e9df4624ead48f3f356d87773 Mon Sep 17 00:00:00 2001 From: David Laehnemann Date: Fri, 27 Oct 2023 13:44:39 +0200 Subject: [PATCH 7/9] include comment about pinning not necessarily being decided, yet --- recipes/bioconductor-rhdf5/meta.yaml | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/recipes/bioconductor-rhdf5/meta.yaml b/recipes/bioconductor-rhdf5/meta.yaml index ec3fbde4200d2..69799ac5992d3 100644 --- a/recipes/bioconductor-rhdf5/meta.yaml +++ b/recipes/bioconductor-rhdf5/meta.yaml @@ -19,6 +19,12 @@ build: - lib/R/lib/ - lib/ run_exports: + # This pinning is preliminary. It should be changed if either: + # * a general policy for pinning bioconductor packages is decided and differs: + # https://github.com/bioconda/bioconda-recipes/issues/43905 + # * the author of this package assures us that he adheres to semantic + # versioning, in which case we can unpin the minor version, see: + # https://github.com/grimbough/rhdf5/issues/131#issuecomment-1782567153 - {{ pin_subpackage(full_name, max_pin="x.x") }} # Suggests: bit64, BiocStyle, knitr, rmarkdown, testthat, bench, dplyr, ggplot2, mockery, BiocParallel # SystemRequirements: GNU make From a70733e9997fb14341c8b5aec5ad5b434bc96d46 Mon Sep 17 00:00:00 2001 From: David Laehnemann Date: Fri, 27 Oct 2023 13:45:18 +0200 Subject: [PATCH 8/9] move the build section to the start of requirements --- recipes/bioconductor-rhdf5/meta.yaml | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/recipes/bioconductor-rhdf5/meta.yaml b/recipes/bioconductor-rhdf5/meta.yaml index 69799ac5992d3..2621b0ac404eb 100644 --- a/recipes/bioconductor-rhdf5/meta.yaml +++ b/recipes/bioconductor-rhdf5/meta.yaml @@ -29,6 +29,11 @@ build: # Suggests: bit64, BiocStyle, knitr, rmarkdown, testthat, bench, dplyr, ggplot2, mockery, BiocParallel # SystemRequirements: GNU make requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - automake + - make host: - 'bioconductor-rhdf5filters >=1.12.0,<1.13.0' - 'bioconductor-rhdf5lib >=1.22.0,<1.23.0' @@ -39,11 +44,6 @@ requirements: - 'bioconductor-rhdf5filters >=1.12.0,<1.13.0' - 'bioconductor-rhdf5lib >=1.22.0,<1.23.0' - r-base - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - automake - - make test: commands: - '$R -e "library(''{{ name }}'')"' From 1642bfb9bac353caed7b8c904d6b4b8212338b87 Mon Sep 17 00:00:00 2001 From: David Laehnemann Date: Fri, 27 Oct 2023 13:52:04 +0200 Subject: [PATCH 9/9] fix typo --- recipes/bioconductor-rhdf5/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/bioconductor-rhdf5/meta.yaml b/recipes/bioconductor-rhdf5/meta.yaml index 2621b0ac404eb..22e76300066cf 100644 --- a/recipes/bioconductor-rhdf5/meta.yaml +++ b/recipes/bioconductor-rhdf5/meta.yaml @@ -57,6 +57,6 @@ extra: - biotools:rhdf5 parent_recipe: name: '{{ full_name }}' - path: `recipes/{{ full_name }}' + path: 'recipes/{{ full_name }}' version: 2.24.0