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update bioconductor-rhdf5: rebuild after including libcurl dependency downstream in bioconductor-rhdf5lib, include pin_subpackage syntax #43900

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merged 9 commits into from
Oct 30, 2023
Merged

update bioconductor-rhdf5: rebuild after including libcurl dependency downstream in bioconductor-rhdf5lib, include pin_subpackage syntax #43900

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a0c8abd
fix: [bioconductor-rhdf5] explicitly include libcurl dependency
dlaehnemann Oct 26, 2023
37bf42e
bump version number
dlaehnemann Oct 26, 2023
381f64b
Update bioconductor-rhdf5: include `run_exports` with `pin_subpackage`
dlaehnemann Oct 26, 2023
bc26c45
introduce full_name variable to include `bioconductor-` prefix
dlaehnemann Oct 26, 2023
837378f
remove libcurl again, as this is handled downstream in bioconductor-r…
dlaehnemann Oct 27, 2023
cba4901
clean up full_name usage
dlaehnemann Oct 27, 2023
d8bf847
include comment about pinning not necessarily being decided, yet
dlaehnemann Oct 27, 2023
a70733e
move the build section to the start of requirements
dlaehnemann Oct 27, 2023
1642bfb
fix typo
dlaehnemann Oct 27, 2023
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29 changes: 19 additions & 10 deletions recipes/bioconductor-rhdf5/meta.yaml
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Original file line number Diff line number Diff line change
@@ -1,25 +1,39 @@
{% set version = "2.44.0" %}
{% set name = "rhdf5" %}
{% set full_name = "bioconductor-" ~ name|lower %}
{% set bioc = "3.17" %}

package:
name: 'bioconductor-{{ name|lower }}'
name: '{{ full_name }}'
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: 0
number: 1
rpaths:
- 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
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'
Expand All @@ -30,11 +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 }}'')"'
Expand All @@ -47,7 +56,7 @@ extra:
identifiers:
- biotools:rhdf5
parent_recipe:
name: bioconductor-rhdf5
path: recipes/bioconductor-rhdf5
name: '{{ full_name }}'
path: 'recipes/{{ full_name }}'
version: 2.24.0

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