Matrix extension fails to load for Seurat

[verdurin]

Matrix 1.5-1 is now in the Archive, and there needs to be a URL specific for it in the Archive, not for the main enclosing package i.e. Seurat.

[branfosj]

https://cran.r-project.org/src/contrib/Archive/Matrix/Matrix_1.5-1.tar.gz

[branfosj]

Does that mean

source_urls = [
    'https://cran.r-project.org/src/contrib/Archive/%(name)s',  # package archive
    'https://cran.r-project.org/src/contrib/',  # current version of packages
    'https://cran.freestatistics.org/src/contrib',  # mirror alternative for current packages
]

The first item is expanding %(name)s as Seurat instead of Matrix?

[branfosj]

And testing that, we see

== fetching files...
  >> download failed: https://cran.r-project.org/src/contrib/Archive/Seurat/Matrix_1.5-1.tar.gz
  >> download failed: https://cran.r-project.org/src/contrib/Matrix_1.5-1.tar.gz
  >> download failed: https://cran.freestatistics.org/src/contrib/Matrix_1.5-1.tar.gz
  >> download failed: https://sources.easybuild.io/s/Seurat/Matrix_1.5-1.tar.gz

In the Seurat easyconfig change:

exts_default_options = {'sources': ['%(name)s_%(version)s.tar.gz']}

to be

exts_default_options = {
    'sources': ['%(name)s_%(version)s.tar.gz'],
    'source_urls': source_urls,
}

[branfosj]

In fact, we should be setting

exts_default_options = {
    'sources': ['%(name)s_%(version)s.tar.gz'],
    'source_urls': [
        'https://cran.r-project.org/src/contrib/Archive/%(name)s',  # package archive
        'https://cran.r-project.org/src/contrib/',  # current version of packages
        'https://cran.freestatistics.org/src/contrib',  # mirror alternative for current packages
    ],
}

and removing the top level source_urls.

[branfosj]

#17830 fixes the Seurat 4.x easyconfigs.

Some method for searching is we need to do this elsewhere is needed. From my quick check this only looks to be impacting the Seurat easyconfigs.