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Package descriptions and patches for Fink
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bioconductor-* source URL #704

Open babayoshihiko opened 3 years ago

babayoshihiko commented 3 years ago

bioconductor-* source URLs have changed and these packages are not available.

Currently, in our .info file, we have set http://www.bioconductor.org/packages/3.10/bioc/src/contrib/ (Note that 3.12 is the upstream's latest version).

Now, the sources have moved to: https://www.bioconductor.org/packages/release/bioc/src/contrib/

And when a newer version is available, they will move to: http://bioconductor.org/packages/3.12/bioc/src/contrib/Archive/PACKAGENAME/ 3.12 is for BioC 3.12 packages only. The value may change.

So, we can solve by modifying as: Source: mirror:custom:PACKAGENAME_%v.tar.gz CustomMirror: << Primary: https://www.bioconductor.org/packages/release/bioc/src/contrib/ Secondary: http://bioconductor.org/packages/3.12/bioc/src/contrib/Archive/PACKAGENAME/ <<

nieder commented 3 years ago

By 'newer version', do you mean a newer version of bioconductor (say 3.14 vs current 3.12), or newer version of the specific package? http://bioconductor.org/packages/3.12/bioc/src/contrib/Archive/affy/affy_1.68.0.tar.gz currently returns a 404, but https://www.bioconductor.org/packages/release/bioc/src/contrib/affy_1.68.0.tar.gz works.

babayoshihiko commented 3 years ago

By 'newer version', do you mean a newer version of bioconductor (say 3.14 vs current 3.12), or newer version of the specific package? http://bioconductor.org/packages/3.12/bioc/src/contrib/Archive/affy/affy_1.68.0.tar.gz currently returns a 404, but https://www.bioconductor.org/packages/release/bioc/src/contrib/affy_1.68.0.tar.gz works.

for

And when a newer version is available, they will move to:

The source of affy is now at https://www.bioconductor.org/packages/release/bioc/src/contrib/ [1]

When a new version of affy for bioconductor is available, the 1.68.0 source will be moved to http://bioconductor.org/packages/3.12/bioc/src/contrib/Archive/affy/ [2]

So, 1.68.0 is either at [1] or [2], not at both of them until 3.14 comes.

babayoshihiko commented 3 years ago

For a newer bioconductor (say 3.14), it seems the below is better:

CustomMirror: << Primary: http://bioconductor.org/packages/3.12/bioc/src/contrib/ Secondary: http://bioconductor.org/packages/3.12/bioc/src/contrib/Archive/PACKAGENAME/ <<