AnnotationDbi 1.46.0 not available in archive of Bioconductor 3.9 release?
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@kennethhoste-8269
Last seen 3.1 years ago
Belgium

Apparently the version of AnnotationDbi packages in the Bioconductor 3.9 release was bumped recently.

It was 1.46.0 before, now it's at 1.46.1 (see https://bioconductor.org/packages/3.9/bioc/html/AnnotationDbi.html).

This is usually not a problem since package versions that were once included in a Bioconductor release are usually still available for download via the archive since recently (see https://support.bioconductor.org/p/102555/).

However, in this case there simply is no AnnotationDbi listed at http://bioconductor.org/packages/3.9/bioc/src/contrib/Archive/, so the source tarball for AnnotationDbi 1.46.0 is no longer available.

Is there a specific reason for this, or can this be fixed?

(related: https://bioconductor.org/packages/3.9/bioc/news/AnnotationDbi/NEWS is horribly outdated, is there an overview of changes for recent versions available somewhere?)

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@kaylainterdonato-17327
Last seen 5 weeks ago
United States

We are looking a bit deeper into the archive issue. As far as the outdated NEWS file, you can take a look at the commits made to AnnotationDbi on the GitHub repo.

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The archive is now available and can be found here or at the end of the landing page for AnnotationDbi.

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Thank you very much for restoring the download of AnnotationDbi 1.46.0!

There's another problem though: it seems like this is not the original source tarball that was available originally, it's a re-created one?

Here's the diff between the old and new source tarball:

diff -ru AnnotationDbi_1.46.0_old AnnotationDbi_1.46.0_new
diff -ru AnnotationDbi_1.46.0_old/DESCRIPTION AnnotationDbi_1.46.0_new/DESCRIPTION
--- AnnotationDbi_1.46.0_old/DESCRIPTION    2019-05-03 01:45:31.000000000 +0200
+++ AnnotationDbi_1.46.0_new/DESCRIPTION    2019-08-28 22:39:07.000000000 +0200
@@ -31,11 +31,6 @@
 License: Artistic-2.0
 biocViews: Annotation, Microarray, Sequencing, GenomeAnnotation
 VignetteBuilder: knitr
-Packaged: 2019-05-02 23:45:31 UTC; biocbuild
+Packaged: 2019-08-28 20:39:07 UTC; biocbuild
 Video: 
-git_url: https://git.bioconductor.org/packages/AnnotationDbi
-git_branch: RELEASE_3_9
-git_last_commit: 431257d
-git_last_commit_date: 2019-05-02
-Date/Publication: 2019-05-02
 NeedsCompilation: no
Binary files AnnotationDbi_1.46.0_old/build/vignette.rds and AnnotationDbi_1.46.0_new/build/vignette.rds differ
Binary files AnnotationDbi_1.46.0_old/inst/doc/AnnotationDbi.pdf and AnnotationDbi_1.46.0_new/inst/doc/AnnotationDbi.pdf differ
Binary files AnnotationDbi_1.46.0_old/inst/doc/IntroToAnnotationPackages.pdf and AnnotationDbi_1.46.0_new/inst/doc/IntroToAnnotationPackages.pdf differ

Is it possible to restore the original source tarball?

That's important because many people (including myself) verify the checksum of downloaded source tarballs (to detect corrupted downloads and protect against malicious activitiy). Since the source tarball is different now, the checksum is also different...

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This was due to an issue with the build code. This tarball had to be created by hand, hence the minor differences such as time stamps. Unfortunately, we are not able to restore the original source tarball but the code is now more robust to decrease the occurrence of this issue in the future.

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