[Bioc-devel] List of Deprecated Packages for Bioc3.21

[Kern, Lori]

Because of the way the builders are set up we only see CRAN dependency disappear when we do a new install of R or manually flush the repository.  Therefore there can be a delay in seeing these failures/ERROR's.   If it is due to a Bioconductor package,  we normally notify reverse dependencies once a package is listed as deprecated (not necessarily only failing).

We try to be very fair to package maintainers so depending on when we (and they) are aware of the failure, we may give them extra time moving into a release as we realize package maintenance is not everyone's top priority (even tho we would like it to be)


Lori Shepherd - Kern

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

________________________________
From: Llu�s Revilla <lluis.revilla using gmail.com>
Sent: Saturday, March 29, 2025 4:05 AM
To: Kern, Lori <Lori.Shepherd using RoswellPark.org>
Cc: bioc-devel <bioc-devel using r-project.org>
Subject: Re: [Bioc-devel] List of Deprecated Packages for Bioc3.21

Hi Lori,

There is some documentation<https://secure-web.cisco.com/1CaaN3K9FoTk2Yod51sOa073f3kslapZhz7-LVKYRBmE93Yq1qBXI4SRYWldRJEjARLQRUbqtbWxUO8xJrGXFZs6h3-B6ge0M7EdxtpwKgJAVFhA8R2zE7GkKmWorRq7eQ7UvSZFnj-hPRzxJw8nmGAqsJx_bjDQBVuUEIjD_mDmplcj1IgsAVBbzdD8Kkjzfetcxv4eR_9zCQfnpb0DgFOvThpu6M7zp6rZ8djT-_4SyjfCX-Wu5yVL6Qt-lnAIt03FWlt3zJakrcdbCo0KdTYN8iBqm7Hwi0ICpEa8W1gp7wR7yl0d_uQMCSoRShNGo/https%3A%2F%2Fcontributions.bioconductor.org%2Fpackage-end-of-life-policy.html%23criteria-for-package-deprecation-by-core-team> about how to keep a package on Bioconductor (and when they are archived). Among other conditions it mentions that they shouldn't be failing checks.

There are currently two packages on Bioconductor 3.20 that depend on a package no longer available, as a consequence they fail some checks. One dependency is a software package on CRAN and the other an experimental data package.
These packages do not have the dependency removed on the devel branch as far as I can tell or the maintainers are aware of the situation ( no activity on their issue tracker).

However, I don't see these packages on this list. Are these cases handled differently?

Best,

Llu�s



On Thu, 27 Mar 2025 at 15:56, Kern, Lori via Bioc-devel <bioc-devel using r-project.org<mailto:bioc-devel using r-project.org>> wrote:
The Bioconductor Team is continuing to identify packages that will be deprecated in the next release to allow for the Bioconductor community to respond accordingly. This is the current list of deprecated packages for Bioc 3.21.

It should be noted, we did try to reach out to these package maintainers multiple times and they were either unresponsive or had emails bounce. We encourage anyone that is familiar with a package maintainer on this list to reach out to them and notify them directly. Packages can be un-deprecated if a maintainer fixes the package to build/check cleanly before the next release and requests un-deprecation on the bioc-devel using r-project.org<mailto:bioc-devel using r-project.org> mailing list

Do not un-deprecate a package yourself. You must request un-deprecation from the Bioconductor core team at bioc-devel using r-project.org<mailto:bioc-devel using r-project.org>. We will not recognize a self un-deprecation

Software User Requested:
- Director
- erma
- girafe
- RBioinf
- Rtreemix
- synapter
- zlibbioc

Software Unresponsive:

- AneuFinder
- BEARscc
- CBEA
- chromstaR
- coMET
- crossmeta
- dce
- DeProViR
- DIAlignR
- GeneGeneInteR
- genoCN
- gespeR
- GraphPAC
- HTSeqGenie
- iPAC
- MAGeCKFlute
- netDx
- NeuCA
- PanViz
- pareg
- paxtoolsr
- PICS
- PING
- QuartPAC
- ReactomeContentService4R
- RGMQL
- SpacePAC
- staRank
- STdeconvolve
- supraHex
- trigger
- TypeInfo

Experiment Data Requested

-  parathyroidSE
- benchmarkfdrData2019
- synapterdata

Workflow Requested

- BiocMetaWorkflow

Annotation Data Requested

- mirbase.db
- targetscan.Hs.eg.db
- targetscan.Mm.eg.db




Lori Shepherd - Kern

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


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