News: Initial List of Deprecated Package Bioc 3.9
0
gravatar for shepherl
12 months ago by
shepherl ♦♦ 1.7k
United States
shepherl ♦♦ 1.7k 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. The list will be updated monthly.

The current list of deprecated packages for Bioc 3.9 is as follows:

Maintainer requested deprecation:

  • Software:

    • flowQ

Unresponsive/not-maintained packages:

  • Software:

    • ProCoNA
  • Experiment Data Package:

    • PGPC

We will be sending emails out to packages that have been broken across all platforms for an extended period of time, and therefore are now broken in Bioconductor Release 3.8 and Bioconductor Devel 3.9, as those are packages that are up for immediate deprecation if not corrected in a timely fashion. Thank you

news package release deprecate • 371 views
ADD COMMENTlink modified 12 months ago by Wolfgang Huber13k • written 12 months ago by shepherl ♦♦ 1.7k
Answer: Initial List of Deprecated Package Bioc 3.9
0
gravatar for Wolfgang Huber
12 months ago by
EMBL European Molecular Biology Laboratory
Wolfgang Huber13k wrote:

RFC:
I have a question regarding best practice for packages like PGPC, which provides not a general-purpose resource, but a reproducible transcript of the (complete) set of analyses presented in a specific, singular paper (in the case of PGPC, published 2015). That means that it's important for the scientific record to have this package and its vignette building with the versions of R and packages that were used at the time, but not really essential to keep it working with all current and future versions of R and packages. So we could now simply deprecate it, but OTOH one could also imagine creating a corner in the Bioconductor package ecosystem for packages that are only ever supposed to build and check with a single release. What do others think about this?

ADD COMMENTlink written 12 months ago by Wolfgang Huber13k
1

Maybe we could start by having a BiocViews term that we use to identify this type of package. Although this would make them "findable" only if you search/browse the right BioC version because our view trees are version specific: https://bioconductor.org/packages/release/BiocViews.html#___Software

Probably worth moving this discussion to the bioc-devel mailing list?

H.

ADD REPLYlink written 12 months ago by Hervé Pagès ♦♦ 14k

I did move this to https://stat.ethz.ch/pipermail/bioc-devel/2018-November/014301.html

ADD REPLYlink written 12 months ago by Martin Morgan ♦♦ 24k
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