News:List of Deprecated Packages for Bioc3.18
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shepherl 3.8k
@lshep
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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 3.18:

Software:

User Requested

  • biodbMirbase
  • DeepBlueR
  • exomeCopy
  • gaggle
  • LPEadj
  • macat
  • Ringo
  • trena

Unresponsive:

  • baySeq
  • BGmix
  • bigPint
  • BioMM
  • biomvRCNS
  • Clonality
  • CSSP
  • deco
  • DMRforPairs
  • fcoex
  • GCSscore
  • genbankr
  • GISPA
  • GOsummaries
  • GRridge
  • HPAStainR
  • imageHTS
  • LineagePulse
  • logitT
  • LowMACA
  • mAPKL
  • mbOmic
  • MEIGOR
  • Metab
  • MSstatsSampleSize
  • multiSight
  • netbiov
  • OmicsLonDA
  • PFP
  • plethy
  • pwrEWAS
  • qrqc
  • ReportingTools
  • RNAdecay
  • SCATE
  • SEPIRA
  • seqbias
  • seqCNA
  • SISPA
  • snapCGH
  • sscore
  • Travel

ExperimentData:

User Requested

  • ccTutorial
  • MAQCsubsetILM
  • stjudem

Unresponsive

  • ChIC.data
  • DLBCL
  • mAPKLData
  • MIGSAdata
  • pwrEWAS.data
  • SCATEData
  • seqCNA.annot

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@r-project.org mailing list

Please do not undeprecate a package yourself. You must request undeprecation from the Bioconductor core team at bioc-devel@r-project.org.

Deprecation Bioconductor devel Devel • 2.4k views
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Hi!

What about https://bioconductor.org/checkResults/3.18/bioc-LATEST/CancerInSilico/ ?

The project fails on Linux due to changes in GLIBC.

There is no activity in the Github repo since 2019.

The Bioc repo has only bump version commits too by the Bioc team.

Regards, Martin

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Its in consideration. We are cautious when a package is only failing on one platform with deprecation.

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Also the source package is not available in BioC 3.17 which means that the package has been broken on Linux since at least November 2022 when we started the 3.17 builds.

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shepherl 3.8k
@lshep
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biomvRCNS has been fixed and is undeprecated

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shepherl 3.8k
@lshep
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motifbreakR is making updates and will be undeprecated

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shepherl 3.8k
@lshep
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SOMNiBUS is making updates and will be undeprecated

tweeDEseq / tweeDEseqdata has found a replacement maintainer and will be undeprecated

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shepherl 3.8k
@lshep
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YAPSA has been fixed in devel and will be undeprecated

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shepherl 3.8k
@lshep
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shinyMethyl has been fixed in devel and will be undeprecated

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shepherl 3.8k
@lshep
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United States

TCseq has fixed their package and will be undeprecated

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shepherl 3.8k
@lshep
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GEOexplorer has been responsive and will be undeprecated

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shepherl 3.8k
@lshep
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United States

hypeR has fixed there package and will be undeprecated

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shepherl 3.8k
@lshep
Last seen 8 hours ago
United States

ReportingTools has been fixed and a replacement maintainer found. It has also been undeprecated

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shepherl 3.8k
@lshep
Last seen 8 hours ago
United States

DLBCL has been fixed and will remain in Bioconductor.

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shepherl 3.8k
@lshep
Last seen 8 hours ago
United States

RNAdecay has been fixed and will be undeprecated

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