News:Final List of Deprecated Packages for Bioc3.10
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shepherl 2.8k
@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.

The final list for this release is as follows:

Maintainer requested deprecation:

  • Software:

    • SNPchip
    • GenomeGraphs
    • HTSanalyzeR
    • Rchemcpp
    • charm
    • Pbase
  • Experiment Data Package:

    • charmData

Unresponsive/not-maintained packages:

  • Software:

    • dSimer
    • flipflop
    • exomePeak
    • CNPBayes
    • brainImageR
    • plateCore
    • rHVDM
    • SEPA
    • condcomp
    • PathNet
    • scone
    • birte
    • mlm4omics
    • RnaSeqSampleSize
  • Experiment Data Package:

    • facopy.annot
    • allenpvc

Renaming The package CAMTHC is marked for deprecation. This package has been renamed to debCAM

The following Annotation Packages have been user requested deprecated:

    • MafDb.gnomADex.r2.0.1.GRCh38
    • MafDb.gnomAD.r2.0.1.GRCh38
    • MafDb.gnomADex.r2.0.1.hs37d5
    • MafDb.gnomAD.r2.0.1.hs37d5

They are replaced with

    • MafDb.gnomADex.r2.1.GRCh38
    • MafDb.gnomAD.r2.1.GRCh38
    • MafDb.gnomADex.r2.1.hs37d5
    • MafDb.gnomAD.r2.1.hs37d5

The Bioconductor team will continue to send emails out to packages that have been broken across all platforms for an extended period of time as those are packages that are up for immediate deprecation if not corrected in a timely fashion. Packages that are ERRORing and not fixed before the October 30th 3.10 release will immediately be marked as deprecated in devel 3.11.

Thank you

annotation experimentdata deprecation release software News • 349 views
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shepherl 2.8k
@lshep
Last seen 1 day ago
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scone will be un-deprecated and remain in Bioconductor.

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Entering edit mode
shepherl 2.8k
@lshep
Last seen 1 day ago
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  • MafDb.ESP6500SI.V2.SSA137.hs37d5
  • MafDb.EXP6500SI.V2.SSA137.GRCh38

have been deprecated in 3.10 and removed from 3.11.

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