[Bioc-devel] EXTERNAL: Final List of Deprecated Packages for Bioc3.11

[Interdonato, Kayla]

org.At.tair.db has been updated and will be undeprecated. This package will remain in Bioconductor.

On 3/30/20, 11:37 AM, "Bioc-devel on behalf of Shepherd, Lori" <bioc-devel-bounces using r-project.org on behalf of Lori.Shepherd using RoswellPark.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. The list will be updated monthly. This is the current list of deprecated packages for Bioc 3.11 :

    Maintainer requested deprecation:

    Software:

    QUALIFIER
    motifRG
    triform
    CVE
    proteoQC
    affypdnn
    splicegear
    Genominator
    IdMappingAnalysis
    IdMappingRetrieval
    manta
    RefNet
    AnalysisPageServer
    scfind
    kimod
    plw
    cn.mops
    cobindR
    LMGene
    sRAP
    gCMAP
    gCMAPWeb
    DESeq


    Annotation:

    org.At.tair.db
    hom.At.inp.db
    hom.Ce.inp.db
    hom.Dm.inp.db
    hom.Dr.inp.db
    hom.Hs.inp.db
    hom.Mm.inp.db
    hom.Rn.inp.db
    hom.Sc.inp.db
    KEGG.db (use KEGGREST instead)


    Unresponsive/not-maintained packages:

    Software:

    SELEX
    CTDquerier
    MTseeker
    readat
    anamiR
    MEAL
    BiSeq
    CALIB
    cellGrowth
    chroGPS
    DEDS
    LVSmiRNA
    MANOR
    MCRestimate
    nem
    PAPi
    pcaGoPromoter
    pint
    RIPSeeker
    SANTA
    waveTiling
    BayesPeak
    bgafun
    lol
    M3D
    MergeMaid
    IPPD
    biosvd
    birta
    DupChecker
    FEM
    geecc
    MaxContrastProjection
    mitoODE
    MoPS
    PowerExplorer
    Vega


    ExpermentData:

    MTseekerData
    RIPSeekerData


    The follow Annotation packages were deprecated in 3.10 and removed from 3.11 but not previously announced.

    MafDb.ESP6500SI.V2.SSA137.hs37d5
    MafDb.EXP6500SI.V2.SSA137.GRCh38

    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 mailing list.

    We will be sending 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.

    We will still be keeping track of failing packages and compiling a list to deprecate immediately after the release. This could have been because the package has reverse dependencies or was identified to late to deprecate in 3.11. We encourage anyone that knows the maintainers of these packages to reach out to them to fix their package to avoid deprecation. The current list for immediate deprecation in 3.12 is:

    DESeq
    MotIV
    NOISeq
    omicade4
    PGSEA
    Starr
    VanillaICE


    Thank you


    Lori Shepherd

    Bioconductor Core Team

    Roswell Park Comprehensive Cancer Center

    Department of Biostatistics & Bioinformatics

    Elm & Carlton Streets

    Buffalo, New York 14263


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