[Bioc-devel] EXTERNAL: Re: List of Deprecated Packages Bioc 3.11

Thu Feb 27 20:40:58 CET 2020

When generating this annotation package, we believed the data we were downloading was stale which is why we chose to deprecate it.  Upon seeing the deprecation list email, a user informed us of a different location where the data may be more up to date. We are currently working through our annotation pipeline with the new data to be sure we can generate all the information needed in the org.At.tair.db package. Once we have finished this pipeline and compared, we will determine if the package should in fact be deprecated and if so, what will the supplement be. 

Best,
Kayla

On 2/27/20, 1:24 PM, "Bioc-devel on behalf of Ludwig Geistlinger" <bioc-devel-bounces using r-project.org on behalf of Ludwig.Geistlinger using sph.cuny.edu> wrote:

    Why will org.At.tair.db be deprecated and by what will it be replaced? It's the org package for Arabidopsis and thus central for gene ID mapping when working with Arabidopsis data ...

    Thanks,
    Ludwig

    --
    Dr. Ludwig Geistlinger
    Department of Epidemiology and Biostatistics
    CUNY School of Public Health
    New York, NY 10027

    ________________________________________
    From: Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of Shepherd, Lori <Lori.Shepherd using RoswellPark.org>
    Sent: Thursday, February 27, 2020 12:32 PM
    To: bioc-devel using r-project.org
    Subject: [Bioc-devel] List of Deprecated Packages Bioc 3.11

    ***ATTENTION: This email came from an external source. Do not open attachments or click on links from unknown senders or unexpected emails.***

    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 3.11 is as follows:

    Maintainer requested deprecation:

    Software:

    QUALIFIER
    motifRG
    triform
    CVE
    proteoQC
    affypdnn
    splicegear
    Genominator
    IdMappingAnalysis
    IdMappingRetrieval
    manta
    RefNet
    AnalysisPageServer
    scfind
    kimod
    plw

    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
    RCAS
    bgafun
    lol
    M3D
    MergeMaid

    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.

    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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