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List:       bioc-devel
Subject:    Re: [Bioc-devel]  EXTERNAL: Re:  List of Deprecated Packages Bioc 3.11
From:       Ludwig Geistlinger <Ludwig.Geistlinger () sph ! cuny ! edu>
Date:       2020-02-27 21:26:09
Message-ID: 1582838769395.94296 () sph ! cuny ! edu
[Download RAW message or body]

Great, thanks for the update!

________________________________________
From: Interdonato, Kayla <Kayla.Morrell@RoswellPark.org>
Sent: Thursday, February 27, 2020 2:40 PM
To: Ludwig Geistlinger; bioc-devel@r-project.org
Subject: Re: EXTERNAL: Re: [Bioc-devel] List of Deprecated Packages Bioc 3.11

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@r-project.org on behalf of Ludwig.Geistlinger@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@r-project.org> on behalf of Shepherd, Lori \
<Lori.Shepherd@RoswellPark.org>  Sent: Thursday, February 27, 2020 12:32 PM
    To: bioc-devel@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@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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