[Bioc-devel] List of Deprecated Packages Bioc 3.11

Shepherd, Lori Lor|@Shepherd @end|ng |rom Ro@we||P@rk@org
Mon Jan 6 18:54:09 CET 2020

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
  *   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
     *   MIGSA
     *   nem
     *   PAPi
     *   pcaGoPromoter
     *   pint
     *   RIPSeeker
     *   SANTA
     *   waveTiling
     *   BayesPeak
     *   RCAS
     *   schex
  *   ExpermentData:

     *   MTseekerData

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

The PathNet package has been un-deprecated and will remain in Bioconductor.

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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