[Bioc-devel] List of Deprecated Packages Bioc 3.11

[Ludwig Geistlinger]

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

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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 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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