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

[Shepherd, Lori]

BiSeq has fixed their package and reached out for undeprecation. The package will remain in Bioconductor.


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

________________________________
From: Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of Shepherd, Lori <Lori.Shepherd using RoswellPark.org>
Sent: Monday, March 30, 2020 11:36 AM
To: bioc-devel using r-project.org <bioc-devel using r-project.org>
Subject: [Bioc-devel] Final List of Deprecated Packages for Bioc3.11

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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