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@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
