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 3.15 :
Software:
User Requested:
- caOmicsV
- clonotypeR
- GCSFileSystem
- GCSConnection
- genphen
- ppiStats
- ProteomicsAnnotationHubData
- PSICQUIC
- PubScore
- Rgin
- RpsiXML
- ScISI
- SLGI
- Sushi
Unresponsive:
- ABAEnrichment
- Autotuner
- CAnD
- CHETAH
- CountClust
- diffloop
- GenoGAM
- gprege
- Onassis
- perturbatr
- phemd
- RmiR
- tofsims
- TSRchitect
ExperimentData
User Requested:
- ppiData
- DREAM4
Unresponsive:
- MSstatsBioData
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.
The workflow proteomics is also deprecated.
networkBMA is also deprecated
phemd has been fixed and will be undeprecated.
CHETAH has been fixed and will be undeprecated