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 package scone has been added to the list. Pbase has been maintainer requested deprecated as well. The current list of deprecated packages for Bioc 3.10 is as follows:
Maintainer requested deprecation:
-
Software:
- SNPchip
- GenomeGraphs
- HTSanalyzeR
- Rchemcpp
- charm
- Pbase
-
Experiment Data Package:
- charmData
Unresponsive/not-maintained packages:
-
Software:
- diggit
- dSimer
- flipflop
- exomePeak
- CNPBayes
- brainImageR
- plateCore
- rHVDM
- SEPA
- viper
- condcomp
- PathNet
- scone
-
Experiment Data Package:
- facopy.annot
- diggitdata
- allenpvc
The following Annotation Packages have been user requested deprecated:
- MafDb.gnomADex.r2.0.1.GRCh38
- MafDb.gnomAD.r2.0.1.GRCh38
- MafDb.gnomADex.r2.0.1.hs37d5
- MafDb.gnomAD.r2.0.1.hs37d5
They are replaced with
- MafDb.gnomADex.r2.1.GRCh38
- MafDb.gnomAD.r2.1.GRCh38
- MafDb.gnomADex.r2.1.hs37d5
- MafDb.gnomAD.r2.1.hs37d5
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
