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. This is the current list of deprecated packages for Bioc 3.18:
Software:
User Requested
- biodbMirbase
- DeepBlueR
- exomeCopy
- gaggle
- LPEadj
- macat
- Ringo
- trena
Unresponsive:
- BGmix
- bigPint
- BioMM
- Clonality
- COHCAP
- CSSP
- deco
- DMRforPairs
- fcoex
- GCSscore
- genbankr
- GISPA
- GOsummaries
- GRridge
- HPAStainR
- imageHTS
- IntOMICS
- LineagePulse
- logitT
- LowMACA
- mAPKL
- mbOmic
- Metab
- MSstatsSampleSize
- multiSight
- netbiov
- OmicsLonDA
- PFP
- plethy
- pwrEWAS
- qrqc
- SCATE
- SEPIRA
- seqbias
- seqCNA
- SISPA
- snapCGH
- sscore
- Travel
ExperimentData:
User Requested
- ccTutorial
- MAQCsubsetILM
- stjudem
Unresponsive
- ChIC.data
- mAPKLData
- MIGSAdata
- pwrEWAS.data
- SCATEData
- seqCNA.annot
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
Please do not undeprecate a package yourself. You must request undeprecation from the Bioconductor core team at bioc-devel@r-project.org.
Hi!
What about https://bioconductor.org/checkResults/3.18/bioc-LATEST/CancerInSilico/ ?
The project fails on Linux due to changes in GLIBC.
There is no activity in the Github repo since 2019.
The Bioc repo has only bump version commits too by the Bioc team.
Regards, Martin
Its in consideration. We are cautious when a package is only failing on one platform with deprecation.
Also the source package is not available in BioC 3.17 which means that the package has been broken on Linux since at least November 2022 when we started the 3.17 builds.