[Bioc-devel] List of Deprecated Packages for Bioc 3.12

[Ludwig Geistlinger]

The (very popular) safe package breaks due the quite disruptive class(matrix) update in R-4.0.0 which I could easily fix if given access.

Marcel and I contacted the maintainer of the safe package (William T Barry), but received the following automatic notice.

"AUTOMATIC NOTICE: Please note that as of March 17th, 2018, I am no longer employed at Dana-Farber Cancer Institute, nor affiliated with DF/HCC, HMS, B&CB and the Alliance Statistics and Data Center. Please contact individuals in each organization with urgent or new matters.  For ongoing activities, I will receive and respond to this message as I am able. Cheers,"

Could you please advise how to proceed as breaking of safe (and the package not being available for bioc-devel) currently prevents me from building my enrichOmics workshop for Bioc2020, and I would thus be interested in resolving this asap.

Many thanks,
Ludwig

________________________________________
From: Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of Shepherd, Lori <Lori.Shepherd using RoswellPark.org>
Sent: Monday, June 8, 2020 11:50 AM
To: bioc-devel using r-project.org
Subject: [Bioc-devel] List of Deprecated Packages for Bioc 3.12

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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 3.12 :



Maintainer requested deprecation:

Software:

CGEN
DESeq: please see DESeq2
chimera
flowFit
flowSpy
netReg
metaseqR: please see metaseqR2
MPFE
OGSA
prada
PWMEnrich
rTANDEM
scsR
shinyTANDEM
spotSegmentation


Unresponsive/not-maintained packages:

Software:


adaptest
ArrayTV
BioNet
BioSeqClass
CHARGE
CNVtools
CorMut
flowType
flowVS
focalCall
FourCSeq
gage
GeneOverlap
GenRank
GOFunction
ImpulseDE
ImpulseDE2
joda
JunctionSeq
LINC
Logolas
MAIT
Mirsynergy
MotIV
NarrowPeaks
netbenchmark
NOISeq
omicade4
omicRexposome
OmicsMarkeR
pathprint
PathwaySplice
PGSEA
plrs
Prize
reb
Roleswitch
safe
sampleClassifier
sigaR
signet
Starr



Experiment Data Package:

FunciSNP.data
mitoODEdata
Mulder2012
PWMEnrich.Dmelanogaster.background
PWMEnrich.Hsapiens.background
PWMEnrich.Mmusculus.background
RNAinteractMAPK
RnaSeqSampleSizeData




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.

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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