[Bioc-devel] EXTERNAL: Re: List of Deprecated Packages Bioc 3.11
When generating this annotation package, we believed the data we were downloading was stale which is why we chose to deprecate it. Upon seeing the deprecation list email, a user informed us of a different location where the data may be more up to date. We are currently working through our annotation pipeline with the new data to be sure we can generate all the information needed in the org.At.tair.db package. Once we have finished this pipeline and compared, we will determine if the package should in fact be deprecated and if so, what will the supplement be.
Best,
Kayla
?On 2/27/20, 1:24 PM, "Bioc-devel on behalf of Ludwig Geistlinger" <bioc-devel-bounces at r-project.org on behalf of Ludwig.Geistlinger at sph.cuny.edu> wrote:
Why will org.At.tair.db be deprecated and by what will it be replaced? It's the org package for Arabidopsis and thus central for gene ID mapping when working with Arabidopsis data ...
Thanks,
Ludwig
--
Dr. Ludwig Geistlinger
Department of Epidemiology and Biostatistics
CUNY School of Public Health
New York, NY 10027
From: Bioc-devel <bioc-devel-bounces at r-project.org> on behalf of Shepherd, Lori <Lori.Shepherd at RoswellPark.org>
Sent: Thursday, February 27, 2020 12:32 PM
To: bioc-devel at r-project.org
Subject: [Bioc-devel] List of Deprecated Packages Bioc 3.11
Sent: Thursday, February 27, 2020 12:32 PM
To: bioc-devel at r-project.org
Subject: [Bioc-devel] List of Deprecated Packages Bioc 3.11
***ATTENTION: This email came from an external source. Do not open attachments or click on links from unknown senders or unexpected emails.***
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 current list of deprecated packages for Bioc 3.11 is as follows:
Maintainer requested deprecation:
Software:
QUALIFIER
motifRG
triform
CVE
proteoQC
affypdnn
splicegear
Genominator
IdMappingAnalysis
IdMappingRetrieval
manta
RefNet
AnalysisPageServer
scfind
kimod
plw
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
RCAS
bgafun
lol
M3D
MergeMaid
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 at 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
This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited. If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you.
[[alternative HTML version deleted]]
_______________________________________________
Bioc-devel at r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
_______________________________________________
Bioc-devel at r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited. If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you.