Great, thanks for the update!
________________________________________
From: Interdonato, Kayla <kayla.morr...@roswellpark.org>
Sent: Thursday, February 27, 2020 2:40 PM
To: Ludwig Geistlinger; bioc-devel@r-project.org
Subject: Re: EXTERNAL: Re: [Bioc-devel] 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-boun...@r-project.org on behalf of ludwig.geistlin...@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-boun...@r-project.org> on behalf of Shepherd,
Lori <lori.sheph...@roswellpark.org>
Sent: Thursday, February 27, 2020 12:32 PM
To: bioc-devel@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@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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