________________________________
From: Ludwig Geistlinger <Ludwig.Geistlinger at sph.cuny.edu>
Sent: Wednesday, December 4, 2019 1:32 PM
To: Shepherd, Lori <Lori.Shepherd at RoswellPark.org>; bioc-devel at r-project.org <bioc-devel at r-project.org>
Subject: Re: Final List of Deprecated Packages for Bioc3.10
Yes, I could do that if needed.
________________________________
From: Shepherd, Lori <Lori.Shepherd at RoswellPark.org>
Sent: Wednesday, December 4, 2019 1:28 PM
To: Ludwig Geistlinger; bioc-devel at r-project.org
Subject: Re: Final List of Deprecated Packages for Bioc3.10
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Are you volunteering to permanently take over as maintainer of this package?
Lori Shepherd
Bioconductor Core Team
Roswell Park Comprehensive Cancer Center
Department of Biostatistics & Bioinformatics
Elm & Carlton Streets
Buffalo, New York 14263
________________________________
From: Ludwig Geistlinger <Ludwig.Geistlinger at sph.cuny.edu>
Sent: Wednesday, December 4, 2019 1:22 PM
To: Shepherd, Lori <Lori.Shepherd at RoswellPark.org>; bioc-devel at r-project.org <bioc-devel at r-project.org>
Subject: Re: Final List of Deprecated Packages for Bioc3.10
Hi Lori,
Is it possible to undeprecate the "PathNet" package?
I just checked, the problem is a failing unit test, causing the otherwise well working package to fail R CMD check.
I fixed this here on a local clone of https://git.bioconductor.org/packages/PathNet<https://urldefense.proofpoint.com/v2/url?u=https-3A__git.bioconductor.org_packages_PathNet&d=DwMFAg&c=mRWFL96tuqj9V0Jjj4h40ddo0XsmttALwKjAEOCyUjY&r=OdfcI7SrMMnS3DAUJULIgzR9ZFOeXSyzUMNqMKXj4yE&m=hXVVPnvQ8N1q2LgQkQOS5W7zBluTCo4kY2Gmj4i4RXY&s=q1rBhXn6bs7NDTSKvbP9xKPMjQ4tUSuSwBvC-YYzWSI&e=> and could push these minor changes if granted access.
The PathNet package implements a solid network-based enrichment method and the corresponding paper has some 50 citations - it would thus be unfortunate to see it gone.
Thanks,
Ludwig
________________________________________
From: Bioc-devel <bioc-devel-bounces at r-project.org> on behalf of Shepherd, Lori <Lori.Shepherd at RoswellPark.org>
Sent: Monday, October 7, 2019 9:41 AM
To: bioc-devel at r-project.org
Subject: [Bioc-devel] Final List of Deprecated Packages for Bioc3.10
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 final list for the 3.10 release is as follows:
Maintainer requested deprecation:
Software:
SNPchip
GenomeGraphs
HTSanalyzeR
Rchemcpp
charm
Pbase
Experiment Data Package:
charmData
Unresponsive/not-maintained packages:
Software:
dSimer
flipflop
exomePeak
CNPBayes
brainImageR
plateCore
rHVDM
SEPA
condcomp
PathNet
scone
birte
mlm4omics
RnaSeqSampleSize
Experiment Data Package:
facopy.annot
allenpvc
Renaming The package CAMTHC is marked for deprecation. This package has been renamed to debCAM
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
The Bioconductor team will continue to send 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. Packages that are ERRORing and not fixed before the October 30th 3.10 release will immediately be marked as deprecated in devel 3.11.
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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