[Bioc-devel] un-deprecation Request biomvRCNS

Mon Dec 4 13:10:46 CET 2023

Thank you. I will undeprecate and add back into devel (3.19) manifest/report.

Cheers,

Lori Shepherd - Kern

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

________________________________
From: Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of Dan Du <tooyoung using gmail.com>
Sent: Monday, December 4, 2023 5:48 AM
To: bioc-devel using r-project.org <bioc-devel using r-project.org>
Subject: Re: [Bioc-devel] un-deprecation Request biomvRCNS

Dear CoreTeam staff,

Sorry this email didn't come to my attention, due to loss of access to this
gmail account for quite some time.

Someone notified me about the failing status in build/check, I have made
some quickfix in the past week using my github account, in both release and
devel, appear to be warning free except the deprecation notice. I will
monitor the status change in the next build, and please kindly let me know
if there are other issues.

Best Regards,
Dan

@release

commit 978f184eb4e2850231c98127de4c6a08c62c9860 (*HEAD -> **RELEASE_3_18*,
*origin/RELEASE_3_18*)

Author: yd23 <idananan using gmail.com>

Date:   Fri Dec 1 16:03:31 2023 +0800

    version bump to push it through in the new build.

commit 6087e31bf63bf64c7d152fdc9b37e6779cbcca81

Author: yd23 <idananan using gmail.com>

Date:   Mon Nov 27 08:31:38 2023 +0800

    resave variosm.rda as version 2 to reduce R version dependance

commit 794eddfe3dfb2078c6b38c546d991feee73c4608

Author: yd23 <idananan using gmail.com>

Date:   Thu Nov 23 10:30:44 2023 +0800

    rename c macro in branch remotes/origin/RELEASE_3_18

commit b79c4400f9a48032a2a7e151e6745d330f6970b5

Author: J Wokaty <jennifer.wokaty using sph.cuny.edu>

Date:   Tue Oct 24 09:52:56 2023 -0400

    bump x.y.z version to even y prior to creation of RELEASE_3_18 branch

commit a2fc19b9faec2bfe52f8f0c2126a655b82dab0d3

Author: lshep <lori.shepherd using roswellpark.org>

Date:   Tue Jun 27 08:46:40 2023 -0400

    Deprecate

     - unresponsive

@devel

commit ee30c51457e1720d9c27758cb75c86d28c107c07 (*HEAD -> **master*,
*origin/master*, *origin/HEAD*)

Author: yd23 <idananan using gmail.com>

Date:   Mon Nov 27 08:33:45 2023 +0800

    resave variosm.rda as version 2 to reduce R version dependance

commit 2e1fd423dad9ce248fcb4a54e98349d477b35399 (*origin/devel*)

Author: yd23 <idananan using gmail.com>

Date:   Tue Nov 21 09:33:30 2023 +0800

    rename c macro ;)

commit a83b8b4f60ec33aa72304e235095a3bbfa415108

Author: J Wokaty <jennifer.wokaty using sph.cuny.edu>

Date:   Tue Oct 24 09:52:56 2023 -0400

    bump x.y.z version to odd y following creation of RELEASE_3_18 branch

commit b79c4400f9a48032a2a7e151e6745d330f6970b5

Author: J Wokaty <jennifer.wokaty using sph.cuny.edu>

Date:   Tue Oct 24 09:52:56 2023 -0400

    bump x.y.z version to even y prior to creation of RELEASE_3_18 branch

commit a2fc19b9faec2bfe52f8f0c2126a655b82dab0d3

Author: lshep <lori.shepherd using roswellpark.org>

Date:   Tue Jun 27 08:46:40 2023 -0400

    Deprecate

     - unresponsive

On Tue, Jun 27, 2023 at 9:06 PM Kern, Lori <Lori.Shepherd using roswellpark.org>
wrote:

> 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 3.17:
>
>
>
> Software:
>
> Unresponsive:
>
>   *   baySeq
>   *   BGmix
>   *   BioMM
>   *   biomvRCNS
>   *   deco
>   *   genbankr
>   *   HPAStainR
>   *   hypeR
>   *   imageHTS
>   *   motifbreakR
>   *   netbiov
>   *   plethy
>   *   qrqc
>   *   RNAdecay
>   *   SOMNiBUS
>   *   TCseq
>   *   Travel
>   *   tweeDEseq
>
> 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
>
> Please do not undeprecate a package yourself. You must request
> undeprecation from the Bioconductor core team at bioc-devel using r-project.org.
>
>
>
> Lori Shepherd - Kern
>
> Bioconductor Core Team
>
> Roswell Park Comprehensive Cancer Center
>
> Department of Biostatistics & Bioinformatics
>
> Elm & Carlton Streets
>
> Buffalo, New York 14263
>
>
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> agent responsible for the delivery of this message to the intended
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