[Bioc-devel] about deprecate package DNABarcode

Fri Sep 20 11:27:57 CEST 2024

Hi everyone,

I updated/fixed the package some time ago and DNABarcodes builds and 
tests successfully on all Bioconductor platforms. I have a working setup 
to continue working on any problems with the package. Therefore, I would 
like to request the package to be un-deprecated.

Regards,

Tilo

On 27.03.24 15:27, Kern, Lori wrote:
> You'll have to remind them to request un-deprecation here or on the 
> emails they were reached out to.  We will not un-deprecate until the 
> package is fixed and they request the package not be deprecated to 
> prove they have an active email.
>
> Lori Shepherd - Kern
>
> Bioconductor Core Team
>
> Roswell Park Comprehensive Cancer Center
>
> Department of Biostatistics & Bioinformatics
>
> Elm & Carlton Streets
>
> Buffalo, New York 14263
>
> ------------------------------------------------------------------------
> *From:* Pedro Sánchez Sánchez <bio.pedro.technology using gmail.com>
> *Sent:* Wednesday, March 27, 2024 10:23 AM
> *To:* Sun Wenjie <wenjie.sun using curie.fr>
> *Cc:* Kern, Lori <Lori.Shepherd using RoswellPark.org>; 
> bioc-devel using r-project.org <bioc-devel using r-project.org>; 
> buschmann using b-n-w.org <buschmann using b-n-w.org>
> *Subject:* Re: [Bioc-devel] about deprecate package DNABarcode
> Hi Sun,
>
> Yes! I was about to write the same to you hahaha
>
> It's great news!
>
> Best,
>
> Pedro
>
>
> On Wed, Mar 27, 2024, 15:18 Sun Wenjie <wenjie.sun using curie.fr> wrote:
>
>     Hi Pedro,
>
>     Tilo has responded and is currently updating the DNABarcode package.
>
>     Best,
>     Wenjie
>
>     ________________________________________
>     From: Pedro Sánchez Sánchez <bio.pedro.technology using gmail.com>
>     Sent: Wednesday, March 20, 2024 1:58 PM
>     To: Kern, Lori
>     Cc: Sun Wenjie; bioc-devel using r-project.org
>     Subject: Re: [Bioc-devel] about deprecate package DNABarcode
>
>     WARNING: This email originated from outside of Institut Curie.
>     Please validate the sender's email address before clicking on
>     links or attachments as they may not be safe.
>
>     Hi all,
>
>     I also tried to contact the author on the available email contacts
>     (waiting for response from
>     tilo.buschmann.ac using gmail.com<mailto:tilo.buschmann.ac using gmail.com>;
>     depreciated email
>     tilo.buschmann using izi.fraunhofer.de<mailto:tilo.buschmann using izi.fraunhofer.de>)
>     I found on the internet. If I get a response, I'll let you know.
>
>     It will be a pity if DNABarcodes is depreciated for lacking of
>     maintenance.
>
>     Just in case, it is helpful for someone, I just want to mention
>     there is an apparently similar repository on GitHub with the same
>     goal as DNABarcodes, by other developers and written in
>     Python/Jupyter Notebooks: https://github.com/feldman4/dna-barcodes
>     <https://secure-web.cisco.com/1apD5NMnNtMjEjs9vEqX18MVGxCO8MShxqR-qjMPFVhSwyP0pu91zeYne0Xke-0sY4TwWe9k6enUSTxs7T7NzRPMaF1o7X7Sudv_yBcA7MyqU4Rkr0JysgcZi4NDH-DGNG5NwCWYDuFYcwAZvo3PJxFsYoUs3DuuzjNCF6LTZUCwYx7HbDkI5egJHxtvLW3nLHHxCraI2tTk0Nr9bYwXfbDppHD_2urEZfSlOFri_PBHFt7_j8p0a5YHO-CyIfqLkIee405IJadEV36I3bVHk95UIDY9NfAda54OGyE2Fw8m_4ybIp_Djhw8BEGvmX2f6/https%3A%2F%2Fgithub.com%2Ffeldman4%2Fdna-barcodes>.
>
>     Best,
>
>     Pedro
>
>     El mar, 12 mar 2024 a las 13:18, Kern, Lori via Bioc-devel
>     (<bioc-devel using r-project.org<mailto:bioc-devel using r-project.org>>)
>     escribió:
>     The package is deprecated in devel.  It will remain listed in the
>     next Bioc 3.19 release, but deprecated, and removed from
>     anticipated 3.20.  The package will have up until the fall release
>     (generally late Oct / early Nov) to reinstate before it will be
>     removed.
>
>     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<mailto:bioc-devel-bounces using r-project.org>>
>     on behalf of Sun Wenjie
>     <wenjie.sun using curie.fr<mailto:wenjie.sun using curie.fr>>
>     Sent: Tuesday, March 12, 2024 8:07 AM
>     To: bioc-devel using r-project.org<mailto:bioc-devel using r-project.org>
>     <bioc-devel using r-project.org<mailto:bioc-devel using r-project.org>>
>     Subject: [Bioc-devel] about deprecate package DNABarcode
>
>     Hi Bioconductor core team,
>
>     I saw the package of DNABarcode is listed as to be deprecated.
>
>     I am trying to reach the author. Do you know when will be the
>     deadline?
>
>     Best,
>     Wenjie
>
>     ------------------------------------------
>     Wenjie SUN
>     Postdoctoral researcher
>     UMR168, Curie Institute
>     E-mail: wenjie.sun using curie.fr<mailto:wenjie.sun using curie.fr>
>     Address: batiment Curie, RDC.13A
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