[Bioc-devel] about deprecate package DNABarcode

[Kern, Lori]

Thank you for letting us know.  We will undeprecate DNABarcodes in 3.19 and readd to 3.20


Lori Shepherd - Kern

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

________________________________
From: Tilo Buschmann <buschmann using b-n-w.org>
Sent: Friday, September 20, 2024 5:27 AM
To: Kern, Lori <Lori.Shepherd using RoswellPark.org>; Pedro S�nchez S�nchez <bio.pedro.technology using gmail.com>; Sun Wenjie <wenjie.sun using curie.fr>
Cc: bioc-devel using r-project.org <bioc-devel using r-project.org>; maintainer using bioconductor.org <maintainer using bioconductor.org>
Subject: Re: [Bioc-devel] about deprecate package DNABarcode


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 S�nchez S�nchez <bio.pedro.technology using gmail.com><mailto:bio.pedro.technology using gmail.com>
Sent: Wednesday, March 27, 2024 10:23 AM
To: Sun Wenjie <wenjie.sun using curie.fr><mailto:wenjie.sun using curie.fr>
Cc: Kern, Lori <Lori.Shepherd using RoswellPark.org><mailto:Lori.Shepherd using RoswellPark.org>; 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>; buschmann using b-n-w.org<mailto:buschmann using b-n-w.org> <buschmann using b-n-w.org><mailto: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<mailto:wenjie.sun using curie.fr>> wrote:
Hi Pedro,

Tilo has responded and is currently updating the DNABarcode package.

Best,
Wenjie

________________________________________
From: Pedro S�nchez S�nchez <bio.pedro.technology using gmail.com<mailto: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<mailto: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><mailto: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><mailto: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><mailto:bioc-devel using r-project.org<mailto:bioc-devel using r-project.org>>>) escribi�:
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><mailto: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><mailto:wenjie.sun using curie.fr<mailto:wenjie.sun using curie.fr>>>
Sent: Tuesday, March 12, 2024 8:07 AM
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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><mailto:wenjie.sun using curie.fr<mailto:wenjie.sun using curie.fr>>
Address: batiment Curie, RDC.13A
11 rue Pierre et Marie Curie, 75005 Paris
https://secure-web.cisco.com/1-TBJw4o6EGDXK_14o3XCIp7DQhMLTaxvVR4NCL9q9sGYrycpujC_OYkx7ortrnjf5crYpYXyRsFEcpldkHYYLTfw-V9oZUKv8flhupsI5LV_JzcWwDb1FnvBDTYwcj0cXxmA3GNJQVF3Mnc1QnR55FA-_sO9AKIMHbDHD2U1y9HvFChc3nLydpoM4IZQhFrkC01Z7BtNAdt0gmfJzyF8AM4qlM40FR8g5KAPURr03QM4ukAWrszSyzsi9jEVmrUnL0Tjcsf1thPL1wOBupAU-UZtzsKkLIae_8gglI6k6W8kBMlUjp2SvfS4iEIah835/https%3A%2F%2Fcurie.fr%2Fequipe%2Fperie

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