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 <buschm...@b-n-w.org> Sent: Friday, September 20, 2024 5:27 AM To: Kern, Lori <lori.sheph...@roswellpark.org>; Pedro S�nchez S�nchez <bio.pedro.technol...@gmail.com>; Sun Wenjie <wenjie....@curie.fr> Cc: bioc-devel@r-project.org <bioc-devel@r-project.org>; maintai...@bioconductor.org <maintai...@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.technol...@gmail.com><mailto:bio.pedro.technol...@gmail.com> Sent: Wednesday, March 27, 2024 10:23 AM To: Sun Wenjie <wenjie....@curie.fr><mailto:wenjie....@curie.fr> Cc: Kern, Lori <lori.sheph...@roswellpark.org><mailto:lori.sheph...@roswellpark.org>; bioc-devel@r-project.org<mailto:bioc-devel@r-project.org> <bioc-devel@r-project.org><mailto:bioc-devel@r-project.org>; buschm...@b-n-w.org<mailto:buschm...@b-n-w.org> <buschm...@b-n-w.org><mailto:buschm...@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....@curie.fr<mailto:wenjie....@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.technol...@gmail.com<mailto:bio.pedro.technol...@gmail.com>> Sent: Wednesday, March 20, 2024 1:58 PM To: Kern, Lori Cc: Sun Wenjie; bioc-devel@r-project.org<mailto:bioc-devel@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...@gmail.com<mailto:tilo.buschmann...@gmail.com><mailto:tilo.buschmann...@gmail.com<mailto:tilo.buschmann...@gmail.com>>; depreciated email tilo.buschm...@izi.fraunhofer.de<mailto:tilo.buschm...@izi.fraunhofer.de><mailto:tilo.buschm...@izi.fraunhofer.de<mailto:tilo.buschm...@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@r-project.org<mailto:bioc-devel@r-project.org><mailto:bioc-devel@r-project.org<mailto:bioc-devel@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-boun...@r-project.org<mailto:bioc-devel-boun...@r-project.org><mailto:bioc-devel-boun...@r-project.org<mailto:bioc-devel-boun...@r-project.org>>> on behalf of Sun Wenjie <wenjie....@curie.fr<mailto:wenjie....@curie.fr><mailto:wenjie....@curie.fr<mailto:wenjie....@curie.fr>>> Sent: Tuesday, March 12, 2024 8:07 AM To: bioc-devel@r-project.org<mailto:bioc-devel@r-project.org><mailto:bioc-devel@r-project.org<mailto:bioc-devel@r-project.org>> <bioc-devel@r-project.org<mailto:bioc-devel@r-project.org><mailto:bioc-devel@r-project.org<mailto:bioc-devel@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....@curie.fr<mailto:wenjie....@curie.fr><mailto:wenjie....@curie.fr<mailto:wenjie....@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 _______________________________________________ Bioc-devel@r-project.org<mailto:Bioc-devel@r-project.org><mailto:Bioc-devel@r-project.org<mailto:Bioc-devel@r-project.org>> mailing list https://secure-web.cisco.com/1l6kli-5ER6TfFRoWON7eg605W9-aPQ1auinsEup1uN5OFQqRFc_QRRlrkmssHncngEABAwXz4PYezr9ontykNdw3OQlPlaKaQJXx9J_ey5JecbnynELh3K-b_GgnpbL94Du22Rl80OCRrkiU3mGuPhIqnUgFxA9Bo9QsZmZHs3u4yuLvZK9QVQxgvloJXJO8Z0H8rBvABpOzApweEY8hv8ovHZBVkWCCPX1r-yGlLt9G_Y1GJvdqruefoEmWpUBxngKD3odX73chnPmSKwS0X31BlZezoSG7BeE5KK_SR8tKGHjf8oxPHoNBTC1WTP6x/https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel This email message may contain legally privileged and/or confidential information. 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