Re: [Bioc-devel] about deprecate package DNABarcode
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 Sent: Wednesday, March 27, 2024 10:23 AM To: Sun Wenjie Cc: Kern, Lori ; bioc-devel@r-project.org ; 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 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 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 (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 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 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>> 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
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 wrote: > Hi Pedro, > > Tilo has responded and is currently updating the DNABarcode package. > > Best, > Wenjie > > > From: Pedro Sánchez Sánchez > Sent: Wednesday, March 20, 2024 1:58 PM > To: Kern, Lori > Cc: Sun Wenjie; 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 tilo.buschmann...@gmail.com>; depreciated email > 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. > > 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>>) 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-boun...@r-project.org>> on behalf of Sun Wenjie < > 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> < > 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> > 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> 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. If you are not the intended recipient(s), or the employee or > agent responsible for the delivery of this message to the intended > recipient(s), you are hereby notified that any disclosure, copying, > distribution, or use of this email message is prohibited. If you have > received this message in error, please notify the sender immediately by > e-mail and delete this email message from your computer. Thank you. > [[alternative HTML version deleted]] > > ___ > Bioc-devel@r-project.org<mailto:Bioc-devel@r-project.org> mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] about deprecate package DNABarcode
Hi Pedro, Tilo has responded and is currently updating the DNABarcode package. Best, Wenjie From: Pedro Sánchez Sánchez Sent: Wednesday, March 20, 2024 1:58 PM To: Kern, Lori Cc: Sun Wenjie; 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>; depreciated email 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. Best, Pedro El mar, 12 mar 2024 a las 13:18, Kern, Lori via Bioc-devel (mailto:bioc-devel@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 mailto:bioc-devel-boun...@r-project.org>> on behalf of Sun Wenjie 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>> 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> 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> 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. If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited. If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you. [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org<mailto:Bioc-devel@r-project.org> mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] about deprecate package DNABarcode
Hi all, I also tried to contact the author on the available email contacts (waiting for response from tilo.buschmann...@gmail.com; depreciated email 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. Best, Pedro El mar, 12 mar 2024 a las 13:18, Kern, Lori via Bioc-devel (< bioc-devel@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 on behalf of Sun > Wenjie > Sent: Tuesday, March 12, 2024 8:07 AM > To: 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 > 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 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. If you are not the intended recipient(s), or the employee or > agent responsible for the delivery of this message to the intended > recipient(s), you are hereby notified that any disclosure, copying, > distribution, or use of this email message is prohibited. If you have > received this message in error, please notify the sender immediately by > e-mail and delete this email message from your computer. Thank you. > [[alternative HTML version deleted]] > > ___ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] about deprecate package DNABarcode
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 on behalf of Sun Wenjie Sent: Tuesday, March 12, 2024 8:07 AM To: 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 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 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. If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited. If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you. [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
