Re: [Bioc-devel] Can not push to bioconductor! please help me!
Dear BioMedR Maintainer I'm sorry that you never responded to our many earlier emails and notifications. I recommend checking your email systems to make sure emails from Bioconductor and RoswellPark are not being blocked or spammed. To address your first point: Your github repository is not what we use at Bioconductor as the canonical location. That is your personal local repository. When the package was accepted you received instructions for updating the package in Bioconductor using svn. Since then, Bioconductor has moved to git version control, which was announced multiple times with instructions on how to update package. We posed FAQs and instructions for git on the website. http://bioconductor.org/developers/how-to/git/ It is your responsibilty to make sure your package works with any dependencies you required and that it builds on our Bioconductor systems (not your independent systems) http://bioconductor.org/checkResults/ . Your package has already been removed from Bioconductor following the end of life procedure for packages found at https://www.bioconductor.org/developers/package-end-of-life/ Please resubmit to the tracker for re-review and inclusion in Bioc 3.8 https://github.com/Bioconductor/Contributions/issues Lori Shepherd Bioconductor Core Team Roswell Park Cancer Institute Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 From: Zhu MF Sent: Wednesday, April 18, 2018 2:04:40 AM To: Shepherd, Lori Cc: bioc-devel@r-project.org Subject: Re:Re: [Bioc-devel] Can not push to bioconductor! please help me! Dear sir, Thank you for your letter. Firstly, Actually, I don't know why does the content in GitHub and Bioconductor are not the same when the package was firstly releaed in bioconductor? In the GitHub we have removed the error file since the first release. Then, the tips of the checked error was caused by the expired function of rcdk not BioMedR. The error is in the unitest that actually worked well in other cases, so in our local machine, this error have not been triggerd in the past one year, so we don't know what happened. So, could you help us simple the review process and include in the Bioc 3.7 release? Thank you very much! At 2018-04-17 01:47:51, "Shepherd, Lori" mailto:lori.sheph...@roswellpark.org>> wrote: Dear BioMedR maintainer, Unfortunately BioMedR was removed from Bioconductor as of Release 3.6 (last Oct). We reached out several times before the 3.6 release as your package had been failing since early July 2017. Part of the Bioconductor guidelines require that packages are actively maintained and fixed in a timely manner. Packages are built daily indicating if there are ERROR's or WARNING's and should be occasionally checked: http://bioconductor.org/checkResults/ Besides emailing you privately several times, it was also posted before the release on the support site and devel mailing list (bioc-devel@r-project.org<mailto:bioc-devel@r-project.org>) links given below - giving time to respond before officially being deprecated. And you would have recieved email notifications from bbs-nore...@bioconductor.org<mailto:bbs-nore...@bioconductor.org> indicating build failures. https://support.bioconductor.org/p/100984/ https://support.bioconductor.org/p/100199/ https://stat.ethz.ch/pipermail/bioc-devel/2017-September/011522.html As you remained unresponsive and the package remained broken it began the deprecation and end-of-life process. If you would like to revive the package, it would need to go through the package review process again and at this point is too late to be included in the Bioc 3.7 release. You can have it reviewed and accepted to be re-included in Bioc 3.8 later this year. Lori Shepherd Bioconductor Core Team Roswell Park Cancer Institute Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 From: Bioc-devel mailto:bioc-devel-boun...@r-project.org>> on behalf of Zhu MF mailto:wind2...@163.com>> Sent: Monday, April 16, 2018 12:32:10 PM To: bioc-devel@r-project.org<mailto:bioc-devel@r-project.org> Subject: [Bioc-devel] Can not push to bioconductor! please help me! dear sir: contents in GitHub and that in bioconductor are not the same. I want to update the package to follow the contents in github, but falied: git remote -v origin g...@github.com<mailto:g...@github.com>:wind22zhu/BioMedR.git (fetch) origin g...@github.com<mailto:g...@github.com>:wind22zhu/BioMedR.git (push) upstream g...@git.bioconductor.org<mailto:g...@git.bioconductor.org>:packages/BioMedR.git (fetch) upstream g...@git.bioconductor.org<mailto:g...@git.bioconductor.org>:packages/BioMedR.git (push) $ git push upstream master Enter passphrase for key '/c/Users/ifyo
Re: [Bioc-devel] Can not push to bioconductor! please help me!
Dear sir, Thank you for your letter. Firstly, Actually, I don't know why does the content in GitHub and Bioconductor are not the same when the package was firstly releaed in bioconductor? In the GitHub we have removed the error file since the first release. Then, the tips of the checked error was caused by the expired function of rcdk not BioMedR. The error is in the unitest that actually worked well in other cases, so in our local machine, this error have not been triggerd in the past one year, so we don't know what happened. So, could you help us simple the review process and include in the Bioc 3.7 release? Thank you very much! At 2018-04-17 01:47:51, "Shepherd, Lori" wrote: Dear BioMedR maintainer, Unfortunately BioMedR was removed from Bioconductor as of Release 3.6 (last Oct). We reached out several times before the 3.6 release as your package had been failing since early July 2017. Part of the Bioconductor guidelines require that packages are actively maintained and fixed in a timely manner. Packages are built daily indicating if there are ERROR's or WARNING's and should be occasionally checked: http://bioconductor.org/checkResults/ Besides emailing you privately several times, it was also posted before the release on the support site and devel mailing list (bioc-devel@r-project.org) links given below - giving time to respond before officially being deprecated. And you would have recieved email notifications from bbs-nore...@bioconductor.org indicating build failures. https://support.bioconductor.org/p/100984/ https://support.bioconductor.org/p/100199/ https://stat.ethz.ch/pipermail/bioc-devel/2017-September/011522.html As you remained unresponsive and the package remained broken it began the deprecation and end-of-life process. If you would like to revive the package, it would need to go through the package review process again and at this point is too late to be included in the Bioc 3.7 release. You can have it reviewed and accepted to be re-included in Bioc 3.8 later this year. Lori Shepherd Bioconductor Core Team Roswell Park Cancer Institute Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 From: Bioc-devel on behalf of Zhu MF Sent: Monday, April 16, 2018 12:32:10 PM To:bioc-devel@r-project.org Subject: [Bioc-devel] Can not push to bioconductor! please help me! dear sir: contents in GitHub and that in bioconductor are not the same. I want to update the package to follow the contents in github, but falied: git remote -v origin g...@github.com:wind22zhu/BioMedR.git (fetch) origin g...@github.com:wind22zhu/BioMedR.git (push) upstream g...@git.bioconductor.org:packages/BioMedR.git (fetch) upstream g...@git.bioconductor.org:packages/BioMedR.git (push) $ git push upstream master Enter passphrase for key '/c/Users/ifyoung/.ssh/id_rsa': FATAL: W any packages/BioMedR wind22zhu DENIED by fallthru (or you mis-spelled the reponame) fatal: Could not read from remote repository. Please make sure you have the correct access rights and the repository exists. $ ssh -T g...@git.bioconductor.org R packages/BioMedR No WRITE(W) permissions? Why? Can you help me ? I have been stucked here for several days! [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-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
Re: [Bioc-devel] Can not push to bioconductor! please help me!
Dear BioMedR maintainer, Unfortunately BioMedR was removed from Bioconductor as of Release 3.6 (last Oct). We reached out several times before the 3.6 release as your package had been failing since early July 2017. Part of the Bioconductor guidelines require that packages are actively maintained and fixed in a timely manner. Packages are built daily indicating if there are ERROR's or WARNING's and should be occasionally checked: http://bioconductor.org/checkResults/ Besides emailing you privately several times, it was also posted before the release on the support site and devel mailing list (bioc-devel@r-project.org) links given below - giving time to respond before officially being deprecated. And you would have recieved email notifications from bbs-nore...@bioconductor.org indicating build failures. https://support.bioconductor.org/p/100984/ https://support.bioconductor.org/p/100199/ https://stat.ethz.ch/pipermail/bioc-devel/2017-September/011522.html As you remained unresponsive and the package remained broken it began the deprecation and end-of-life process. If you would like to revive the package, it would need to go through the package review process again and at this point is too late to be included in the Bioc 3.7 release. You can have it reviewed and accepted to be re-included in Bioc 3.8 later this year. Lori Shepherd Bioconductor Core Team Roswell Park Cancer Institute Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 From: Bioc-devel on behalf of Zhu MF Sent: Monday, April 16, 2018 12:32:10 PM To: bioc-devel@r-project.org Subject: [Bioc-devel] Can not push to bioconductor! please help me! dear sir: contents in GitHub and that in bioconductor are not the same. I want to update the package to follow the contents in github, but falied: git remote -v origin g...@github.com:wind22zhu/BioMedR.git (fetch) origin g...@github.com:wind22zhu/BioMedR.git (push) upstream g...@git.bioconductor.org:packages/BioMedR.git (fetch) upstream g...@git.bioconductor.org:packages/BioMedR.git (push) $ git push upstream master Enter passphrase for key '/c/Users/ifyoung/.ssh/id_rsa': FATAL: W any packages/BioMedR wind22zhu DENIED by fallthru (or you mis-spelled the reponame) fatal: Could not read from remote repository. Please make sure you have the correct access rights and the repository exists. $ ssh -T g...@git.bioconductor.org R packages/BioMedR No WRITE(W) permissions? Why? Can you help me ? I have been stucked here for several days! [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-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
Re: [Bioc-devel] Can not push to bioconductor! please help me!
Hi Zhu, You submitted your keys with the wrong username. Please use your SVN ID “m.zhu” and resubmit Best, Nitesh > On Apr 16, 2018, at 12:32 PM, Zhu MF wrote: > > dear sir: > > > contents in GitHub and that in bioconductor are not the same. I want to > update the package to follow the contents in github, but falied: > > > git remote -v > origin g...@github.com:wind22zhu/BioMedR.git (fetch) > origin g...@github.com:wind22zhu/BioMedR.git (push) > upstream g...@git.bioconductor.org:packages/BioMedR.git (fetch) > upstream g...@git.bioconductor.org:packages/BioMedR.git (push) > > > > > $ git push upstream master > Enter passphrase for key '/c/Users/ifyoung/.ssh/id_rsa': > FATAL: W any packages/BioMedR wind22zhu DENIED by fallthru > (or you mis-spelled the reponame) > fatal: Could not read from remote repository. > Please make sure you have the correct access rights > and the repository exists. > > > > > > > $ ssh -T g...@git.bioconductor.org > > > > > R packages/BioMedR > > > No WRITE(W) permissions? > Why? > Can you help me ? I have been stucked here for several days! > [[alternative HTML version deleted]] > > ___ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-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. ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] Can not push to bioconductor! please help me!
dear sir: contents in GitHub and that in bioconductor are not the same. I want to update the package to follow the contents in github, but falied: git remote -v origin g...@github.com:wind22zhu/BioMedR.git (fetch) origin g...@github.com:wind22zhu/BioMedR.git (push) upstream g...@git.bioconductor.org:packages/BioMedR.git (fetch) upstream g...@git.bioconductor.org:packages/BioMedR.git (push) $ git push upstream master Enter passphrase for key '/c/Users/ifyoung/.ssh/id_rsa': FATAL: W any packages/BioMedR wind22zhu DENIED by fallthru (or you mis-spelled the reponame) fatal: Could not read from remote repository. Please make sure you have the correct access rights and the repository exists. $ ssh -T g...@git.bioconductor.org R packages/BioMedR No WRITE(W) permissions? Why? Can you help me ? I have been stucked here for several days! [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel