Re: [Bioc-devel] Bioconductor Git Credentials error
Hi Nitesh, I am Ashish Jain, author, and maintainer of the package "TissueEnrich". I am also facing a similar issue as I am not able to login to the BiocCredentials website. I need to update my package with some fixes. Can you please also look into this? Regards, Ashish Jain On Fri, Apr 2, 2021 at 8:48 AM Nitesh Turaga wrote: > Hi Raman, > > You should have access to the package. Please check again. > > Best, > > Nitesh > > From: raman sethi > Date: Friday, April 2, 2021 at 1:38 AM > To: Nitesh Turaga , Chen Jinmiao < > chen_jinm...@immunol.a-star.edu.sg> > Subject: Re: [Bioc-devel] Bioconductor Git Credentials error > > Hi Nitesh, > > We have activated the account using the email ID : ramanseth...@gmail.com > <mailto:ramanseth...@gmail.com> and added SSH keys to the account. > > We want to submit the code of the R package cytofkit2 ( > https://github.com/raman91/cytofkit2) to Bioconductor which was modified > from the package : https://github.com/JinmiaoChenLab/cytofkit2 > > The author of the Package cytofkit (Dr. Chen Jinmiao) is copied in this > email as per your request. > > Thank you > > Best Regards > Raman > > > > On Wed, Mar 31, 2021 at 10:46 PM Nitesh Turaga <mailto:nturaga.b...@gmail.com>> wrote: > Hi Raman, > > I’ve created your own BiocCredentials account for you now. > > Email: ramanseth...@gmail.com<mailto:ramanseth...@gmail.com> > > Please activate the account, add your Github username or SSH keys. ( > https://git.bioconductor.org/BiocCredentials/account_activation) > > Once you know which packages you want access to, let me know and please > copy on the email the authors of those packages. > > You should be accessing these packages with your own SSH keys and > Credentials account. > > Best, > > Nitesh > > > > From: raman sethi mailto:ramanseth...@gmail.com>> > Date: Wednesday, March 31, 2021 at 6:49 AM > To: Nitesh Turaga mailto:nturaga.b...@gmail.com>> > Subject: Re: [Bioc-devel] Bioconductor Git Credentials error > > Hi Nitesh, > > Sorry for the late reply. > I am running gitch fetch --all but i am getting an error message: > > g...@git.bioconductor.org<mailto:g...@git.bioconductor.org>: Permission > denied (publickey). > fatal: Could not read from remote repository. > > Please make sure you have the correct access rights > and the repository exists. > error: Could not fetch upstream > > Can you please tell me how can i solve this problem? > > Thank you > > Best Regards > Raman > > On Mon, Mar 22, 2021 at 8:23 PM Nitesh Turaga <mailto:nturaga.b...@gmail.com>> wrote: > Hi, > > You cannot have two maintainers to a package. We operate under the > assumption that there is a single maintainer per package. The user that has > access to the package is “j.chen2”., there are no SSH keys with that > username so there is no access. I’ve deleted the other account with > username “raman..” under the same email as “j.chen2”. > > The best way forward is to add keys under j.chen2 and get access to the > package. > > https://github.com/JinmiaoChenLab/cytofkit2/blob/master/DESCRIPTION#L10 > > Take a look at this link: > http://bioconductor.org/developers/package-guidelines/#description > > > “Only one person should be listed as the Maintainer to ensure a single > point of contact. This person by default will have commit access to the git > repository on git.bioconductor.org<http://git.bioconductor.org>. Commit > access can be given to other developers by request on the bioc-devel > mailing list. Another option is to add collaborators to the github > repository. This approach enables development by many but restricts push > access to git.bioconductor.org.” > > > Best, > > Nitesh > > > > From: raman sethi mailto:ramanseth...@gmail.com>> > Date: Monday, March 22, 2021 at 2:40 AM > To: Nitesh Turaga mailto:nturaga.b...@gmail.com>> > Cc: Bioc-devel mailto:bioc-devel@r-project.org>> > Subject: Re: [Bioc-devel] Bioconductor Git Credentials error > > Hi Nitesh, > > Our account is activated already. > > Thank you > > Best Regards > Raman > > > On Sat, Mar 20, 2021 at 10:31 PM Nitesh Turaga <mailto:nturaga.b...@gmail.com>> wrote: > Did you activate your account first? > > > > From: raman sethi mailto:ramanseth...@gmail.com>> > Date: Friday, March 19, 2021 at 10:33 PM > To: Nitesh Turaga mailto:nturaga.b...@gmail.com>> > Cc: Bioc-devel mailto:bioc-devel@r-project.org>> > Subject: Re: [Bioc-devel] Bioconductor Git Credentials error > > Hi Nitesh, > > I am using the URL :
[Bioc-devel] Not able to login or reset password on BiocCredentials website
Hi All, I am Ashish Jain, author, and maintainer of the package "TissueEnrich". I mistakenly lost the SSH key required for accessing the Bioconductor repository. I tried to log in to the BiocCredentials website to access/update it but it seems like my email (j...@iastate.edu) is not linked to the repository. Can someone please help me with this as I need to push some fixes to the package. -- Regards, Ashish Jain Ph +1-317-529-7973 [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Fwd: TissueEnrich problems reported in the Multiple platform build/check report for BioC 3.9
Hi Lori, Thank you for your help. I was able to reproduce the issue locally after updating the packages. I updated the vignette with the changes and pushed it on both RELEASE_3_9 and the development (3_10) branches. Again thank you for your help! Regards, Ashish Jain On Tue, Sep 17, 2019 at 7:06 AM Shepherd, Lori < lori.sheph...@roswellpark.org> wrote: > I am able to reproduce the ERROR. It seems to be an issue of trying to > subset. > > > head(exp %>% gather(Tissue)) Tissue value > 1 Adipose Tissue 1.63226821549951 > 2 Adipose Tissue 0 > 3 Adipose Tissue 0 > 4 Adipose Tissue 0.485426827170242 > 5 Adipose Tissue 0.584962500721156 > 6 Adipose Tissue 3.05311133645956> head(exp %>% > gather(Tissue=1:(ncol(exp)-1)))Error: 1 components of `...` had unexpected > names. > > We detected these problematic arguments: > * `Tissue` > > Did you misspecify an argument?Call `rlang::last_error()` to see a backtrace > > > > > You can see if there were any recent changes to package you depend on that > could have caused this. A package you depend on may have changed their > functionality. I needed to update packages (with BiocManager::install() > update all ) in order to reproduce. > > Cheers, > > 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 Ashish > Jain > *Sent:* Monday, September 16, 2019 3:08 PM > *To:* bioc-devel@r-project.org > *Subject:* [Bioc-devel] Fwd: TissueEnrich problems reported in the > Multiple platform build/check report for BioC 3.9 > > Hi All, > > I just got the message that my package is giving an error during the build > process on Bioconductor build server. I saw the logs and found it is > failing while building the vignette. I am not sure why it's happening as I > have not updated the package since release and it was building without any > errors. Can someone look into this? > > Regards, > Ashish Jain > > -- Forwarded message - > From: > Date: Mon, Sep 16, 2019 at 1:59 PM > Subject: TissueEnrich problems reported in the Multiple platform > build/check report for BioC 3.9 > To: > > > [This is an automatically generated email. Please don't reply.] > > Hi TissueEnrich maintainer, > > According to the Multiple platform build/check report for BioC 3.9, > the TissueEnrich package has the following problem(s): > > o ERROR for 'R CMD build' on malbec2. See the details here: > > > https://master.bioconductor.org/checkResults/3.9/bioc-LATEST/TissueEnrich/malbec2-buildsrc.html > > Please take the time to address this by committing and pushing > changes to your package at git.bioconductor.org > > Notes: > > * This was the status of your package at the time this email was sent to > you. > Given that the online report is updated daily (in normal conditions) > you > could see something different when you visit the URL(s) above, > especially if > you do so several days after you received this email. > > * It is possible that the problems reported in this report are false > positives, > either because another package (from CRAN or Bioconductor) breaks your > package (if yours depends on it) or because of a Build System problem. > If this is the case, then you can ignore this email. > > * Please check the report again 24h after you've committed your changes > to the > package and make sure that all the problems have gone. > > * If you have questions about this report or need help with the > maintenance of your package, please use the Bioc-devel mailing list: > > https://bioconductor.org/help/mailing-list/ > > (all package maintainers are requested to subscribe to this list) > > For immediate notification of package build status, please > subscribe to your package's RSS feed. Information is at: > > https://bioconductor.org/developers/rss-feeds/ > > Thanks for contributing to the Bioconductor project! > > > > -- > Regards, > Ashish Jain > Ph.D. Candidate > Bioinformatics and Computational Biology > Iowa State University > Ph +1-317-529-7973 > Website: *https://ashishjain1988.github.io > <https://ashishjain1988.github.io/>/* > > [[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 privil
[Bioc-devel] Fwd: TissueEnrich problems reported in the Multiple platform build/check report for BioC 3.9
Hi All, I just got the message that my package is giving an error during the build process on Bioconductor build server. I saw the logs and found it is failing while building the vignette. I am not sure why it's happening as I have not updated the package since release and it was building without any errors. Can someone look into this? Regards, Ashish Jain -- Forwarded message - From: Date: Mon, Sep 16, 2019 at 1:59 PM Subject: TissueEnrich problems reported in the Multiple platform build/check report for BioC 3.9 To: [This is an automatically generated email. Please don't reply.] Hi TissueEnrich maintainer, According to the Multiple platform build/check report for BioC 3.9, the TissueEnrich package has the following problem(s): o ERROR for 'R CMD build' on malbec2. See the details here: https://master.bioconductor.org/checkResults/3.9/bioc-LATEST/TissueEnrich/malbec2-buildsrc.html Please take the time to address this by committing and pushing changes to your package at git.bioconductor.org Notes: * This was the status of your package at the time this email was sent to you. Given that the online report is updated daily (in normal conditions) you could see something different when you visit the URL(s) above, especially if you do so several days after you received this email. * It is possible that the problems reported in this report are false positives, either because another package (from CRAN or Bioconductor) breaks your package (if yours depends on it) or because of a Build System problem. If this is the case, then you can ignore this email. * Please check the report again 24h after you've committed your changes to the package and make sure that all the problems have gone. * If you have questions about this report or need help with the maintenance of your package, please use the Bioc-devel mailing list: https://bioconductor.org/help/mailing-list/ (all package maintainers are requested to subscribe to this list) For immediate notification of package build status, please subscribe to your package's RSS feed. Information is at: https://bioconductor.org/developers/rss-feeds/ Thanks for contributing to the Bioconductor project! -- Regards, Ashish Jain Ph.D. Candidate Bioinformatics and Computational Biology Iowa State University Ph +1-317-529-7973 Website: *https://ashishjain1988.github.io <https://ashishjain1988.github.io/>/* [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] "TissueEnrich" is failing on windows server in the BioC 3.7 build
Hi All, My package "TissueEnrich" which was building and installing fine on all the servers is suddenly failed on the windows server in today's build report. The report says that * checking for file 'TissueEnrich/DESCRIPTION' ... OK * preparing 'TissueEnrich': * checking DESCRIPTION meta-information ... OK * installing the package to build vignettes * creating vignettes ... ERROR Error: processing vignette 'TissueEnrich.Rmd' failed with diagnostics: undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_detect, st Execution halted Anybody knows why this is happening? -- Regards, Ashish Jain BCB-Graduate Student Iowa State University Ph +1-317-529-7973 Website: *https://ashishjain1988.github.io/ <https://ashishjain1988.github.io/>* Github: https://github.com/ashishjain1988/ [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Transition from Google Sheet to Web App
Hi Valerie, Thank you for this information. It is the email of my PI. I will tell her to register on this website. Again thank you for the information. Regards, Ashish Jain On Fri, Apr 20, 2018 at 3:26 PM, Obenchain, Valerie < valerie.obench...@roswellpark.org> wrote: > Hi Ashish Jain, > > The email you registered with the Google Sheet was 'ge...@iastate.edu'. > > The email in the DESCRIPTION file often goes stale. If a maintainer > registered with the Google Sheet with an address different from DESCRIPTION > we performed several checks. If the username provided in the Google Sheet > matched the config and keys we have on file, it was assumed the email in > the Google Sheet was more current. > > Is ge...@iastate.edu an email for you or no? > > Valerie > > > > On 04/20/2018 01:02 PM, Ashish Jain wrote: > > Hi, > > I am the developer of the "TissueEnrich" package and I tried to activate > my account using my email id in DESCRIPTION file (j...@iastate.edu) but > the site is saying "j...@iastate.edu is not associated with a maintainer > of a Bioconductor package". Can you please help me with this. > > Regards, > Ashish Jain > > On Wed, Apr 18, 2018 at 1:05 PM, Turaga, Nitesh < > nitesh.tur...@roswellpark.org> wrote: > >> The Web App for managing SSH keys is now available at >> >> https://git.bioconductor.org/BiocCredentials/ >> >> Accounts have been created for all package maintainers. Note the central >> identifier, i.e., how you login is your email. This email was taken from >> the DESCRIPTION of your package or the Google Sheet if you registered a key >> there. >> >> When you first visit the App you'll need to activate your account. An >> activation link will be sent to your email. Once your account is activated >> you can login. Trying to login without activation will lead to an error. >> >> Let us know if you have any questions or problems. >> >> Best Regards, >> >> >> >> > On Apr 18, 2018, at 8:56 AM, Obenchain, Valerie >> <valerie.obench...@roswellpark.org> wrote: >> > >> > This transition will start at 9am EST today. We'll post back when it's >> done. >> > >> > Valerie >> > >> > >> > On 04/17/2018 10:27 AM, Obenchain, Valerie wrote: >> > >> > Hi developers, >> > >> > Tomorrow we are bringing a web app online to help with the management >> of SSH keys. The app will replace the Google Sheet currently used to add >> keys. Through the web interface you'll be able to add keys and change your >> email or github username. There is also an option to see what packages you >> have access to. >> > >> > Using the app is not a requirement. It's intended to help package >> authors get setup with keys and access to their package in the Bioconductor >> git repository. Those of you already set up with keys and access may never >> need to use it. >> > >> > Tomorrow, April 18, we'll have downtime from 9-11am EST while we take >> down the Google Sheet and bring up the app. >> > >> > Thanks. >> > >> > Valerie and Nitesh >> > >> > >> > 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 >> > >> > >> > >> > >> > >> > 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
Re: [Bioc-devel] Transition from Google Sheet to Web App
Hi, I am the developer of the "TissueEnrich" package and I tried to activate my account using my email id in DESCRIPTION file (j...@iastate.edu) but the site is saying "j...@iastate.edu is not associated with a maintainer of a Bioconductor package". Can you please help me with this. Regards, Ashish Jain On Wed, Apr 18, 2018 at 1:05 PM, Turaga, Nitesh < nitesh.tur...@roswellpark.org> wrote: > The Web App for managing SSH keys is now available at > > https://git.bioconductor.org/BiocCredentials/ > > Accounts have been created for all package maintainers. Note the central > identifier, i.e., how you login is your email. This email was taken from > the DESCRIPTION of your package or the Google Sheet if you registered a key > there. > > When you first visit the App you'll need to activate your account. An > activation link will be sent to your email. Once your account is activated > you can login. Trying to login without activation will lead to an error. > > Let us know if you have any questions or problems. > > Best Regards, > > > > > On Apr 18, 2018, at 8:56 AM, Obenchain, Valerie > > <valerie.obench...@roswellpark.org> > wrote: > > > > This transition will start at 9am EST today. We'll post back when it's > done. > > > > Valerie > > > > > > On 04/17/2018 10:27 AM, Obenchain, Valerie wrote: > > > > Hi developers, > > > > Tomorrow we are bringing a web app online to help with the management of > SSH keys. The app will replace the Google Sheet currently used to add keys. > Through the web interface you'll be able to add keys and change your email > or github username. There is also an option to see what packages you have > access to. > > > > Using the app is not a requirement. It's intended to help package > authors get setup with keys and access to their package in the Bioconductor > git repository. Those of you already set up with keys and access may never > need to use it. > > > > Tomorrow, April 18, we'll have downtime from 9-11am EST while we take > down the Google Sheet and bring up the app. > > > > Thanks. > > > > Valerie and Nitesh > > > > > > 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 > > > > > > > > > > > > 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 > > > > 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 > -- Regards, Ashish Jain BCB-Graduate Student Iowa State University Ph +1-317-529-7973 Website: *https://ashishjain1988.github.io/ <https://ashishjain1988.github.io/>* Github: https://github.com/ashishjain1988/ [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] "TissueEnrich" is missing in the BioC 3.7 build report
Hi Martin, Thank you for the reply. I think I accidently updated the DESCRIPTION file. I will fix it now. Regards, Ashish Jain On Sun, Apr 15, 2018 at 4:35 PM, Martin Morgan < martin.mor...@roswellpark.org> wrote: > I made a clean 'read only' clone of your git repository > > git$ git clone https://git.bioconductor.org/packages/TissueEnrich > > then tried to build it > > git$ Rdev CMD build TissueEnrich > Bioconductor version 3.7 (BiocInstaller 1.29.6), ?biocLite for help > * checking for file 'TissueEnrich/DESCRIPTION' ... OK > * preparing 'TissueEnrich': > * checking DESCRIPTION meta-information ... ERROR > Authors@R field gives more than one person with maintainer role: > Ashish Jain <j...@iastate.edu> [aut, cre] > Geetu Tuteja <ge...@iastate.edu> [aut, cre] > > See section 'The DESCRIPTION file' in the 'Writing R Extensions' > manual. > > Have you tried to correct this? > > Martin > > On 04/15/2018 05:30 PM, Ashish Jain wrote: > >> Hi All, >> >> I am the developer of the "TissueEnrich" package which got accepted 6 days >> back. After the acceptance, the package was included in the Bioc 3.7 build >> and I was able to see it in the build report. But suddenly for last two >> days, it is not there in the Bioc 3.7 build report. Can somebody help me >> with this? >> >> > > 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. > -- Regards, Ashish Jain BCB-Graduate Student Iowa State University Ph +1-317-529-7973 Website: *https://ashishjain1988.github.io/ <https://ashishjain1988.github.io/>* Github: https://github.com/ashishjain1988/ [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] "TissueEnrich" is missing in the BioC 3.7 build report
Hi All, I am the developer of the "TissueEnrich" package which got accepted 6 days back. After the acceptance, the package was included in the Bioc 3.7 build and I was able to see it in the build report. But suddenly for last two days, it is not there in the Bioc 3.7 build report. Can somebody help me with this? -- Regards, Ashish Jain BCB-Graduate Student Iowa State University Ph +1-317-529-7973 Website: *https://ashishjain1988.github.io/ <https://ashishjain1988.github.io/>* Github: https://github.com/ashishjain1988/ [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
