I think I have successfully pushed my package files with version 1.9.1 to both *Bioconductor* and GitHub repositories, and repeated for the release branch with version 1.8.1. So what next I should do to make my updated package available to users? Thank you again for all your help!
Best wishes, Tingting On Thu, Jan 25, 2018 at 1:58 PM, Shepherd, Lori < lori.sheph...@roswellpark.org> wrote: > So you are missing the upstream remote. I'm not exactly sure how it got > deleted and how you have been able to push to master. > > It looks like you have created a github repository for your package and > should be following > > Create a new GitHub repository tutorial: > > > > http://bioconductor.org/developers/how-to/git/maintain-github-bioc/ > > > using origin will push/pull to your github repository > > using upstream (once it is added) will push/pull to our > git.bioconductor.org server > > > You'll want to pick up the above page at step 6 for adding the upstream > remote. > > > Cheers, > > > > Lori Shepherd > > Bioconductor Core Team > > Roswell Park Cancer Institute > > Department of Biostatistics & Bioinformatics > > Elm & Carlton Streets > > Buffalo, New York 14263 > ------------------------------ > *From:* Zhai, Tingting <tingting.z...@uky.edu> > *Sent:* Thursday, January 25, 2018 1:47:51 PM > *To:* Shepherd, Lori > *Cc:* Martin Morgan; Turaga, Nitesh > > *Subject:* Re: [Bioc-devel] NanoStringDiff package update > > > the results of > > > git remote -v : > > > origin g...@github.com:tingtina/NanoStringDiff.git (fetch) > > origin g...@github.com:tingtina/NanoStringDiff.git (push) > > > > I'm trying to change the version on the master branch to 1.9.1. > > > Thanks, > > Tingting > > On Thu, Jan 25, 2018 at 1:26 PM, Shepherd, Lori < > lori.sheph...@roswellpark.org> wrote: > > Can you please send the results of > > > git remote -v > > > > Also please note: > > > The version on the master branch (devel) should be 1.9.1 > > > The 1.8.1 will be for RELEASE_3_6 > > > Versions are package_x.y.z the y in devel is always odd, y in release > is always even, and devel y > release y > > > > > > Lori Shepherd > > Bioconductor Core Team > > Roswell Park Cancer Institute > > Department of Biostatistics & Bioinformatics > > Elm & Carlton Streets > > Buffalo, New York 14263 > ------------------------------ > *From:* Zhai, Tingting <tingting.z...@uky.edu> > *Sent:* Thursday, January 25, 2018 1:17:22 PM > > *To:* Shepherd, Lori > *Cc:* Martin Morgan > *Subject:* Re: [Bioc-devel] NanoStringDiff package update > > Hi Lori, > Sorry to bother you again. Now I have successfully pushed my package > files with version 1.8.1 to both *Bioconductor* and GitHub repositories. But > when I repeat for the release branch with "git push upstream > RELEASE_3_6", I get following error: > > fatal: 'upstream' does not appear to be a git repository > > fatal: Could not read from remote repository. > > > Please make sure you have the correct access rights > and the repository exists. > > Could you help me fix this out? > > Thanks, > Tingting > > On Thu, Jan 25, 2018 at 11:50 AM, Shepherd, Lori < > lori.sheph...@roswellpark.org> wrote: > > The current release branch is RELEASE_3_6 > > > So the bottom section instructions would use that as the release branch: > > http://bioconductor.org/developers/how-to/git/maintain-bioc-only/ > > I do see the changes on the git.bioconductor.org so your push was > successful however this is one issue: > > > Please pay attention to version numbers. I just did a quick glance at the > changes that were uploaded and the version number committed is less than > the current devel version : > > > http://bioconductor.org/checkResults/3.7/bioc-LATEST/NanoStr > ingDiff/malbec2-buildsrc.html > > > The current devel version we have is 1.9.0 and you submitted changes with > 1.7.1 > > > Please see the section on versioning > > http://bioconductor.org/developers/how-to/version-numbering/ > > and the recent devel post > > https://stat.ethz.ch/pipermail/bioc-devel/2018-January/012657.html > > > While your changes are on the git server the package won't be rebuild > because of the lower Description version number. It needs to be corrected > on the master branch to 1.9.1. > > > When you submit your changes on the RELEASE_3_6 branch the current version > we have is 1.8.0 so the changes should be committed with 1.8.1 ... > > > > The version increases happen at release time. You should pull from the > git repository after a release happens and periodically. > > > http://bioconductor.org/developers/how-to/git/pull-upstream-changes/ > > Cheers, > > > Lori Shepherd > > Bioconductor Core Team > > Roswell Park Cancer Institute > > Department of Biostatistics & Bioinformatics > > Elm & Carlton Streets > > Buffalo, New York 14263 > ------------------------------ > *From:* Zhai, Tingting <tingting.z...@uky.edu> > *Sent:* Thursday, January 25, 2018 11:13:44 AM > *To:* Shepherd, Lori > *Cc:* Martin Morgan > > *Subject:* Re: [Bioc-devel] NanoStringDiff package update > > Hi Lori and Morgan, > I am taking the "Maintain a Bioconductor-only repository tutorial". I'm > done with "Push your local commits to the *Bioconductor* repository" so > far. So what next I should do to make my new package available to the > user community? > I guess I need to do the next step "Merge changes to the current release > branch", but I don't know my current release branch. > Could you all help me out? > > Thank you! > Best wishes, > Tingting > > On Thu, Jan 25, 2018 at 9:58 AM, Shepherd, Lori < > lori.sheph...@roswellpark.org> wrote: > > Sorry for the delay. Please try again. We have just processed the keys > again and it should be accessible. If you continue to have issues please > reply all so that it stays on the devel mailing list thread and other > members of the team can also assist. > > > Cheers > > > Lori Shepherd > > Bioconductor Core Team > > Roswell Park Cancer Institute > > Department of Biostatistics & Bioinformatics > > Elm & Carlton Streets > > Buffalo, New York 14263 > ------------------------------ > *From:* Zhai, Tingting <tingting.z...@uky.edu> > *Sent:* Thursday, January 25, 2018 9:49:47 AM > *To:* Shepherd, Lori > *Subject:* Re: [Bioc-devel] NanoStringDiff package update > > Hi Lori, > You are so helpful! I really appreciate it! > I submitted the form you mentioned above two days ago (Jan. 23). But when > I run "git clone g...@git.bioconductor.org:packages/NanoStringDiff.git", I > still get the error that "Permission denied (publickey). > fatal: Could not read from remote repository." Does it mean that my key > has not been added to your system? > > Thank you again for your help. > > > Best wishes, > Tingting > > > > > On Thu, Jan 25, 2018 at 7:13 AM, Shepherd, Lori < > lori.sheph...@roswellpark.org> wrote: > > Bioconductor has switched from svn to git, and was announced back in > August 2017, so you are correct that you are no longer able to use svn to > upload changes to the new location for the Bioconductor repository > > > git.bioconductor.org > > > You don't have to use github to maintain your package locally (we do > recommend it but not necessary) but we do require git for maintaining the > Bioconductor canonical location. There are lots of scenarios and useful > FAQ section on the Bioconductor website > > > http://bioconductor.org/developers/how-to/git/ > > > Create a new GitHub repository tutorial - will take you through how to > convert an existing directory onto github and how to maintain the two > locations (local github and bioconductor git location) > > > Maintain a Bioconductor-only repository tutorial - will take you through > how to link to the Bioconductor git.bioconductor.org repository without > creating a github. > > > There are many tutorials with how to push changes and how to pull from the > Bioconductor repo (after a release happens this is necessary) and how to > trouble shoot common issues. > > > The first step will be to submit an id and ssh-key to the following form > to gain access to the package > > > https://docs.google.com/forms/d/1CCwUhjtG82rnmcTWYqY43WcmBx5 > YyQm5UD4pcs1dhEs/viewform?edit_requested=true > > > You will need to enter your email - because you had an svn account your > svn.id - and a ssh public key - > > > Cheers, > > > > Lori Shepherd > > Bioconductor Core Team > > Roswell Park Cancer Institute > > Department of Biostatistics & Bioinformatics > > Elm & Carlton Streets > > Buffalo, New York 14263 > ------------------------------ > *From:* Bioc-devel <bioc-devel-boun...@r-project.org> on behalf of Zhai, > Tingting <tingting.z...@uky.edu> > *Sent:* Wednesday, January 24, 2018 2:17:17 PM > *To:* bioc-devel@r-project.org > *Subject:* [Bioc-devel] NanoStringDiff package update > > I’m one of the maintainers of NanoStringDiff package on Bioconductor. Now I > want to update this package and add some useful functions. I’m using SVN, > but when committing, it gives me this error: The new canonical location for > Bioconductor software and > > data experiment packages is git.bioconductor.org > > > The recommended way to maintain your Bioconductor software > > or data experiment package is to use GitHub. > > > > Does this mean I’m not able to use SVN to maintain my package any more? I’m > not familiar with github. > > > Thank you very much for any help in advance. > > > Best wishes, > > Tingting > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > Bioc-devel Info Page - ETH Zurich > <https://stat.ethz.ch/mailman/listinfo/bioc-devel> > stat.ethz.ch > Your email address: Your name (optional): You may enter a privacy password > below. 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