Dear Lori: Thank you very much for your very helpful response. I am sorry to say that I still am having difficulty seeing errors I think I resolved locally get successfully pushed to my devel branch. I would really appreciate your feedback to help me possibly identify the problem.
First, I checked that my git remotes are set up correctly. Below is my output: origin https://github.com/lindsayrutter/bigPint.git (fetch) origin https://github.com/lindsayrutter/bigPint.git (push) upstream g...@git.bioconductor.org:packages/bigPint.git (fetch) upstream g...@git.bioconductor.org:packages/bigPint.git (push) In an attempt to push changes to my devel branch, I updated my DESCRIPTION file to contain version 1.3.2. My last commit can be seen here <https://github.com/lindsayrutter/bigPint/commit/1f61951168d5ba35be6464c3f082e006ff2dd220>. I waited a few days and see that my builder <http://bioconductor.org/checkResults/devel/bioc-LATEST/bigPint/malbec2-checksrc.html> is still failing. The ERROR seems to be coming from my R/convertSEPair.R script in the line: vapply(colnames(oldData), function(x) strsplit(x, "[.]")[[1]][1]) I had updated this command, changing “vapply” to “lapply”. It now reads: lapply(colnames(oldData), function(x) strsplit(x, "[.]")[[1]][1]) I double-checked the R/convertSEPair.R file on my latest GitHub commit <https://github.com/lindsayrutter/bigPint/blob/1f61951168d5ba35be6464c3f082e006ff2dd220/R/convertSEPair.R> and indeed the “vapply” command is no longer present. I also note that my “Last commit” field on the builder website <http://bioconductor.org/checkResults/devel/bioc-LATEST/bigPint/malbec2-checksrc.html> is b810b6a from February 29, whereas my latest intended GitHub commit for the devel branch was 1f61951 from March 8. I should also state that I had tried a few times and kept bumping up my version number. So, on March 7 (Commit c75da1e), I had version 1.3.5. In my latest commit, I reduced my version number to 1.3.2 just to check that the reason my devel branch was still failing was not simply because my z (x.y.z) number was increased by more than a value of 1. However, it seems my pushed changes on GitHub are not updating to the devel builder website. I really thank you for sharing your advice with me. I wanted to ask if you may have any ideas on what I may be missing at this stage. Thank you again for your support. Sincerely, Lindsay 2020年3月3日(火) 21:30 Shepherd, Lori <lori.sheph...@roswellpark.org>: > It can take up to 24 from a push to be reflected on the build report. > > For release 3.10 (RELEASE_3_10 branch) we see a version number of 1.2.0 > http://bioconductor.org/checkResults/release/bioc-LATEST/bigPint/ > and > For devel 3.11 (master branch) we see a version number of 1.3.1 as well > http://bioconductor.org/checkResults/devel/bioc-LATEST/bigPint/ > > The landing page > http://bioconductor.org/packages/3.11/bioc/html/bigPint.html will only > be updated on a successful build/check of the package so we don't propagate > broken packages to users. If the fixes did not allow for a clean build and > check it would not be reflected. > > Also remember that in order for a change to propagate you need a valid > version bump. So your release version 1.2.0 in order to take effect would > have needed to be 1.2.1. And for devel master branch you would need a > version of 1.3.2. > > Never apologize for asking questions. We are here to help. And we > appreciate that you are taking the time to fix the package and learn how to > push the changes up correct. > > > I'll answer your specific questions below: > > Firstly make sure your git remotes are set up correctly where origin is > your github repository and upstream is pointing to the bioconductor > repositories > http://bioconductor.org/developers/how-to/git/sync-existing-repositories/ > > origin (your github) > origin (your github) > upstream g...@git.bioconductor.org:packages/bigPint.git (fetch) > upstream g...@git.bioconductor.org:packages/bigPint.git (push) > > 1) Is it acceptable for me to push what is on my GitHub master branch > (1.3.1) to the development branch of Bioconductor? > Yes. however you will want to bump the version number in the DESCRIPTION > to 1.3.2 because we have version 1.3.1 on our builders as indicated > http://bioconductor.org/checkResults/devel/bioc-LATEST/bigPint/. This > page reflects 1.3.0 because 1.3.1 has not built without ERROR and we would > not propagate broken packages to users > http://bioconductor.org/packages/3.11/bioc/html/bigPint.html. > > 2) Is it acceptable for me to likewise push what is on my GitHub master > branch (1.3.1) to the release branch of Bioconductor? I am assuming I am > only supposed to push the "cherry-pick" commits that resolve what had been > causing an error originally? This may be difficult for me as I have since > added many more changes to the master branch on GitHub after resolving that > release error. > Yes although not recommended but we would rather have a working package > than one ERRORing so if you don't think you can cherry-pick than yes. The > best option for that would be to checkout the RELEASE_3_10 branch and do a > git merge master. You will have to change the version number in the > DESCRIPTION to be consistent with release version numbers. (1.2.1) AFTER > the merge. > > 3) Is it possible to ask if there is anything else identifiably "out of > line" with my setup (on my GitHub master, development branch, or release > branch)? I am sure that once I complete this process successfully I will > have be better positioned to critically think of what is happening - but > right now I worry that due to my earlier mistakes, something may be "off" > with my setup that will make it difficult for me to successfully follow any > set of instructions. > I think you were on the right track so no further comments. > Some helpful hints : > > 1. git fetch --all will fetch all branches from your origin github and > the upstream bioconductor location (this will be important to do after the > next release in april to get the next RELEASE_3_11 branch) > 2. it is always a good idea to do a git pull upstream (branch name) > to pull any changes we have made. occasionally if we made an infrastructure > change bioconductor will apply patches. We also do the version bump > changes at release time. So for your master devel branch git pull > upstream master (git pull upstream RELEASE_3_10 for the current release) > 3. If you do git merge read the out message carefully and make sure > there are no conflicts. Conflicts means there is code that was changes in > both files (locally and on the branch you want to merge) so you will have > to check the file to make sure you don't include merge conflicts - The > code conflicts are indicated with >>>>> and <<<<<. you delete those > and keep the changes you want to commit. Then add and commit like normal > and git should give you messages about resolving conflicts. > > > Hope this helps. Let me know if you run into any further trouble. > > Cheers > > > Lori Shepherd > > Bioconductor Core Team > > Roswell Park Comprehensive Cancer Center > > Department of Biostatistics & Bioinformatics > > Elm & Carlton Streets > > Buffalo, New York 14263 > ------------------------------ > *From:* L Rutter <lindsayannerut...@gmail.com> > *Sent:* Tuesday, March 3, 2020 5:55 AM > *To:* Shepherd, Lori <lori.sheph...@roswellpark.org> > *Cc:* bioc-devel@r-project.org <bioc-devel@r-project.org> > *Subject:* Re: [Bioc-devel] R CMD build error for 3.10 (but not 3.11) > > Dear Lori: > > Thank you for this helpful advice. I did successfully now manage to change > my keys and name on the git.credentials app you suggested on February 25. > > At that time, my development version was building but my release version > was failing. So, I followed the instructions in the link you provided on > February 3 ( > http://bioconductor.org/developers/how-to/git/bug-fix-in-release-and-devel/) > to update my release version. I was able to also follow the "Sync existing > repositories" tab at the beginning of the guideline. > > After waiting for the updates, when I checked into my package (bigPint), I > noticed now both the development ( > https://bioconductor.org/packages/devel/bioc/html/bigPint.html) and > release (https://bioconductor.org/packages/release/bioc/html/bigPint.html) > version are not building. I was surprised because I did not think I was > making any changes to the development version through these instructions. I > also notice my development version is 1.3.0, my release version is 1.2.0, > and my GitHub master branch ( > https://github.com/lindsayrutter/bigPint/blob/master/DESCRIPTION) is > version 1.3.1. It also seems that the version on my local computer reversed > to 1.2.0. > > I tentatively plan to: > > 1) Clone my GitHub master branch (version 1.3.1) back to my local computer > (to make sure I do not lose many recent changes I have made to my package). > 2) Try to push my most current version (1.3.1) to the development branch > of Bioconductor. > 3) Try to push changes to the release branch of Bioconductor. > > I am pretty stuck even to the point where it is hard for me to formulate > questions but below are a few questions that might help me identify the > point of confusion: > 1) Is it acceptable for me to push what is on my GitHub master branch > (1.3.1) to the development branch of Bioconductor? > 2) Is it acceptable for me to likewise push what is on my GitHub master > branch (1.3.1) to the release branch of Bioconductor? I am assuming I am > only supposed to push the "cherry-pick" commits that resolve what had been > causing an error originally? This may be difficult for me as I have since > added many more changes to the master branch on GitHub after resolving that > release error. > 3) Is it possible to ask if there is anything else identifiably "out of > line" with my setup (on my GitHub master, development branch, or release > branch)? I am sure that once I complete this process successfully I will > have be better positioned to critically think of what is happening - but > right now I worry that due to my earlier mistakes, something may be "off" > with my setup that will make it difficult for me to successfully follow any > set of instructions. > > I apologize for reaching out about this headache of an issue now. I am > just concerned I may not be able to resolve this in a timely manner with my > current scope of knowledge. > > Sincerely, > Lindsay > > > 2020年2月25日(火) 21:14 Shepherd, Lori <lori.sheph...@roswellpark.org>: > > Thank you for reaching out. Have you tried checking your keys and > changing your name on the git.credentials app? > > https://git.bioconductor.org/BiocCredentials/login/?next=/BiocCredentials/ > > Lori Shepherd > > Bioconductor Core Team > > Roswell Park Comprehensive Cancer Center > > Department of Biostatistics & Bioinformatics > > Elm & Carlton Streets > > Buffalo, New York 14263 > ------------------------------ > *From:* L Rutter <lindsayannerut...@gmail.com> > *Sent:* Tuesday, February 25, 2020 1:55 AM > *To:* Shepherd, Lori <lori.sheph...@roswellpark.org> > *Cc:* bioc-devel@r-project.org <bioc-devel@r-project.org> > *Subject:* Re: [Bioc-devel] R CMD build error for 3.10 (but not 3.11) > > Dear Lori: > > Thanks for the suggestions. I tried to follow the linked instructions on > February 4 and February 9, but was unsuccessful both times (i.e. did not > see the changes pushed to the release branch). I tried following the > instructions again today. I notice that when I issue the command: > > git merge upstream/master > > I receive the message: > > merge: upstream/master - not something we can merge > > So, I clicked on the "Sync existing repositories" tab and checked that the > instructions there were working. After adding the upstream branch as > follows: > > git remote add upstream g...@git.bioconductor.org:packages/bigPint.git > > When I then try to fetch all (git fetch --all), I receive the following > error: > > Fetching origin > Fetching upstream > FATAL: R any packages/bigpint lrutter 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. > error: Could not fetch upstream > > I changed my GitHub userName about one year ago from "lrutter" to > "lindsayrutter". By doing "git remote -v", I can see that my origin > branches are correctly at "lindsayrutter", but I am unable to see about my > upstream branches on git.bioconductor. This is my output from "git remote > -v": > > origin https://github.com/lindsayrutter/bigPint (fetch) > origin https://github.com/lindsayrutter/bigPint (push) > upstream g...@git.bioconductor.org:packages/bigpint.git (fetch) > upstream g...@git.bioconductor.org:packages/bigpint.git (push) > > Do you have any advice on how I can fix this issue with fetch upstream > possibly expecting my older userName? Thank you for sharing advice. > > Sincerely, > Lindsay > > > 2020年2月3日(月) 21:54 Shepherd, Lori <lori.sheph...@roswellpark.org>: > > It looks like you only pushed changes to the master branch which is our > devel branch (3.11). > > Please see the instructions for > http://bioconductor.org/developers/how-to/git/bug-fix-in-release-and-devel/ > > where RELEASE_X_Y would be RELEASE_3_10 for pushing changes to the > release 3.10 branch. > > > > Lori Shepherd > > 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 L > Rutter <lindsayannerut...@gmail.com> > *Sent:* Saturday, February 1, 2020 4:18 AM > *To:* bioc-devel@r-project.org <bioc-devel@r-project.org> > *Subject:* [Bioc-devel] R CMD build error for 3.10 (but not 3.11) > > Dear all: > > I have been receiving messages that my Bionconductor package bigPint is > producing errors on 'R CMD build' on malbec1. I believe I discovered the > source of the error, fixed it, and pushed changes to my GitHub account ( > github.com/lindsayrutter) on December 10, 2019. I continued to receive > this > error notification and was advised to ensure I had pushed the changes to > Bioconductor. I pushed changes following these instructions ( > http://bioconductor.org/developers/how-to/git/) on January 4, 2020. I am > still receiving notifications that my package produces errors on 'R CMD > build' on malbec1 ( > > https://master.bioconductor.org/checkResults/3.10/bioc-LATEST/bigPint/malbec1-buildsrc.html > ). > However, it seems my package is no longer failing daily build reports for > version 3.11 as of January 4, 2020 ( > http://bioconductor.org/checkResults/3.11/bioc-LATEST/). > > I am seeking advice on what a maintainer should try in this situation? Is > it possible my changes were only recognized in version 3.11 but not version > 3.10? Thank you for any advice you may have! > > Sincerely, > L. Rutter > > [[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. > > > 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. > > > 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. 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