Re: [Bioc-devel] GitHub and Bioc sync: issue with dup commit for the sva package
Hi Leo, You are right in that you cannot “force” push to git.bioconductor.org. I’ve just done this for you. The git history looks clean and you can sync your Github and Bioc (http://bioconductor.org/developers/how-to/git/sync-existing-repositories/) for any further changes without any issues now. Let me know if you have trouble. Best regards, Nitesh > On Aug 30, 2018, at 3:33 AM, Claire Ruberman wrote: > > Thank you, Leo! > > On Mon, Aug 27, 2018 at 1:53 PM Leonardo Collado Torres > wrote: > Hi Nitesh, > > After looking more closely, I went with option 1 that you clearly > outlined below. The cherry picked version of the history is now the > origin/master one at > https://github.com/jtleek/sva-devel/commits/master. From > http://bioconductor.org/developers/how-to/git/resolve-duplicate-commits/ > my understanding is that now you have to force the Bioconductor git > history (upstream/master with the default setup) to match the one from > the sva-devel GitHub repo. > > The only complicated commit was > https://github.com/jtleek/sva-devel/commit/e6b80f62d494f77465650cf3d624feaf8913e837 > where I had to use the "theirs" strategy for many files. > > At the end I added this commit > https://github.com/jtleek/sva-devel/commit/05cfab55c893b428061ab703f3abd235889a > that bumps the version of the package to 3.29.1 on bioc-devel to > propagate Claire's recent changes. > > Best, > Leo > > PS I tried the git push -f upstream/master out of curiousity, and yup, > I can't do it: > > $ git push -f upstream master > Counting objects: 111, done. > Delta compression using up to 4 threads. > Compressing objects: 100% (54/54), done. > Writing objects: 100% (111/111), 19.58 KiB | 2.80 MiB/s, done. > Total 111 (delta 83), reused 62 (delta 56) > remote: Resolving deltas: 100% (83/83), completed with 38 local objects. > remote: FATAL: + refs/heads/master packages/sva l.collado-torres > DENIED by fallthru > remote: error: hook declined to update refs/heads/master > To git.bioconductor.org:packages/sva.git > ! [remote rejected] master -> master (hook declined) > error: failed to push some refs to > 'g...@git.bioconductor.org:packages/sva.git' > > PS2 I did push the master_backup branch to GitHub just in case we need > it later https://github.com/jtleek/sva-devel/tree/master_backup > > > On Sat, Aug 25, 2018 at 2:00 AM Turaga, Nitesh > wrote: > > > > Hi Leo, > > > > I’ll try to help you with this issue. > > > > The duplicates commit you have on your package “sva” come from the pre-git > > era of Bioconductor. There are three ways we can fix this, > > > > 1, > > > > You fix your GitHub repo by removing the duplicate commits. They happen > > only after this commit. > > > > commit d12b53824915f0ff7b7906043c7fc9237521e8f3 > > Author: Kipper Fletez-Brant > > Date: Sat Apr 22 10:42:29 2017 -0400 > > > > actually did it > > > > > > You can do the cherry-picking of the commits (only one from a set of > > duplicate commits, one after the other to construct your git history). It > > is outlined in this document here, > > > > > > http://bioconductor.org/developers/how-to/git/resolve-duplicate-commits/. > > > > If you choose this method, I can help with any questions you may have. > > > > Some help if you decide to choose this route, > > > > A. > > > > You might face issues with this commit (7e4aa44 Merge pull request > > #26 from cafletezbrant/master) while doing the cherry-pick. > > You can ignore this, because the commits themselves will be in the > > git history. > > > > d12b538 actually did it > > 7cedd49 needed to use tcrossprod(t(...)) a bunch > > > > > > B. > > > > If you hit a lot of merge conflicts while doing the cherry-pick, > > the best way I’ve gotten used to is by using > > > > `git mergetool`. > > > > (I personally use the option `git mergetool -t vimdiff`, but feel > > free to use whatever merge tool you’d like) > > > > C. > > > > Make sure you cherry-pick the RELEASE commits which come from the > > core team while doing the cherry-pick process. > > > > 2, > > > > I can fix the bioconductor repo on my end to show no duplicate commits. > > Then you’d have to force your Github master branch to be the same as the > > Bioconductor repo and then put Claire’s commits on top of them. This is a > > slightly less optimal solution because I might make some mistakes resolving > > the conflicts, since I don’t know the details of code. > > > > 3, > > > > Since the issue of duplicate commits was pre-git era, we can just ignore > > the duplicates. It is pretty straightforward to disable the duplicate > > commit check, but it should only be a worst case. I don’t recommend this > > for your repo because there are very few issues and it seems we can resolve > > them. I reserve this option for packages which have extensively fractured > > their git history. > > > > > > Best
Re: [Bioc-devel] Logolas package broken for R (3.4) users
Thanks so much Valerie and Kasper for the helpful comments...I will look into the issue as you suggested. Best Kushal On Wednesday, 29 August 2018, Obenchain, Valerie < valerie.obench...@roswellpark.org> wrote: > Kasper is right, you can only update code in the current release (Bioc > 3.7) or devel (Bioc 3.8). Sorry I didn't read your question carefully > enough. You could, however, use the AMI suggested below to attempt to > reproduce the reported error. > > This is the last build report for Bioc 3.6 and Logolas is not broken: > > https://www.bioconductor.org/checkResults/3.6/bioc-20180412/ > > If you can reproduce the error (with the AMI) you probably did not have a > comprehensive set of tests which is why the build report is green. If you > can't reproduce the error, the people reporting problems may be using > mismatched R/Bioconductor package versions. The output of their > sessionInfo() should be informative. > > Valerie > > > > On 08/29/2018 09:45 AM, Kasper Daniel Hansen wrote: > > I think the "correct" answer to this, is that it is impossible. Old > releases are locked. > > The way to discover such things is to have appropriate test functions > which will signal an error if things break. > > Best, > Kasper > > On Tue, Aug 28, 2018 at 2:17 PM Obenchain, Valerie roswellpark.org> wrote: > >> You could use an AMI with R 3.4 installed. See the 'AMI IDs' section: >> >> https://www.bioconductor.org/help/bioconductor-cloud-ami/#ami_ids >> >> Valerie >> >> >> On 08/27/2018 11:48 AM, kushal kumar dey wrote: >> >> Hi, >> >> I just found based on user reports that the old version of my package >> Logolas for R 3.4 and Bioc 3.6 is broken. It does install fine but the >> main >> function does not run. Everything seems to be fine however for R 3.5 and >> Bioc 3.7. I would like to produce either an error message if someone < R >> 3.5 tries to install Logolas, or to mend the old version. Can you please >> let me know what is the procedure for either of these cases? >> >> Thanks so much. >> >> Kushal >> >> >> >> >> >> 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. -- Kushal K. Dey Graduate Student 5 th Year, Department of Statistics University of Chicago Contact: +1 312-709-0680 | kk...@uchicago.edu [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Pushing to Bioconductor devel version...
Bioconductor assumes the master branch of a github repository is the devel branch. There is no devel branch on the git.bioconductor server so you will have to push the changes to upstream master. This is slightly confusing but stated on the git help pages http://bioconductor.org/developers/how-to/git/ http://bioconductor.org/developers/how-to/git/push-to-github-bioc/ 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 Paul Brennan Sent: Thursday, August 30, 2018 7:14:05 AM To: bioc-devel@r-project.org Subject: [Bioc-devel] Pushing to Bioconductor devel version... Hi, Sorry but this is a new developer question but I can't find an answer on any of the help pages. I have written some new function (and tests) in my package (drawProteins) and I would like to push them onto the devel version of Bioconductor. I have tried git push upstream devel but this is giving me an error message: ! [remote rejected] devel -> devel (hook declined) I don't know what to do next so any guidance would be very much appreciated. Thanks in advance, Paul Paul Brennan Cardiff University Github: brennanpincardiff [[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
[Bioc-devel] Pushing to Bioconductor devel version...
Hi, Sorry but this is a new developer question but I can't find an answer on any of the help pages. I have written some new function (and tests) in my package (drawProteins) and I would like to push them onto the devel version of Bioconductor. I have tried git push upstream devel but this is giving me an error message: ! [remote rejected] devel -> devel (hook declined) I don't know what to do next so any guidance would be very much appreciated. Thanks in advance, Paul Paul Brennan Cardiff University Github: brennanpincardiff [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
