Thanks Sean. -- Fathi
Fathi Elloumi, PhD Bioinformatics Software Engineer Contractor CSRA Developmental Therapeutics Branch NIH/NCI/CCR Phone: 240-760-6601 From: Sean Davis <seand...@gmail.com> Date: Monday, October 30, 2017 at 8:41 AM To: "Elloumi, Fathi (NIH/NCI) [C]" <fathi.ello...@nih.gov> Cc: "Turaga, Nitesh" <nitesh.tur...@roswellpark.org>, Bioc-devel <bioc-devel@r-project.org> Subject: Re: [Bioc-devel] rcellminer Bioconductor package Hi, Fathi. On Fri, Oct 27, 2017 at 5:12 PM, Elloumi, Fathi (NIH/NCI) [C] <fathi.ello...@nih.gov<mailto:fathi.ello...@nih.gov>> wrote: Hi Nitesh, I started merging and updating package rcellminerData following the instructions here : https://bioconductor.org/developers/how-to/git/sync-existing-repositories/ I have conflict merge in step 7: git merge --allow-unrelated-histories upstream/master warning: Cannot merge binary files: data/molData.RData (HEAD vs. upstream/master) warning: Cannot merge binary files: data/drugData.RData (HEAD vs. upstream/master) Auto-merging inst/extdata/CellLineToOncoTree.txt CONFLICT (add/add): Merge conflict in inst/extdata/CellLineToOncoTree.txt Auto-merging data/molData.RData CONFLICT (add/add): Merge conflict in data/molData.RData Auto-merging data/drugData.RData CONFLICT (add/add): Merge conflict in data/drugData.RData Auto-merging NAMESPACE CONFLICT (add/add): Merge conflict in NAMESPACE Auto-merging DESCRIPTION CONFLICT (add/add): Merge conflict in DESCRIPTION Automatic merge failed; fix conflicts and then commit the result. $git status On branch master Your branch is up-to-date with 'origin/master'. You have unmerged paths. (fix conflicts and run "git commit") (use "git merge --abort" to abort the merge) Changes to be committed: new file: data/datalist new file: external_data_store.txt new file: inst/extdata/make_rcellminerdata.R new file: inst/tests/test_rcellminerData.R new file: tests/runTests.R Unmerged paths: (use "git add <file>..." to mark resolution) both added: DESCRIPTION both added: NAMESPACE both added: data/drugData.RData both added: data/molData.RData both added: inst/extdata/CellLineToOncoTree.txt I was able to edit files DESCRIPTION and NAMESPACE and solve the conflict however it is not DOABLE for data files (*.txt and .Rdata) to make edit and remove undesirable parts. I want to check that the solution is to run: git checkout –ours data/drugData.RData git checkout –ours data/molData.RData git checkout –ours inst/extdata/CellLineToOncoTree.txt I think that will work. You may have to try it. Note that you can do tests like this on your local repo (or any number of copies) to confirm that things work as expected. As long as there are no pushes, you can feel free to experiment. When things are as you expect in your local copy, then push changes to upstream. git add * git commit and then step 9 Another question: should I go through step 10 for RELEASE_3_5 (what about the others 3_1 to 3_4). Please advise. In general, think of all RELEASE branches as read-only unless you have significant bug fixes. No new features should be added to release and no changes to current functionality should be introduced (except for bug fixes). In general, there is no need to fix older releases, as the recommendation to is to use the latest release. Sean Best, -- Fathi Fathi Elloumi, PhD Bioinformatics Software Engineer Contractor CSRA Developmental Therapeutics Branch NIH/NCI/CCR Phone: 240-760-6601<tel:240-760-6601> Here are my remotes: origin https://github.com/CBIIT/rcellminerData.git (fetch) origin https://github.com/CBIIT/rcellminerData.git (push) upstream g...@git.bioconductor.org:packages/rcellminerData.git (fetch) upstream g...@git.bioconductor.org:packages/rcellminerData.git (push) On 10/10/17, 10:25 AM, "Turaga, Nitesh" <nitesh.tur...@roswellpark.org> wrote: You should have access if you have submitted the new key. We suggest your link your GitHub ID. And add keys to your Github, and we can get them from there. If you have submitted your GitHub ID once to the google form, you won’t have to resubmit. Best, Nitesh > On Oct 7, 2017, at 9:04 AM, Elloumi, Fathi (NIH/NCI) [C] <fathi.ello...@nih.gov<mailto:fathi.ello...@nih.gov>> wrote: > > Hi Nitesh, > > I added a new ssh key to allow access from Laptop. Could you grant me permission for my 2 ssh keys? > > Thanks. > > Fathi > 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<mailto:Bioc-devel@r-project.org> mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel -- Sean Davis, MD, PhD Center for Cancer Research National Cancer Institute National Institutes of Health Bethesda, MD 20892 https://seandavi.github.io/ https://twitter.com/seandavis12 [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
