[Bioc-devel] rcellminer Bioconductor package

[Sean Davis]

Hi, Fathi.

On Fri, Oct 27, 2017 at 5:12 PM, Elloumi, Fathi (NIH/NCI) [C] <
fathi.elloumi at 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
>
>
> Here are my remotes:
> origin  https://github.com/CBIIT/rcellminerData.git (fetch)
> origin  https://github.com/CBIIT/rcellminerData.git (push)
> upstream        git at git.bioconductor.org:packages/rcellminerData.git
> (fetch)
> upstream        git at git.bioconductor.org:packages/rcellminerData.git
> (push)
>
>
>
> On 10/10/17, 10:25 AM, "Turaga, Nitesh" <Nitesh.Turaga at 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.elloumi at 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
>     >
>
>
>
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-- 
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

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