[Bioc-devel] rcellminer Bioconductor package

Mon Oct 30 17:27:43 CET 2017

Thanks Sean.

-- Fathi

Fathi Elloumi, PhD
Bioinformatics Software Engineer
Contractor CSRA
Developmental Therapeutics Branch
NIH/NCI/CCR
Phone: 240-760-6601

From: Sean Davis <seandavi at gmail.com>
Date: Monday, October 30, 2017 at 8:41 AM
To: "Elloumi, Fathi (NIH/NCI) [C]" <fathi.elloumi at nih.gov>
Cc: "Turaga, Nitesh" <Nitesh.Turaga at roswellpark.org>, Bioc-devel <bioc-devel at 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.elloumi at nih.gov<mailto: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<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        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<mailto: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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