[Bioc-devel] rcellminer Bioconductor package

Elloumi, Fathi (NIH/NCI) [C] fathi.elloumi at nih.gov
Fri Oct 27 23:12:11 CEST 2017

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

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.


-- Fathi
Fathi Elloumi, PhD
Bioinformatics Software Engineer 
Contractor CSRA
Developmental Therapeutics Branch
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. 
    > 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
    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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