[Bioc-devel] Git failing to push upstream to Bioc devel

[Turaga, Nitesh]

Hi Koen,

It seems you have not followed the support documentation to sync the Github and Bioconductor repositories first.

http://bioconductor.org/developers/how-to/git/sync-existing-repositories/

If you follow the steps, you’d get this. 


/tmp ❯❯❯ git clone https://github.com/statOmics/stageR
Cloning into 'stageR'...
remote: Counting objects: 783, done.
remote: Compressing objects: 100% (94/94), done.
remote: Total 783 (delta 88), reused 86 (delta 44), pack-reused 645
Receiving objects: 100% (783/783), 1.15 MiB | 204.00 KiB/s, done.
Resolving deltas: 100% (498/498), done.

/tmp ❯❯❯ cd stageR
 1 DESCRIPTION +                                                                                                                      
/t/stageR ❯❯❯ git remote add upstream git using git.bioconductor.org:packages/stageR                    
/t/stageR ❯❯❯ git fetch --all                                                                                                    
Fetching origin
Fetching upstream
remote: Counting objects: 5, done.
remote: Compressing objects: 100% (5/5), done.
remote: Total 5 (delta 3), reused 0 (delta 0)
Unpacking objects: 100% (5/5), done.
From git.bioconductor.org:packages/stageR
 * [new branch]      RELEASE_3_6 -> upstream/RELEASE_3_6
 * [new branch]      RELEASE_3_7 -> upstream/RELEASE_3_7
 * [new branch]      master      -> upstream/master

/t/stageR ❯❯❯ git merge origin/master                                                                                         
Already up-to-date.

/t/stageR ❯❯❯ git merge upstream/master                                                                                   
Auto-merging vignettes/stageRVignette.Rmd
Auto-merging DESCRIPTION
CONFLICT (content): Merge conflict in DESCRIPTION
Automatic merge failed; fix conflicts and then commit the result.

/t/stageR ❯❯❯ git diff                                                                                               ⏎ master:merge ✚ ═
diff --cc DESCRIPTION
index 1380561,dd43712..0000000
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@@ -1,7 -1,7 +1,11 @@@
  Package: stageR
  Type: Package
  Title: stageR: stage-wise analysis of high throughput gene expression data in R
++<<<<<<< HEAD
 +Version: 1.3.27
++=======
+ Version: 1.3.26
++>>>>>>> upstream/master
  Author: Koen Van den Berge and Lieven Clement
  Maintainer: Koen Van den Berge <koen.vdberge using gmail.com>
  Description: The stageR package allows automated stage-wise analysis of high-throughput gene expression data. The method is published

/t/stageR ❯❯❯ vim DESCRIPTION                                                                                          master:merge ✚ ═

/t/stageR ❯❯❯ git status                                                                                               master:merge ✚ ═
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:

	modified:   vignettes/stageRVignette.Rmd

Unmerged paths:
  (use "git add <file>..." to mark resolution)

	both modified:   DESCRIPTION

/t/stageR ❯❯❯ git add DESCRIPTION                                                                                      master:merge ✚ ═

/t/stageR ❯❯❯ git status                                                                                                 master:merge ✚
On branch master
Your branch is up-to-date with 'origin/master'.

All conflicts fixed but you are still merging.
  (use "git commit" to conclude merge)

Changes to be committed:

	modified:   vignettes/stageRVignette.Rmd

/t/stageR ❯❯❯ git commit -m "Modifications"                                                                              master:merge ✚
[master 1bfc1ca] Modifications

/t/stageR ❯❯❯ git status                                                                                                       master ⬆
On branch master
Your branch is ahead of 'origin/master' by 2 commits.
  (use "git push" to publish your local commits)

nothing to commit, working tree clean



Now you should be able to push without the “force” option.

Best,

Nitesh

> On Aug 31, 2018, at 8:32 PM, Koen Van den Berge <koen.vdberge using gmail.com> wrote:
> 
> Hi,
> 
> I did git pull, using `git pull upstream master`, first (see output); is this insufficient?
> 
> Best,
> Koen
> 
> 
> 
>> On 31 Aug 2018, at 17:00, Turaga, Nitesh <Nitesh.Turaga using RoswellPark.org> wrote:
>> 
>> Hi, 
>> 
>> You cannot force push to git.bioconductor.org. 
>> 
>> Please "git pull" before you do anything else.
>> 
>> 
>> Best
>> 
>> Nitesh
>> 
>> 
>> 
>> Get Outlook for Android 
>> 
>> 
>> 
>> 
>> 
>> From: Koen Van den Berge 
>> Sent: Friday, August 31, 8:01 PM 
>> Subject: [Bioc-devel] Git failing to push upstream to Bioc devel 
>> To: bioc-devel using r-project.org 
>> 
>> 
>> Dear All, I have updated the vignette from the stageR package. I successfully committed the edit to my Github repo, and also wanted to push it to Bioc devel. However, Git is rejecting my push, while my working tree seems to be clean. Forcing the push with `git push -f` does not solve the issue. I was wondering if there are any suggestions on how to fix this. You can find the output from Git below. Thank you in advance, Best, Koen w254h198:stageR koenvandenberge$ git status nothing to commit, working tree clean w254h198:stageR koenvandenberge$ git pull upstream master From git.bioconductor.org:packages/stageR * branch master -> FETCH_HEAD Already up-to-date. w254h198:stageR koenvandenberge$ git add . w254h198:stageR koenvandenberge$ git commit . nothing to commit, working tree clean w254h198:stageR koenvandenberge$ git push upstream master To git.bioconductor.org:packages/stageR.git ! [rejected] master -> master (non-fast-forward) error: failed to push some refs to 'git using git.bioconductor.org:packages/stageR.git' hint: Updates were rejected because a pushed branch tip is behind its remote hint: counterpart. Check out this branch and integrate the remote changes hint: (e.g. 'git pull ...') before pushing again. hint: See the 'Note about fast-forwards' in 'git push --help' for details. [[alternative HTML version deleted]] _______________________________________________ Bioc-devel using 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.
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