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neurogenomics / EpiCompare

Comparison, benchmarking & QC of epigenetic datasets
https://doi.org/doi:10.18129/B9.bioc.EpiCompare
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Cannot push to Bioconductor #115

Closed serachoi1230 closed 2 years ago

serachoi1230 commented 2 years ago

Hi @bschilder ,

My slack account has been deactivated, so I thought communicating here would be easier than email! I'm having some issues pushing to Bioconductor. Have you seen this error before?

So, when I push to upstream (Bioconductor), I get merge error:

(base) serachoi@Seras-MBP EpiCompare %  git push upstream master
Enter passphrase for key '/Users/serachoi/.ssh/id_ed25519': 
Enumerating objects: 943, done.
Counting objects: 100% (880/880), done.
Delta compression using up to 4 threads
Compressing objects: 100% (269/269), done.
Writing objects: 100% (813/813), 3.99 MiB | 2.35 MiB/s, done.
Total 813 (delta 561), reused 777 (delta 526), pack-reused 0
remote: Resolving deltas: 100% (561/561), completed with 50 local objects.
remote: Error: You cannot push without resolving merge conflicts.
remote: 
remote: Please check the files in the commit pushed to the git-server
remote: for merge conflict markers like '<<<<<<<', '========', '>>>>>>>'.
remote: 
To git.bioconductor.org:packages/EpiCompare.git
 ! [remote rejected] master -> master (pre-receive hook declined)
error: failed to push some refs to 'git.bioconductor.org:packages/EpiCompare.git'

Which is strange, because I'm not seeing merge conflicts anywhere: 

(base) serachoi@Seras-MBP EpiCompare % git checkout master
Already on 'master'
Your branch is up to date with 'origin/master'.
(base) serachoi@Seras-MBP EpiCompare % git status
On branch master
Your branch is up to date with 'origin/master'.

nothing to commit, working tree clean

I also merged upstream and origin, and I had no problems doing that:

(base) serachoi@Seras-MBP EpiCompare % git merge origin/master
Already up to date.
(base) serachoi@Seras-MBP EpiCompare % git merge upstream/master
Already up to date.

Have you seen anything like this before?

Thank you so much!

bschilder commented 2 years ago

I think this might have to do with the difference between merging from master origin (GitHub) or master upstream (Bioconductor). These instructions might help. https://github.com/neurogenomics/labwiki/wiki/Creating-a-Bioconductor-package#6-bioconductor---future-development

Try this:

## Checkout from upstream
git checkout upstream/master

 git merge origin/master
 git merge upstream/master
 git push upstream master
 git push origin master
bschilder commented 2 years ago

@Al-Murphy might be able to offer some advice too

serachoi1230 commented 2 years ago

Thanks Brian! I followed the labwiki page on Sunday and it didn't work for me then, but it's worked now for some reason! I've pushed to Bioconductor and GitHub :)