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[Bioc-devel] DMCHMM package new release

2 messages · Farhad Shokoohi, Nitesh Turaga

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Hello
I am trying to push the new version of DMCHMM package but I face the following error

farhad at Ghool DMCHMM % git remote add upstream git at git.bioconductor.org:packages/DMCHMM.git
fatal: remote upstream already exists.
farhad at Ghool DMCHMM % git fetch --all
Fetching origin
Fetching upstream
farhad at Ghool DMCHMM %  git checkout master
Already on 'master'
Your branch is up to date with 'origin/master'.
farhad at Ghool DMCHMM % git merge origin/master
Already up to date.
farhad at Ghool DMCHMM % git merge upstream/master
Auto-merging DESCRIPTION
CONFLICT (content): Merge conflict in DESCRIPTION
Automatic merge failed; fix conflicts and then commit the result.



error: Merging is not possible because you have unmerged files.
hint: Fix them up in the work tree, and then use 'git add/rm <file>'
hint: as appropriate to mark resolution and make a commit.
fatal: Exiting because of an unresolved conflict.
farhad at Ghool DMCHMM % git merge upstream/master
error: Merging is not possible because you have unmerged files.
hint: Fix them up in the work tree, and then use 'git add/rm <file>'
hint: as appropriate to mark resolution and make a commit.
fatal: Exiting because of an unresolved conflict.


I do not understand this conflict. I have changed the Description several times but it does not work. Here is the new description:
Would you kindly let me know what I am missing here?

Package: DMCHMM
Type: Package
Title: Differentially Methylated CpG using Hidden Markov Model
Version: 1.11.1
Authors at R: c(person("Farhad", "Shokoohi", role = c("aut", "cre"),
                     email = "shokoohi at icloud.com", comment = c(ORCID = "0000-0002-6224-2609"))
              )
Description: A pipeline for identifying differentially methylated CpG sites 
    using Hidden Markov Model in bisulfite sequencing data.
Depends: R (>= 4.0.0),
    SummarizedExperiment,
    methods,
    S4Vectors,
    BiocParallel,
    GenomicRanges,
    IRanges,
    fdrtool
Imports: utils,
    stats,
    grDevices,
    rtracklayer,
    multcomp,
    calibrate,
    graphics
Suggests: testthat, 
    knitr
VignetteBuilder:
    knitr
biocViews: DifferentialMethylation, Sequencing, HiddenMarkovModel, Coverage
License: GPL-3
Date: 2020-09-27
Encoding: UTF-8
LazyData: true
BugReports: https://github.com/shokoohi/DMCHMM/issues
RoxygenNote: 7.1.1
NeedsCompilation: no
Packaged: 2017-06-23 00:13:02 UTC; Farhad

  
  
1 day later
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Hi Farhad,

It seems you should follow this http://bioconductor.org/developers/how-to/git/resolve-conflicts/ <http://bioconductor.org/developers/how-to/git/resolve-conflicts/> .

Another tip, if you have to locate files with conflicts is 

	git diff --name-only --diff-filter=U

I took a look at your message, I need to know how your remotes are set up to help you more. The DESCRIPTION file you sent me doesn?t have any merge conflicts. If that is the case your should simply be able to `git add`, `git commit` and then `git push`. 

Please take a look at #14 in the FAQ http://bioconductor.org/developers/how-to/git/faq/ <http://bioconductor.org/developers/how-to/git/faq/>. Send me the output of your remotes. 

Best,

Nitesh