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
> On Sep 27, 2020, at 3:58 PM, Farhad Shokoohi via Bioc-devel
> <bioc-devel@r-project.org> wrote:
>
> Hello
> I am trying to push the new version of DMCHMM package but I face the
> following error
>
> farhad@Ghool DMCHMM % git remote add upstream
> g...@git.bioconductor.org:packages/DMCHMM.git
> fatal: remote upstream already exists.
> farhad@Ghool DMCHMM % git fetch --all
> Fetching origin
> Fetching upstream
> farhad@Ghool DMCHMM % git checkout master
> Already on 'master'
> Your branch is up to date with 'origin/master'.
> farhad@Ghool DMCHMM % git merge origin/master
> Already up to date.
> farhad@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@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@R: c(person("Farhad", "Shokoohi", role = c("aut", "cre"),
> email = "shoko...@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
>
>
>
>
>> On Sep 5, 2018, at 6:49 AM, Shepherd, Lori <lori.sheph...@roswellpark.org>
>> wrote:
>>
>> We now see the changes on the git.bioconductor.org
>> <http://git.bioconductor.org/> server. The changes should be reflected in
>> tomorrows build report.
>>
>> Cheers,
>>
>> Lori Shepherd
>> Bioconductor Core Team
>> Roswell Park Cancer Institute
>> Department of Biostatistics & Bioinformatics
>> Elm & Carlton Streets
>> Buffalo, New York 14263
>> From: Farhad Shokoohi <shoko...@icloud.com>
>> Sent: Wednesday, September 5, 2018 9:46:21 AM
>> To: Shepherd, Lori
>> Cc: Obenchain, Valerie; bioc-devel@r-project.org
>> Subject: Re: [Bioc-devel] DMCHMM package new dev release
>>
>> Hello,
>>
>> I followed every command.
>> Everything is up to date.
>>
>>
>>
>> MacBook-Pro:DMCHMM Farhad$ git remote add upstream g...@git.bioconductor.org
>> <mailto:g...@git.bioconductor.org>:packages/DMCHMM.git
>> fatal: remote upstream already exists.
>> MacBook-Pro:DMCHMM Farhad$ git fetch --all
>> Fetching origin
>> Fetching upstream
>> MacBook-Pro:DMCHMM Farhad$ git checkout master
>> Switched to branch 'master'
>> Your branch is up-to-date with 'origin/master'.
>> MacBook-Pro:DMCHMM Farhad$
>> MacBook-Pro:DMCHMM Farhad$ git merge origin/master
>> Already up-to-date.
>> MacBook-Pro:DMCHMM Farhad$ git merge upstream/master
>> Already up-to-date.
>> MacBook-Pro:DMCHMM Farhad$ git push upstream master
>> Everything up-to-date
>> MacBook-Pro:DMCHMM Farhad$ git push origin master
>> Everything up-to-date
>>
>>
>>
>> ———
>> Farhad Shokoohi,
>> Ph.D. in Statistics
>> shoko...@icloud.com <mailto:shoko...@icloud.com>
>>
>>> On Sep 5, 2018, at 9:33 AM, Shepherd, Lori <lori.sheph...@roswellpark.org
>>> <mailto:lori.sheph...@roswellpark.org>> wrote:
>>>
>>> If you didn't set up your remotes this link may be useful
>>>
>>> https://bioconductor.org/developers/how-to/git/sync-existing-repositories/
>>> <https://bioconductor.org/developers/how-to/git/sync-existing-repositories/>
>>>
>>>
>>>
>>> Lori Shepherd
>>> Bioconductor Core Team
>>> Roswell Park Cancer Institute
>>> Department of Biostatistics & Bioinformatics
>>> Elm & Carlton Streets
>>> Buffalo, New York 14263
>>> From: Shepherd, Lori
>>> Sent: Wednesday, September 5, 2018 9:32:08 AM
>>> To: Obenchain, Valerie; Farhad Shokoohi
>>> Subject: Re: [Bioc-devel] DMCHMM package new dev release
>>>
>>> You need to commit changes to git.bioconductor.org
>>> <http://git.bioconductor.org/> . There are no changes pushed to our
>>> Bioconductor server.
>>>
>>> Please ensure you have followed the instructions for setting up your
>>> remotes and pushed to the correct location
>>> https://bioconductor.org/developers/how-to/git/push-to-github-bioc/
>>> <https://bioconductor.org/developers/how-to/git/push-to-github-bioc/>
>>>
>>> I would keep track of the commands you try and if you get any ERRORs please
>>> post the commands with full output as a reply all.
>>>
>>>
>>> Lori Shepherd
>>> Bioconductor Core Team
>>> Roswell Park Cancer Institute
>>> Department of Biostatistics & Bioinformatics
>>> Elm & Carlton Streets
>>> Buffalo, New York 14263
>>> From: Bioc-devel <bioc-devel-boun...@r-project.org
>>> <mailto:bioc-devel-boun...@r-project.org>> on behalf of Farhad Shokoohi via
>>> Bioc-devel <bioc-devel@r-project.org <mailto:bioc-devel@r-project.org>>
>>> Sent: Wednesday, September 5, 2018 9:26:58 AM
>>> To: Obenchain, Valerie
>>> Cc: bioc-devel@r-project.org <mailto:bioc-devel@r-project.org>
>>> Subject: Re: [Bioc-devel] DMCHMM package new dev release
>>>
>>> Hello,
>>>
>>> I did everything mentioned in the link.
>>> I am also using Sourcetree app on Mac to commit changes but noting changes.
>>>
>>> Best,
>>> ———
>>> Farhad Shokoohi,
>>> Ph.D. in Statistics
>>> shoko...@icloud.com <mailto:shoko...@icloud.com>
>>>
>>>> On Sep 4, 2018, at 11:59 AM, Obenchain, Valerie
>>>> <valerie.obench...@roswellpark.org> wrote:
>>>>
>>>> The builds start ~5pm EST daily. Commits made before that time will be
>>>> included in the nightly builds. The build report posts the following day
>>>> (see time at top of page):
>>>>
>>>> https://www.bioconductor.org/checkResults/release/bioc-LATEST/
>>>> <https://www.bioconductor.org/checkResults/release/bioc-LATEST/>
>>>> <https://www.bioconductor.org/checkResults/release/bioc-LATEST/
>>>> <https://www.bioconductor.org/checkResults/release/bioc-LATEST/>>
>>>> https://www.bioconductor.org/checkResults/devel/bioc-LATEST/
>>>> <https://www.bioconductor.org/checkResults/devel/bioc-LATEST/>
>>>> <https://www.bioconductor.org/checkResults/devel/bioc-LATEST/
>>>> <https://www.bioconductor.org/checkResults/devel/bioc-LATEST/>>
>>>>
>>>> If you don't see the package version you expected it's likely you missed
>>>> the cutoff or didn't push to the git.bioconductor.org server. See git
>>>> documentation here:
>>>>
>>>> https://www.bioconductor.org/developers/how-to/git/
>>>> <https://www.bioconductor.org/developers/how-to/git/>
>>>> <https://www.bioconductor.org/developers/how-to/git/
>>>> <https://www.bioconductor.org/developers/how-to/git/>>
>>>>
>>>> Valerie
>>>>
>>>>
>>>> On 09/04/2018 07:58 AM, Farhad Shokoohi via Bioc-devel wrote:
>>>>> Hello,
>>>>>
>>>>> I have made some changes and updated my package DMCHMM and pushed it to
>>>>> GitHub.
>>>>> When the new update appears on bioconductor?
>>>>>
>>>>> Best,
>>>>>
>>>>> ———
>>>>> Farhad Shokoohi,
>>>>> Ph.D. in Statistics
>>>>>
>>>>> [[alternative HTML version deleted]]
>>>>>
>>>>> _______________________________________________
>>>>> Bioc-devel@r-project.org <mailto:Bioc-devel@r-project.org
>>>>> <mailto:Bioc-devel@r-project.org>> mailing list
>>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>>> <https://stat.ethz.ch/mailman/listinfo/bioc-devel>
>>>>> <https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>>> <https://stat.ethz.ch/mailman/listinfo/bioc-devel>>
>>>>>
>>>>
>>>>
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>>>> received this message in error, please notify the sender immediately by
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>>>
>>>
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>>>
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>> agent responsible for the delivery of this message to the intended
>> recipient(s), you are hereby notified that any disclosure, copying,
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>
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>
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