[Bioc-devel] DMCHMM package new release

Nitesh Turaga ntur@g@@b|oc @end|ng |rom gm@||@com
Tue Sep 29 14:47:45 CEST 2020


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 using r-project.org> wrote:
> 
> Hello
> I am trying to push the new version of DMCHMM package but I face the following error
> 
> farhad using Ghool DMCHMM % git remote add upstream git using git.bioconductor.org:packages/DMCHMM.git
> fatal: remote upstream already exists.
> farhad using Ghool DMCHMM % git fetch --all
> Fetching origin
> Fetching upstream
> farhad using Ghool DMCHMM %  git checkout master
> Already on 'master'
> Your branch is up to date with 'origin/master'.
> farhad using Ghool DMCHMM % git merge origin/master
> Already up to date.
> farhad using 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 using 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 using R: c(person("Farhad", "Shokoohi", role = c("aut", "cre"),
>                     email = "shokoohi using 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.Shepherd using 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 <shokoohi using icloud.com>
>> Sent: Wednesday, September 5, 2018 9:46:21 AM
>> To: Shepherd, Lori
>> Cc: Obenchain, Valerie; bioc-devel using 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 git using git.bioconductor.org <mailto:git using 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
>> shokoohi using icloud.com <mailto:shokoohi using icloud.com>
>> 
>>> On Sep 5, 2018, at 9:33 AM, Shepherd, Lori <Lori.Shepherd using RoswellPark.org <mailto:Lori.Shepherd using 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-bounces using r-project.org <mailto:bioc-devel-bounces using r-project.org>> on behalf of Farhad Shokoohi via Bioc-devel <bioc-devel using r-project.org <mailto:bioc-devel using r-project.org>>
>>> Sent: Wednesday, September 5, 2018 9:26:58 AM
>>> To: Obenchain, Valerie
>>> Cc: bioc-devel using r-project.org <mailto:bioc-devel using 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
>>> shokoohi using icloud.com <mailto:shokoohi using icloud.com>
>>> 
>>>> On Sep 4, 2018, at 11:59 AM, Obenchain, Valerie <Valerie.Obenchain using 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]]
>>>>> 
>>>>> _______________________________________________
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>>>>> 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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