[Bioc-devel] DMCHMM package new release

Farhad Shokoohi @hokooh| @end|ng |rom |c|oud@com
Sun Sep 27 21:58:25 CEST 2020 

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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>> >> 
>> > 
>> > 
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