Re: [Bioc-devel] DMCHMM package new release

2020-09-29 Thread Nitesh Turaga 
Hi Farhad,

It seems you should follow this 
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/ 
. Send me the output of 
your remotes. 

Best,

Nitesh 

> On Sep 27, 2020, at 3:58 PM, Farhad Shokoohi via Bioc-devel 
>  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 '
> 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 '
> 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 = 
> "-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  
>> wrote:
>> 
>> We now see the changes on the 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 
>> 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 
>> :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 
>> 
>>> On Sep 5, 2018, at 9:33 AM, Shepherd, Lori >>

Re: [Bioc-devel] DMCHMM package new release

2020-09-27 Thread Farhad Shokoohi via Bioc-devel 
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 '
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 '
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 = 
"-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  
> wrote:
> 
> We now see the changes on the 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 
> 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 
> :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 
> 
>> On Sep 5, 2018, at 9:33 AM, Shepherd, Lori > > wrote:
>> 
>> If you didn't set up your remotes  this link may be useful
>> 
>> 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 
>>  .  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/ 
>>