On Sep 27, 2020, at 3:58 PM, Farhad Shokoohi via Bioc-devel <bioc-devel at r-project.org> wrote:
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
On Sep 5, 2018, at 6:49 AM, Shepherd, Lori <Lori.Shepherd at 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 at icloud.com>
Sent: Wednesday, September 5, 2018 9:46:21 AM
To: Shepherd, Lori
Cc: Obenchain, Valerie; bioc-devel at 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 at git.bioconductor.org <mailto:git at 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 at icloud.com <mailto:shokoohi at icloud.com>
On Sep 5, 2018, at 9:33 AM, Shepherd, Lori <Lori.Shepherd at RoswellPark.org <mailto:Lori.Shepherd at 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 at r-project.org <mailto:bioc-devel-bounces at r-project.org>> on behalf of Farhad Shokoohi via Bioc-devel <bioc-devel at r-project.org <mailto:bioc-devel at r-project.org>>
Sent: Wednesday, September 5, 2018 9:26:58 AM
To: Obenchain, Valerie
Cc: bioc-devel at r-project.org <mailto:bioc-devel at 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 at icloud.com <mailto:shokoohi at icloud.com>
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]]