[Bioc-devel] DMCHMM package new release
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>
On Sep 4, 2018, at 11:59 AM, Obenchain, Valerie <Valerie.Obenchain at 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
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This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited. If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you.