[Bioc-devel] COHCAP GitHub Update

[Sean Davis]

Hi, Charles.

The command is slightly off. Note the first '/' is a ':'.  This worked for
me:

git clone git at git.bioconductor.org:packages/COHCAP.git
Cloning into 'COHCAP'...
remote: Counting objects: 485, done.
remote: Compressing objects: 100% (479/479), done.
remote: Total 485 (delta 329), reused 0 (delta 0)
Receiving objects: 100% (485/485), 104.78 KiB | 0 bytes/s, done.
Resolving deltas: 100% (329/329), done.

Sean


On Mon, Sep 4, 2017 at 2:15 PM, Charles Warden <cwarden45 at gmail.com> wrote:

> Hi Nitesh,
>
> Thanks.  Unfortunately, I can't connect to the Bioconductor repository that
> way:
>
>
> *cwarden$ git clone git at git.bioconductor.org/packages/COHCAP.git
> <http://git@git.bioconductor.org/packages/COHCAP.git>*
>
> *fatal: repository 'git at git.bioconductor.org/packages/COHCAP.git
> <http://git@git.bioconductor.org/packages/COHCAP.git>' does not exist*
>
> However, I can connect and update the GitHub repository with the SSH
> commands:
>
> cwarden$ git clone git at github.com:cwarden45/COHCAP.git
>
> Cloning into 'COHCAP'...
>
> Saving password to keychain failed
>
> Identity added: /Users/cwarden/.ssh/id_rsa ((null))
>
> remote: Counting objects: 59, done.
>
> remote: Compressing objects: 100% (53/53), done.
>
> remote: Total 59 (delta 9), reused 3 (delta 2), pack-reused 0
>
> Receiving objects: 100% (59/59), 56.83 KiB | 0 bytes/s, done.
>
> Resolving deltas: 100% (9/9), done.
>
> Checking connectivity... done.
>
> BR11252:COHCAP cwarden$ git status
>
> On branch master
>
> Your branch is up-to-date with 'origin/master'.
>
> Changes not staged for commit:
>
>   (use "git add <file>..." to update what will be committed)
>
>   (use "git checkout -- <file>..." to discard changes in working directory)
>
>
> modified:   CHANGES
>
>
> no changes added to commit (use "git add" and/or "git commit -a")
>
> BR11252:COHCAP cwarden$ git commit -a -m "test commit"
>
> [master f2aded7] test commit
>
>  1 file changed, 1 insertion(+)
>
> BR11252:COHCAP cwarden$ git push
>
> Warning: Permanently added the RSA host key for IP address '192.30.255.112'
> to the list of known hosts.
>
> Counting objects: 3, done.
>
> Delta compression using up to 8 threads.
>
> Compressing objects: 100% (3/3), done.
>
> Writing objects: 100% (3/3), 302 bytes | 0 bytes/s, done.
>
> Total 3 (delta 2), reused 0 (delta 0)
>
> remote: Resolving deltas: 100% (2/2), completed with 2 local objects.
>
> To git at github.com:cwarden45/COHCAP.git
>
>    5285d59..f2aded7  master -> master
>
> *If it helps with troubleshooting, I can also try to update the
> Bioconductor repository as an upstream link to the GitHub repository, but
> that also does not work (at the push step, see below):*
>
> cwarden$ git clone git at github.com:cwarden45/COHCAP.git
>
> Cloning into 'COHCAP'...
>
> remote: Counting objects: 63, done.
>
> remote: Compressing objects: 100% (55/55), done.
>
> remote: Total 63 (delta 12), reused 7 (delta 4), pack-reused 0
>
> Receiving objects: 100% (63/63), 57.24 KiB | 0 bytes/s, done.
>
> Resolving deltas: 100% (12/12), done.
>
> Checking connectivity... done.
>
> cwarden$ cd COHCAP
>
> COHCAP cwarden$ git remote -v
>
> origin git at github.com:cwarden45/COHCAP.git (fetch)
>
> origin git at github.com:cwarden45/COHCAP.git (push)
>
> COHCAP cwarden$ git remote add upstream git at git.bioconductor.org:
> packages/COHCAP.git
>
> BR11252:COHCAP cwarden$ git remote -v
>
> origin git at github.com:cwarden45/COHCAP.git (fetch)
>
> origin git at github.com:cwarden45/COHCAP.git (push)
>
> upstream git at git.bioconductor.org:packages/COHCAP.git (fetch)
>
> upstream git at git.bioconductor.org:packages/COHCAP.git (push)
>
> COHCAP cwarden$ git fetch upstream
>
> warning: no common commits
>
> remote: Counting objects: 485, done.
>
> remote: Compressing objects: 100% (479/479), done.
>
> remote: Total 485 (delta 328), reused 0 (delta 0)
>
> Receiving objects: 100% (485/485), 110.22 KiB | 0 bytes/s, done.
>
> Resolving deltas: 100% (328/328), done.
>
> From git.bioconductor.org:packages/COHCAP
>
>  * [new branch]      RELEASE_2_14 -> upstream/RELEASE_2_14
>
>  * [new branch]      RELEASE_3_0 -> upstream/RELEASE_3_0
>
>  * [new branch]      RELEASE_3_1 -> upstream/RELEASE_3_1
>
>  * [new branch]      RELEASE_3_2 -> upstream/RELEASE_3_2
>
>  * [new branch]      RELEASE_3_3 -> upstream/RELEASE_3_3
>
>  * [new branch]      RELEASE_3_4 -> upstream/RELEASE_3_4
>
>  * [new branch]      RELEASE_3_5 -> upstream/RELEASE_3_5
>
>  * [new branch]      master     -> upstream/master
>
> COHCAP cwarden$ git merge upstream/master
>
> Auto-merging vignettes/COHCAP.Rnw
>
> CONFLICT (add/add): Merge conflict in vignettes/COHCAP.Rnw
>
> Auto-merging man/COHCAP.site.Rd
>
> CONFLICT (add/add): Merge conflict in man/COHCAP.site.Rd
>
> Auto-merging man/COHCAP.qc.Rd
>
> CONFLICT (add/add): Merge conflict in man/COHCAP.qc.Rd
>
> Auto-merging man/COHCAP.integrate.avg.by.site.Rd
>
> CONFLICT (add/add): Merge conflict in man/COHCAP.integrate.avg.by.site.Rd
>
> Auto-merging man/COHCAP.integrate.avg.by.island.Rd
>
> CONFLICT (add/add): Merge conflict in man/COHCAP.integrate.avg.by.
> island.Rd
>
> Auto-merging man/COHCAP.denovo.Rd
>
> CONFLICT (add/add): Merge conflict in man/COHCAP.denovo.Rd
>
> Auto-merging man/COHCAP.avg.by.site.Rd
>
> CONFLICT (add/add): Merge conflict in man/COHCAP.avg.by.site.Rd
>
> Auto-merging man/COHCAP.avg.by.island.Rd
>
> CONFLICT (add/add): Merge conflict in man/COHCAP.avg.by.island.Rd
>
> Auto-merging man/COHCAP.annotate.Rd
>
> CONFLICT (add/add): Merge conflict in man/COHCAP.annotate.Rd
>
> Auto-merging man/COHCAP.BSSeq.preprocess.Rd
>
> CONFLICT (add/add): Merge conflict in man/COHCAP.BSSeq.preprocess.Rd
>
> Auto-merging NAMESPACE
>
> CONFLICT (add/add): Merge conflict in NAMESPACE
>
> Auto-merging DESCRIPTION
>
> CONFLICT (add/add): Merge conflict in DESCRIPTION
>
> Auto-merging CHANGES
>
> CONFLICT (add/add): Merge conflict in CHANGES
>
> [modified files to keep changes intended for SVN Bioconductor repository]
>
> COHCAP cwarden$ git add CHANGES
>
> COHCAP cwarden$ git add DESCRIPTION
>
> COHCAP cwarden$ git add NAMESPACE
>
> COHCAP cwarden$ git add man/COHCAP.BSSeq.preprocess.Rd
>
> COHCAP cwarden$ git add man/COHCAP.annotate.Rd
>
> COHCAP cwarden$ git add man/COHCAP.avg.by.island.Rd
>
> COHCAP cwarden$ git add man/COHCAP.avg.by.site.Rd
>
> COHCAP cwarden$ git add man/COHCAP.denovo.Rd
>
> COHCAP cwarden$ git add man/COHCAP.integrate.avg.by.island.Rd
>
> COHCAP cwarden$ git add man/COHCAP.integrate.avg.by.site.Rd
>
> COHCAP cwarden$ git add man/COHCAP.qc.Rd
>
> COHCAP cwarden$ git add man/COHCAP.site.Rd
>
> COHCAP cwarden$ git add man/COHCAP.reformatFinalReport.Rd
>
> COHCAP cwarden$ git add vignettes/COHCAP.Rnw
>
> COHCAP cwarden$ git add R/COHCAP.reformatFinalReport.R
>
> COHCAP cwarden$ git push upstream master
>
> To git at git.bioconductor.org:packages/COHCAP.git
>
>  ! [rejected]        master -> master (non-fast-forward)
>
> error: failed to push some refs to 'git at git.bioconductor.org:
> packages/COHCAP.git'
>
> hint: Updates were rejected because the tip of your current branch is
> behind
>
> hint: its remote counterpart. Integrate the remote changes (e.g.
>
> hint: 'git pull ...') before pushing again.
>
> hint: See the 'Note about fast-forwards' in 'git push --help' for details.
>
> Can you please help me troubleshoot updating the Bioconductor COHCAP
> repository via SSH?
>
> Thanks,
>
> Charles
>
> On Sun, Sep 3, 2017 at 7:07 PM, Turaga, Nitesh <
> Nitesh.Turaga at roswellpark.org> wrote:
>
> > Hi
> >
> > You are using HTTPS protocol for cloning your repository. You need to use
> > SSH.
> >
> >
> > http://bioconductor.org/developers/how-to/git/new-package-workflow/
> >
> >         • SSH (developer) read / write access: git at git.bioconductor.org
> >         • HTTPS (public) read only access: https://git.bioconductor.org
> >
> >
> > Nitesh
> >
> > > On Sep 3, 2017, at 4:30 PM, Charles Warden <cwarden45 at gmail.com>
> wrote:
> > >
> > > Hi Martin and Nitesh,
> > >
> > > Thanks for your help - I can now clone from the Bioconductor COHCAP git
> > repository, and I'm now working on syncing the GitHub repository and the
> > Bioconductor repository (or at least updating the Bioconductor
> repository).
> > >
> > > I'm testing making a minor change (not affecting functionality, in the
> > "CHANGES" text file) to one of the files from the Bioconductor repository
> > (without trying to sync the repositories), and I get the following error
> > message when I try to push the changes to the Bioconductor repository
> > (showing prior commands as well):
> > >
> > > cwarden$ git clone https://git.bioconductor.org/packages/COHCAP
> > >
> > > Cloning into 'COHCAP'...
> > >
> > > remote: Counting objects: 485, done.
> > >
> > > remote: Compressing objects: 100% (479/479), done.
> > >
> > > remote: Total 485 (delta 328), reused 0 (delta 0)
> > >
> > > Receiving objects: 100% (485/485), 107.97 KiB | 0 bytes/s, done.
> > >
> > > Resolving deltas: 100% (328/328), done.
> > >
> > > Checking connectivity... done.
> > >
> > > cwarden$ cd COHCAP
> > >
> > > COHCAP cwarden$ git checkout master
> > >
> > > Already on 'master'
> > >
> > > Your branch is up-to-date with 'origin/master'.
> > >
> > > [edit file]
> > >
> > > COHCAP cwarden$ git status
> > >
> > > On branch master
> > >
> > > Your branch is up-to-date with 'origin/master'.
> > >
> > > Changes not staged for commit:
> > >
> > >   (use "git add <file>..." to update what will be committed)
> > >
> > >   (use "git checkout -- <file>..." to discard changes in working
> > directory)
> > >
> > >
> > >
> > > modified:   CHANGES
> > >
> > >
> > >
> > > no changes added to commit (use "git add" and/or "git commit -a")
> > >
> > > COHCAP cwarden$ git commit -a -m "fake commit"
> > >
> > > [master 225f7ac] fake commit
> > >
> > >  1 file changed, 1 insertion(+)
> > >
> > > COHCAP cwarden$ git status
> > >
> > > On branch master
> > >
> > > Your branch is ahead of 'origin/master' by 1 commit.
> > >
> > >   (use "git push" to publish your local commits)
> > >
> > >
> > > nothing to commit, working directory clean
> > >
> > > COHCAP cwarden$ git push origin master
> > >
> > > fatal: remote error: FATAL: W any packages/COHCAP nobody DENIED by
> > fallthru
> > >
> > > (or you mis-spelled the reponame)
> > >
> > >
> > > I tried this on a couple computers and I get the same error message
> with
> > the "git push origin master" command.  Can you please help me identify
> the
> > problem, so I can at least update the Bioconductor repository?
> > >
> > > Thanks,
> > > Charles
> > >
> > > On Thu, Aug 24, 2017 at 11:07 AM, Charles Warden <cwarden45 at gmail.com>
> > wrote:
> > > Hi Martin and Nitesh,
> > >
> > > Thanks for your help.
> > >
> > > I created a public ssh-key, I added it as a deploy key for the
> > Bioconductor package, and I provided that key in the git/svn transition
> > Google Doc file.
> > >
> > > I was trying to provide a key what would only affect the COHCAP
> package,
> > and not the other projects that are not Bioconductor projects.  Please
> let
> > me know if this still works.
> > >
> > > Thanks,
> > > Charles
> > >
> > > On Thu, Aug 24, 2017 at 5:59 AM, Martin Morgan <
> > martin.morgan at roswellpark.org> wrote:
> > > On 08/24/2017 07:27 AM, Turaga, Nitesh wrote:
> > > http://bioconductor.org/developers/how-to/git/<http://
> > bioconductor.org/developers/how-to/git/faq/>faq<http://
> > bioconductor.org/developers/how-to/git/faq/>/<http://
> > bioconductor.org/developers/how-to/git/faq/>
> > >
> > > Get Outlook for Android<https://aka.ms/ghei36>
> > >
> > > ________________________________
> > > From: Charles Warden <cwarden45 at gmail.com>
> > > Sent: Wednesday, August 23, 2017 11:32:42 PM
> > > To: Turaga, Nitesh
> > > Subject: Re: [Bioc-devel] COHCAP GitHub Update
> > >
> > > Hi Nitesh,
> > >
> > > I am getting a slightly different error message, now that I am changing
> > to be within the COHCAP directory:
> > >
> > > ###### Start Code ########
> > >
> > > COHCAP cwarden$ git fetch --all
> > >
> > > Fetching origin
> > >
> > > Fetching upstream
> > >
> > > Permission denied (publickey).
> > >
> > > this means that you do not have permissions to access your repository.
> > This is probably because you, as an existing svn account holder, have not
> > submitted an 'ssh' key to Bioconductor.
> > >
> > > The things you need to do are
> > >
> > >   1. create an ssh key pair, and submit the public key to your github
> > account. Follow the link to 'add your public key to your GitHub account'
> in
> > step 2 of
> > >
> > >     http://bioconductor.org/developers/how-to/git/
> maintain-github-bioc/
> > >
> > >   2. submit your request for ssh access to git.bioconductor.org,
> > following step 1 of
> > >
> > >     http://bioconductor.org/developers/how-to/git/new-
> package-workflow/
> > >
> > > (I will update the instructions at http://bioconductor.org/
> > developers/how-to/git/maintain-github-bioc/ to include this step.
> > >
> > >   3. Wait 24 hours for manual processing
> > >
> > >   4. Try again
> > >
> > > some more below...
> > >
> > >
> > >
> > > fatal: Could not read from remote repository.
> > >
> > >
> > > Please make sure you have the correct access rights
> > >
> > > and the repository exists.
> > >
> > > error: Could not fetch upstream
> > >
> > > ###### End Code ########
> > >
> > > I also don't see COHCAP when I search the Bioconductor repository (when
> > searching https://github.com/Bioconductor?utf8=%E2%9C%93&q=
> > COHCAP&type=&language=), and I also can't clone anything directory from
> > Bioconductor:
> > >
> > > github.com/Bioconductor contains public versions of repositories
> > maintained by the Bioconductor core team; yours will not appear there.
> > >
> > >
> > > ###### Start Code ########
> > >
> > > cwarden$ git clone git at git.bioconductor.org:packages/COHCAP
> > >
> > > Cloning into 'COHCAP'...
> > >
> > > Permission denied (publickey).
> > >
> > > fatal: Could not read from remote repository.
> > >
> > >
> > > Please make sure you have the correct access rights
> > >
> > > and the repository exists.
> > >
> > > ###### End Code ########
> > >
> > > I have my Bioconductor SVN username and password, but does something
> > need to be initialized with the new git system (where I'll have a new
> > Bioconductor username and password)?
> > >
> > > Thanks,
> > > Charles
> > >
> > > On Wed, Aug 23, 2017 at 2:18 PM, Turaga, Nitesh <
> > Nitesh.Turaga at roswellpark.org<mailto:Nitesh.Turaga at roswellpark.org>>
> > wrote:
> > > Hi
> > >
> > > On Aug 23, 2017, at 5:13 PM, Charles Warden <cwarden45 at gmail.com
> <mailto:
> > cwarden45 at gmail.com>> wrote:
> > >
> > > Hi,
> > >
> > > I downloaded code for the COHCAP Bioconductor SVN repository (
> > > https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/COHCAP/),
> > made
> > > some changes, and then tried to commit those changes.  However, I got
> an
> > > error message that the SVN repository is locked, so the changes could
> not
> > > be uploaded because of a switch to git.
> > >
> > > I have a GitHub account, and I uploaded the COHCAP code (with the
> latest
> > > round of changes) to GitHub:
> > >
> > > https://github.com/cwarden45/COHCAP
> > >
> > > So far so good.
> > >
> > > However, I am not sure how to make this the new Bioconductor
> > repository.  I
> > > am trying to follow the instructions available here:
> > >
> > > http://bioconductor.org/developers/how-to/git/sync-
> > existing-repositories/
> > >
> > > However, if I run the command *git remote add upstream
> > > git at git.bioconductor.org:packages/COHCAP.gi**t*, then I get an error
> > > message: *fatal: Not a git repository.*
> > >
> > >
> > > Can you paste the command and the error message as is, this formatting
> > seems off.
> > >
> > > Can you please help me update the COHCAP Bioconductor repository and
> > > understand how this is now managed through GitHub?
> > >
> > > Also, I posted this question on the Support forum, but that may have
> not
> > > been the right venue.  So, I apologize for the confusion.
> > >
> > > Thanks,
> > >
> > > Charles
> > >
> > >        [[alternative HTML version deleted]]
> > >
> > > _______________________________________________
> > > Bioc-devel at r-project.org<mailto:Bioc-devel at r-project.org> mailing list
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> > >
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-- 
Sean Davis, MD, PhD
Center for Cancer Research
National Cancer Institute
National Institutes of Health
Bethesda, MD 20892
https://seandavi.github.io/
https://twitter.com/seandavis12

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