[Bioc-devel] COHCAP GitHub Update
Charles Warden
cwarden45 at gmail.com
Mon Sep 4 21:30:43 CEST 2017
Hi Sean,
I'm admittedly on a different computer now, but I still get an error
message (although it is different than the last one):
git clone git at git.bioconductor.org:packages/COHCAP.git
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.
Also, there was a lot of text in the previous message, but I tried
following the commands to merge and update the Bioconductor and GitHub
COHCAP repositories. On that computer (the computer where I defined the
ssh key), I could run "git remote add upstream git at git.bioconductor.org:
packages/COHCAP.git", but I ran into a problem at the push step:
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.
Is there a way that I should modify the ssh "git clone
git at git.bioconductor.org:packages/COHCAP.git" command?
Thanks,
Charles
On Mon, Sep 4, 2017 at 11:41 AM, Sean Davis <seandavi at gmail.com> wrote:
> 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.is
>> land.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
>> > > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>> > >
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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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