[Bioc-devel] COHCAP GitHub Update

[Charles Warden]

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
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
> >
> >
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