[Bioc-devel] COHCAP GitHub Update
Charles Warden
cwarden45 at gmail.com
Sun Sep 10 02:40:33 CEST 2017
Hi,
I'm sorry, but I am having an issue setting up my ssh key. In particular,
it is not recognizing the passcode (and I've tried copying over a new
id_rsa.pub file as well as double-checking the passcode):
:~/.ssh$ ssh-add id_rsa.pub
Enter passphrase for id_rsa.pub:
Bad passphrase, try again for id_rsa.pub:
I also tried following these github instructions (
https://help.github.com/articles/error-permission-denied-publickey/): I
didn't see a solution, but I can confirm the problem:
~/.ssh$ ssh -T git at github.com
Permission denied (publickey)
Since Sean was able to run "git clone git at git.bioconductor.org:packa
ges/COHCAP.git", is there some other modification I should make to ssh
key? If it matters, the original computer was a Mac OSX and the computer I
am trying to manage COHCAP from is an Ubuntu VM (running within Windows).
Also, the error message is the same if using the bioconductor git instead
of the github:
~/.ssh$ ssh -T git at git.bioconductor.org
Permission denied (publickey).
Thanks,
Charles
On Mon, Sep 4, 2017 at 5:28 PM, Sean Davis <seandavi at gmail.com> wrote:
> Hi, Charles. See replies inline.
>
> On Mon, Sep 4, 2017 at 3:30 PM, Charles Warden <cwarden45 at gmail.com>
> wrote:
>
>> 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.
>>
>
> This error means that there is a problem with your git ssh key. It could
> be that your private key is not present on the new computer or that the ssh
> key on Bioconductor has not been registered. Given the error below, it
> appears that at least one ssh key is working.
>
>
>>
>> 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.
>>
>
> You can often follow the instructions suggested by "hints" given by git.
> In this case, it appears that there are some commits present at
> Bioconductor that are not present in your local clone. Doing a `git pull`
> will fetch and merge those changes. Assuming there are no merge conflicts,
> you should then be able to push.
>
>
>>
>>
>> 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?
>>
>
> You have had a few separate issues on this thread. My last comment about
> `git pull` means that your first two problems (typo in the URL, missing or
> mismatched ssh key) were overcome already. I'd proceed from there.
>
> Hope that helps,
> Sean
>
>
>
>>
>> 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.si
>>>> te.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-gith
>>>> ub-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-w
>>>> orkflow/
>>>> > >
>>>> > > (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
>>>
>>
>>
>
>
> --
> 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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