[Bioc-devel] COHCAP GitHub Update

Sean Davis seandavi at gmail.com
Sun Sep 10 03:06:52 CEST 2017 

Hi, Charles.

See inline.

On Sat, Sep 9, 2017 at 8:40 PM, Charles Warden <cwarden45 at gmail.com> wrote:

> 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:
>

Many folks do not use a passphrase (just hit enter when creating a new key)
for ssh keys. It is potentially not as secure (in reality, probably not by
much), but it does simplify things at least to start.


>
> 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)
>

I'm not sure what the problem is at this point, but it seems pretty likely
that figuring out what is broken and trying to fix it might be challenging.
I would suggest starting over from scratch, using Github as a starting
place.

https://help.github.com/articles/connecting-to-github-with-ssh/

Once you get your key working with github from your various machines, then
you can move ahead with the Bioconductor git server.

- While it is tempting to make new ssh keys every time you need one, that
has some very real disadvantages. Note that the github article has some
notes about finding existing ssh keys. That said, in your case, a clean
slate might be the easiest way to go, particularly since it appears that
you might have misplaced the passphrase.
- The file permissions on key files are important, so pay attention to
notes about setting those correctly.


>
> 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?
>

Git clone does not require permissions for public github repositories or
for bioconductor package repositories. Only operations that involving
"writing" to the git server require authentication, so the fact that I was
able to clone your repo has nothing to do with my having correctly used an
ssh key. Anyone, even without ANY ssh key, could have done so.



> 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:
>

As for machine types and ssh, that does not matter. The ssh protocol is not
machine-type dependent, although how to use ssh keys may vary a bit,
particularly on windows.

Sean


>
> ~/.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
>>>>> > >
>>>>> > >
>>>>> > >
>>>>> > > This email message may contain legally privileged and/or
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>>>>> > information.  If you are not the intended recipient(s), or the
>>>>> employee or
>>>>> > agent responsible for the delivery of this message to the intended
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>>>>> > received this message in error, please notify the sender immediately
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>>>>> > e-mail and delete this email message from your computer. Thank you.
>>>>> > >
>>>>> > >
>>>>> > >
>>>>> > > 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
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>>>>> > >         [[alternative HTML version deleted]]
>>>>> > >
>>>>> > > _______________________________________________
>>>>> > > Bioc-devel at r-project.org mailing list
>>>>> > > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>>> > >
>>>>> > >
>>>>> > >
>>>>> > > 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.
>>>>> > >
>>>>> > >
>>>>> >
>>>>> >
>>>>> >
>>>>> > 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.
>>>>> >
>>>>>
>>>>>         [[alternative HTML version deleted]]
>>>>>
>>>>> _______________________________________________
>>>>> Bioc-devel at r-project.org mailing list
>>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>>>
>>>>
>>>>
>>>>
>>>> --
>>>> 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
>>
>
>


-- 
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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