[Bioc-devel] COHCAP GitHub Update

Charles Warden cwarden45 at gmail.com
Sun Sep 10 06:53:01 CEST 2017 

Hi Martin and Sean,

Thanks for your help - I think the issue may be that I don't have a private
key on the second computer (and the passcode still isn't recognized if I
remove the .pub extension).

I was trying to set up a deploy key on GitHub that would only apply to the
COHCAP repository, but I will test having a public account key for the
account (and do more testing before asking another question).

Thanks,
Charles

On Sep 9, 2017 7:34 PM, "Martin Morgan" <martin.morgan at roswellpark.org>
wrote:

> On 09/09/2017 09:06 PM, Sean Davis wrote:
>
>> 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.
>>
>
> actually, the Bioconductor git repository does not support reading using
> ssh keys, only https. So any could do
>
>  git clone https://git.bioconductor.org/packages/COHCAP
>
> but only people with valid ssh keys AND permissions can use
>
>   git clone git at git.bioconductor.org:packages/COHCAP
>
> (Sean -- you've got magical powers that carry over from svn days).
>
> I notice, Charles, that there are no keys registered with github
>
>   https://github.com/cwarden45.keys
>
> I suggest that you figure things out using github, where you can see your
> keys and where there is more public documentation. Also, note that you can
> look at your local key pairs, for instance on Linux
>
> $ ls ~/.ssh/id*
> /home/mtmorgan/.ssh/id_rsa  /home/mtmorgan/.ssh/id_rsa.pub
>
> and I can confirm that the public part of the key pair
>
> $ cat ~/.ssh/id_rsa.pub
> ssh-rsa AAAAB3NzaC1yc2EAAAABIwAAAIEAwrnfSVn+lfnzSRwylWgC2Q7T0QJWvI8A
> 0WHb8yMHF9OkgnldksS72OzjGr4qcz2kUsCb/ZsQTYj+g29zKUntbCSiLclEXBEz+lKUsdbG9z
> awRiIypW60cfXKnbB3WfxkSqsiLDTtYDuaVAgS1htKwe6GV3aSYuMCge27ZlNhBWc=
> mtmorgan at gopher4
>
> matches the public part of the key pair registered on my github account.
> (both github and Bioconductor support multiple key pairs).
>
> If you get to the point where your github public key is working, submit it
> via the form using your svn id and github id.
>
> Martin
>
>
>
>>
>>
>> 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
>>>>>>>>>
>>>>>>>> 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
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> 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
>>>>
>>>>
>>>
>>>
>>
>>
>
> 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,
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> received this message in error, please notify the sender immediately by
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