[Bioc-devel] COHCAP GitHub Update

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 at git.bioconductor.org/packages/COHCAP.git>*

*fatal: repository 'git at git.bioconductor.org/packages/COHCAP.git
<http://git at 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>

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

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