Re: [Bioc-devel] COHCAP GitHub Update

[Martin Morgan]

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 <cwarde...@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 g...@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 g...@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 g...@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+lfnzSRwylWgC2Q7T0QJWvI8A0WHb8yMHF9OkgnldksS72OzjGr4qcz2kUsCb/ZsQTYj+g29zKUntbCSiLclEXBEz+lKUsdbG9zawRiIypW60cfXKnbB3WfxkSqsiLDTtYDuaVAgS1htKwe6GV3aSYuMCge27ZlNhBWc= 
mtmorgan@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 g...@git.bioconductor.org
Permission denied (publickey).

Thanks,
Charles



On Mon, Sep 4, 2017 at 5:28 PM, Sean Davis <seand...@gmail.com> wrote:

Hi, Charles. See replies inline.

On Mon, Sep 4, 2017 at 3:30 PM, Charles Warden <cwarde...@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 g...@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 g...@git.bioconductor.org:
packages/COHCAP.git", but I ran into a problem at the push step:

COHCAP cwarden$ git push upstream master

To g...@git.bioconductor.org:packages/COHCAP.git

  ! [rejected]        master -> master (non-fast-forward)

error: failed to push some refs to 'g...@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
g...@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 <seand...@gmail.com> wrote:

Hi, Charles.

The command is slightly off. Note the first '/' is a ':'.  This worked
for me:

git clone g...@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 <cwarde...@gmail.com>
wrote:

Hi Nitesh,

Thanks.  Unfortunately, I can't connect to the Bioconductor repository
that
way:


*cwarden$ git clone g...@git.bioconductor.org/packages/COHCAP.git
<http://g...@git.bioconductor.org/packages/COHCAP.git>*

*fatal: repository 'g...@git.bioconductor.org/packages/COHCAP.git
<http://g...@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 g...@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 g...@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 g...@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 g...@github.com:cwarden45/COHCAP.git (fetch)

origin g...@github.com:cwarden45/COHCAP.git (push)

COHCAP cwarden$ git remote add upstream g...@git.bioconductor.org:
packages/COHCAP.git

BR11252:COHCAP cwarden$ git remote -v

origin g...@github.com:cwarden45/COHCAP.git (fetch)

origin g...@github.com:cwarden45/COHCAP.git (push)

upstream g...@git.bioconductor.org:packages/COHCAP.git (fetch)

upstream g...@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 g...@git.bioconductor.org:packages/COHCAP.git

  ! [rejected]        master -> master (non-fast-forward)

error: failed to push some refs to 'g...@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.tur...@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:
g...@git.bioconductor.org
         • HTTPS (public) read only access:
https://git.bioconductor.org


Nitesh

On Sep 3, 2017, at 4:30 PM, Charles Warden <cwarde...@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 <
cwarde...@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.mor...@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 <cwarde...@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 g...@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.tur...@roswellpark.org<mailto:nitesh.tur...@roswellpark.org>>
wrote:
Hi

On Aug 23, 2017, at 5:13 PM, Charles Warden <cwarde...@gmail.com
<mailto:
cwarde...@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
g...@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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https://seandavi.github.io/
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--
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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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