[Bioc-devel] DNAcopy git push issue

Thu Jun 29 16:34:12 CEST 2023

In this iteration of the app I don't believe so I think you can only add.

Lori Shepherd - Kern

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

________________________________
From: Venkat Seshan <veseshan using gmail.com>
Sent: Thursday, June 29, 2023 10:30 AM
To: Kern, Lori <Lori.Shepherd using RoswellPark.org>
Cc: bioc-devel using r-project.org <bioc-devel using r-project.org>
Subject: Re: [Bioc-devel] DNAcopy git push issue

Is there a way to remove all the old ssh keys in BiocCredentials? Thanks.

On Thu, Jun 29, 2023 at 10:21 AM Kern, Lori <Lori.Shepherd using roswellpark.org<mailto:Lori.Shepherd using roswellpark.org>> wrote:
excellent. good to hear!

Lori Shepherd - Kern

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

________________________________
From: Venkat Seshan <veseshan using gmail.com<mailto:veseshan using gmail.com>>
Sent: Thursday, June 29, 2023 10:24 AM
To: Kern, Lori <Lori.Shepherd using RoswellPark.org>
Cc: bioc-devel using r-project.org<mailto:bioc-devel using r-project.org> <bioc-devel using r-project.org<mailto:bioc-devel using r-project.org>>
Subject: Re: [Bioc-devel] DNAcopy git push issue

Thank you for pointing me in the right direction. I deleted the old RSA ssh key generated a new one and added it to both GitHub and BiocCredentials. Now everything works.

seshanv using omega0:~$ ssh -T git using git.bioconductor.org<mailto:git using git.bioconductor.org> | head -5
hello seshanv, this is git using ip-172-30-0-33 running gitolite3 v3.6.6-6-g7c8f0ab on git 2.33.0

 R     admin/..*
 R     packages/..*
 R   admin/BiocManager

and

seshanv using omega0:~/GitRepos/Bioc/DNAcopy$ git push upstream devel
Enumerating objects: 38, done.
Counting objects: 100% (38/38), done.
Delta compression using up to 16 threads
Compressing objects: 100% (15/15), done.
Writing objects: 100% (23/23), 5.68 KiB | 5.68 MiB/s, done.
Total 23 (delta 18), reused 13 (delta 8), pack-reused 0
To git.bioconductor.org:packages/DNAcopy.git
   416a2a0..f953003  devel -> devel

Thank you again.
Venkat

On Thu, Jun 29, 2023 at 10:10 AM Venkat Seshan <veseshan using gmail.com<mailto:veseshan using gmail.com>> wrote:
It is authenticating fine except that it is greeting me as venkatre using mskcc.org<mailto:venkatre using mskcc.org>. Thanks.

seshanv using omega0:~$ ssh -T git using git.bioconductor.org<mailto:git using git.bioconductor.org> | head
hello venkatre using mskcc.org<mailto:venkatre using mskcc.org>, this is git using ip-172-30-0-33 running gitolite3 v3.6.6-6-g7c8f0ab on git 2.33.0

 R     admin/..*
 R     packages/..*
 R   admin/BiocManager
 R   admin/bioconductor.org<http://secure-web.cisco.com/1QzN1prnKLY6gVKlXFGaCtqMR-BYfzgYeUx7gZwZ9Xbrvsj9IOOyThbd537bRAbfK1J8DNydBt4RhN0NubP8MJqXpE1N_1TNTpgHBbmBl9FxTeKb9_mxNFTj0804DJ9gqUiNyKdkmIy9p2ZRtoZrq6g67jzmPseOBudldPRoU4_4fqsqByeRgQwdZ5GtHKM3lm6BbhmSE0jDdvP1cSKtouE2_wIUVDPkwYKl6qSSX4BbE7K90IBixhM-XftgyACqCWM8ZPsccGjj7La_Rn2LlwQw1ARD3A0uK87vBSOAymlC7-CZ7iMp3V0-wQ-dakinv/http%3A%2F%2Fbioconductor.org>
 R   admin/hook_maintainer
 R   admin/manifest
 R   packages/ABAData
 R   packages/ABAEnrichment

On Thu, Jun 29, 2023 at 7:49 AM Kern, Lori <Lori.Shepherd using roswellpark.org<mailto:Lori.Shepherd using roswellpark.org>> wrote:
sorry my previous message didn't render either...
What does the following show:

ssh -T git using git.bioconductor.org<mailto:git using git.bioconductor.org>

Lori Shepherd - Kern

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

________________________________
From: Bioc-devel <bioc-devel-bounces using r-project.org<mailto:bioc-devel-bounces using r-project.org>> on behalf of Venkat Seshan <veseshan using gmail.com<mailto:veseshan using gmail.com>>
Sent: Wednesday, June 28, 2023 5:35 PM
To: bioc-devel using r-project.org<mailto:bioc-devel using r-project.org> <bioc-devel using r-project.org<mailto:bioc-devel using r-project.org>>
Subject: Re: [Bioc-devel] DNAcopy git push issue

I saw an error message close to mine mentioned here
https://secure-web.cisco.com/1NegEFTMGhRUIXTRIBqpAEzGh6yJOCgtz8kTX2CCVjn-vPZfjGkLKQYzNa0w8hx5M-g8YyLDRX5APAVuE78NHrRCnzt6MAfdZbThypyWLV5W9f_hz4pPGzb0BHLZnN7nl98HZzVHKXa6e1RQGa8E9BVGTnbnE5v_rxI6iCkoWxG3dz0BmGp1KBSxf3aItnbH1rgtw_4SkpO_OtKQ1c2LC12ndM-OdJftXETAH32qVcgYb5H5qb7EaCnMv4U4FqH3jrTfpaAasBgUO72II5xoYxhhgLm-OeHcbLnEHjyCNaXbahTwyiEVfUsN4dLbbwVPP/https%3A%2F%2Fgithub.com%2FBioconductor%2Fbioc_git_transition%2Fissues%2F30
I cloned the package using ssh and so could not be the cause.

On Wed, Jun 28, 2023 at 3:53 PM Venkat Seshan <veseshan using gmail.com<mailto:veseshan using gmail.com>> wrote:

> I noticed that my prior message was mangled by outlook and so resending
> from gmail. Thanks.
>
> I cloned the repo afresh and set up the remote.
>
> seshanv using omega0:~/GitRepos/Bioc/DNAcopy$ git remote -v
> origin     git using github.com:veseshan/DNAcopy.git (fetch)
> origin     git using github.com:veseshan/DNAcopy.git (push)
> upstream            git using git.bioconductor.org:packages/DNAcopy.git (fetch)
> upstream            git using git.bioconductor.org:packages/DNAcopy.git (push)
>
> I can run git diff and with upstream and it shows the differences as it
> should be
>
> seshanv using omega0:~/GitRepos/Bioc/DNAcopy$ git diff devel upstream/devel |
> head -12
> diff --git a/DESCRIPTION b/DESCRIPTION
> index a0219f9..c7c59a3 100644
> --- a/DESCRIPTION
> +++ b/DESCRIPTION
> @@ -1,6 +1,6 @@
> Package: DNAcopy
> -Title: DNA Copy Number Data Analysis
> -Version: 1.75.2
> +Title: DNA copy number data analysis
> +Version: 1.75.1
> Author: Venkatraman E. Seshan, Adam Olshen
> Description: Implements the circular binary segmentation (CBS)
>
> I have ensured Github has both my RSA and ED25519 keys and I can push to
> my repo and it uses SSH key appropriately.
>
> seshanv using omega0:~/GitRepos/Bioc/DNAcopy$ git push
> Warning: Permanently added the ECDSA host key for IP address
> '140.82.112.3' to the list of known hosts.
> Enumerating objects: 5, done.
> Counting objects: 100% (5/5), done.
> Delta compression using up to 16 threads
> Compressing objects: 100% (3/3), done.
> Writing objects: 100% (3/3), 331 bytes | 331.00 KiB/s, done.
> Total 3 (delta 2), reused 0 (delta 0), pack-reused 0
> remote: Resolving deltas: 100% (2/2), completed with 2 local objects.
> To github.com:veseshan/DNAcopy.git
>    cdd8cfd..f953003  devel -> devel
>
> I confirmed that BiocCredentials has the SSH keys . However I am getting
> the same error when I try to push upstream
>
> seshanv using omega0:~/GitRepos/Bioc/DNAcopy$ git push upstream devel
> FATAL: W any packages/DNAcopy venkatre using mskcc.org<mailto:venkatre using mskcc.org> DENIED by fallthru
> (or you mis-spelled the reponame)
> fatal: Could not read from remote repository.
>
> Please make sure you have the correct access rights
> and the repository exists.
>
> I can’t figure out what the issue is.
>
> Thanks
>
> On Wed, Jun 28, 2023 at 7:29 AM Kern, Lori <Lori.Shepherd using roswellpark.org<mailto:Lori.Shepherd using roswellpark.org>>
> wrote:
>
>> I'm not sure why the upstream has a mailto: at the start but perhaps
>> try resetting upstream to  `git using git.bioconductor.org<mailto:git using git.bioconductor.org>:
>> packages/DNAcopy.git<mailto:git using git.bioconductor.org<mailto:git using git.bioconductor.org>
>> :packages/DNAcopy.git>`
>>
>> The credentials are set up correctly. Perhaps also adding a new ssh key
>> to the BiocCredentials account might be necessary?
>>
>> Cheers,
>>
>>
>>
>> Lori Shepherd - Kern
>>
>> Bioconductor Core Team
>>
>> Roswell Park Comprehensive Cancer Center
>>
>> Department of Biostatistics & Bioinformatics
>>
>> Elm & Carlton Streets
>>
>> Buffalo, New York 14263
>>
>> ________________________________
>> From: Bioc-devel <bioc-devel-bounces using r-project.org<mailto:bioc-devel-bounces using r-project.org>> on behalf of Seshan,
>> Venkatraman <SeshanV using mskcc.org<mailto:SeshanV using mskcc.org>>
>> Sent: Tuesday, June 27, 2023 5:53 PM
>> To: bioc-devel using r-project.org<mailto:bioc-devel using r-project.org> <bioc-devel using r-project.org<mailto:bioc-devel using r-project.org>>
>> Subject: [Bioc-devel] DNAcopy git push issue
>>
>> After a long time of not needing any change to the package I tried to
>> push changes upstream and got the following error:
>>
>> seshanv using omega0:~/GitRepos/DNAcopy$ git push upstream devel
>> FATAL: W any packages/DNAcopy mailto:venkatre using mskcc.org DENIED by
>> fallthru
>> (or you mis-spelled the reponame)
>> fatal: Could not read from remote repository.
>>
>> Please make sure you have the correct access rights
>> and the repository exists.
>> ---------------------------------------------------------
>>
>> I haven't had the email address venkatre using mskcc.org<mailto:venkatre using mskcc.org> since 2007. The git
>> remotes are correct
>>
>> seshanv using omega0:~/GitRepos/DNAcopy$ git remote -v
>> origin
>> https://secure-web.cisco.com/13GYvlJCqh6qE2EmB3eN4Edje-48SQ9VP9RDQxi8R6smN7YMfzSwExzwR71KtQC68TU3j87nJWZaQHYO9a3rbbPdF3BlW9ZcLSQEc4_xNtXCvcr7t55RYnLObQ0HqTdQeMME0pMgsINGhJUwFd3jTZvZM84FXKyIRiWpKDCqrzROjERuTjqrpnbWjvIDPM0ms5nZrKow2sZx3HZ3zjOnHGdhl5TU872hM5LOtQ4H_Yl8iTkNDoyNPYceSt_8I9yReZ50DjFAdK6Rx2sGoQW_gFl70SS1OrIYpUzbBuO4sN-IM84-6pPEB4JlF1clbBzm-/https%3A%2F%2Fgithub.com%2Fveseshan%2FDNAcopy.git
>> (fetch)
>> origin
>> https://secure-web.cisco.com/13GYvlJCqh6qE2EmB3eN4Edje-48SQ9VP9RDQxi8R6smN7YMfzSwExzwR71KtQC68TU3j87nJWZaQHYO9a3rbbPdF3BlW9ZcLSQEc4_xNtXCvcr7t55RYnLObQ0HqTdQeMME0pMgsINGhJUwFd3jTZvZM84FXKyIRiWpKDCqrzROjERuTjqrpnbWjvIDPM0ms5nZrKow2sZx3HZ3zjOnHGdhl5TU872hM5LOtQ4H_Yl8iTkNDoyNPYceSt_8I9yReZ50DjFAdK6Rx2sGoQW_gFl70SS1OrIYpUzbBuO4sN-IM84-6pPEB4JlF1clbBzm-/https%3A%2F%2Fgithub.com%2Fveseshan%2FDNAcopy.git
>> (push)
>> upstream        mailto:git using git.bioconductor.org:packages/DNAcopy.git
>> (fetch)
>> upstream        mailto:git using git.bioconductor.org:packages/DNAcopy.git
>> (push)
>> ---------------------------------------------------------
>>
>> And Bioconductor Git Credentials app shows my correct email address
>> seshanv using mskcc.org<mailto:seshanv using mskcc.org>
>>
>> I don't understand what the issue is. Any help in fixing this will be
>> greatly appreciated.
>>
>> Thanks,
>> Venkat Seshan
>>
>> =====================================================================
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