[Bioc-devel] DNAcopy git push issue

Venkat Seshan ve@e@h@n @end|ng |rom gm@||@com
Thu Jun 29 16:24:15 CEST 2023 

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 | 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> wrote:

> It is authenticating fine except that it is greeting me as
> venkatre using mskcc.org. Thanks.
>
> seshanv using omega0:~$ ssh -T git using git.bioconductor.org | head
> hello 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
>  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>
> wrote:
>
>> sorry my previous message didn't render either...
>> What does the following show:
>>
>> ssh -T 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> on behalf of
>> Venkat Seshan <veseshan using gmail.com>
>> *Sent:* Wednesday, June 28, 2023 5:35 PM
>> *To:* bioc-devel using r-project.org <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> 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 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>
>> > 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:
>> >> packages/DNAcopy.git<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> on behalf of
>> Seshan,
>> >> Venkatraman <SeshanV using mskcc.org>
>> >> Sent: Tuesday, June 27, 2023 5:53 PM
>> >> To: bioc-devel using r-project.org <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
>> <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 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
>> <git using git.bioconductor.org:packages/DNAcopy.git>
>> >> (fetch)
>> >> upstream        mailto:git using git.bioconductor.org:packages/DNAcopy.git
>> <git using git.bioconductor.org:packages/DNAcopy.git>
>> >> (push)
>> >> ---------------------------------------------------------
>> >>
>> >> And Bioconductor Git Credentials app shows my correct email address
>> >> 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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