[Bioc-devel] DNAcopy git push issue

Venkat Seshan ve@e@h@n @end|ng |rom gm@||@com
Thu Jun 29 16:30:01 CEST 2023 

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>
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>
> *Sent:* Thursday, June 29, 2023 10:24 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
>
> 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
> <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>
> 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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