[Bioc-devel] Fixing autonomics - ssh: connect to host git.bioconductor.org port 22: Connection timed out

Wed Apr 5 14:56:22 CEST 2023

Thank you very much Lori,

$ git remote -v
origin  https://github.com/bhagwataditya/autonomics.git (fetch)
origin  https://github.com/bhagwataditya/autonomics.git (push)
upstream        git using git.bioconductor.org:packages/autonomics.git (fetch)
upstream        git using git.bioconductor.org:packages/autonomics.git (push)

$ ssh -T -v git using git.bioconductor.org
OpenSSH_8.8p1, OpenSSL 1.1.1m  14 Dec 2021
debug1: Reading configuration data /etc/ssh/ssh_config
debug1: Connecting to git.bioconductor.org [34.192.48.227] port 22.
debug1: connect to address 34.192.48.227 port 22: Connection timed out
ssh: connect to host git.bioconductor.org port 22: Connection timed out

I also went through the troubleshooting FAQ but so far could not  
identify the cause.

The ssh key that I have on my machine is there in BiocCredentials.
I noticed that it was not in my github account, which I have now added.
That didnt seem to make a difference though.

Thank you very much for helping.

Aditya

> It would help to show some of the commands and output in the FAQ for  
> git help and working through some of the trouleshooting there.
>
> http://contributions.bioconductor.org/git-version-control.html#faq
>
> Particularly showing your
> git remote  -v
>
> and trying
>
>
>  ssh -T -v 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  
> Aditya Bhagwat via Bioc-devel <bioc-devel using r-project.org>
> Sent: Wednesday, April 5, 2023 7:33 AM
> To: Sarvesh Nikumbh <sarvesh.nikumbh using gmail.com>
> Cc: bioc-devel using r-project.org <bioc-devel using r-project.org>
> Subject: Re: [Bioc-devel] Fixing autonomics - ssh: connect to host  
> git.bioconductor.org port 22: Connection timed out
>
> Thank you very much Sarvesh, lovely also to hear from you - how are you? .
>
> I had indeed failed to do these branch renamings which I now have.
> Unfortunately, my ssh issue remains:
>
> git push upstream devel
> ssh: connect to host git.bioconductor.org port 22: Connection timed out
> fatal: Could not read from remote repository.
>
> Dear BioC team, could you help out, am a bit at loss here ?
>
> Thank you very much,
>
> Aditya
>
>
>
>> Hi Aditya,
>>
>> Can you check if this is due to the recent branch name changes: default
>> branch name changed from 'main' to 'devel'
>> This was announced on the mailing-list, and also on this blogpost:
>> https://secure-web.cisco.com/1n72fvF59dD6BZtBdt6wi9Th7fr3G7_rRtSP9FgXzBRpHnSq-VrSgmyZlsAZ4KjMK-pSsxbs9F2zruBwHjVrdFmi4KD7vdnC-vhDy3qDgan2xX9UGFvUBU0MvtXSbXn-0RJfroqoyy3xj4ETCHFaoJ6cPKaoO-tqdefMvlf5zDYW5d4V0RKW61PLY4Qy0F_vqKxqQ2aTb_0DxWbnYs-I84vMG_6QA2TWTUGyFqE9D9gbvVQMu5GMxw6G7t7xZF_BUpdUBrgPEQKJEkundypNCsh3Of95OHse3VzpxIPUn-8j8QCV8ZgC8aZ-tVcnokUlF/https%3A%2F%2Fbioconductor.github.io%2Fbiocblog%2Fposts%2F2023-03-01-transition-to-devel%2F
>>
>> Sarvesh
>>
>> On Tue, 4 Apr 2023 at 19:38, Aditya Bhagwat via Bioc-devel <
>> bioc-devel using r-project.org> wrote:
>>
>>> Dear BioC team,
>>>
>>> I am having the same error as many others (the missing BiocStyle
>>> issue) and I wanted to fix it. But I somehow am not getting into
>>> git.bioconductor.org anymore :
>>>
>>> $ git fetch --all
>>> Fetching origin
>>> Fetching upstream
>>> ssh: connect to host git.bioconductor.org port 22: Connection timed out
>>> 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
>>>
>>> I checked BiocCredentials and my public key is visible there.
>>>
>>> What else could this be ? I changed institutes since my last push, in
>>> my current setup things go through a proxyserver, could that be the
>>> reason?
>>>
>>> Thank you for feedback.
>>>
>>> Aditya
>>>
>>>
>>> --
>>> Aditya Bhagwat
>>> Statistics ∙ Bioinformatics ∙ Data Science
>>> Translational Proteomics ∙ Philipps-University Marburg
>>> Karl-von-Frisch-Str 2 ∙ 35043 Marburg ∙ Germany
>>> Tel.: +49 6421 28 27403
>>>
>>> _______________________________________________
>>> Bioc-devel using r-project.org mailing list
>>> https://secure-web.cisco.com/1WSmgk-KPuAvx2yiy7_CfLoJSFFXcVGygfQznt_qB7SQzYIOTZOS1jnbIlMfheyKx9-wSPjP2sVqdPJJNmmvga9wi8cTqmeUh9t1N_wRtyS0YXMH081klK8t7HHOsECW405BsZJMDrRD9Xae5g0NPzAyPh5a48WuH2iXg5nt8JtuUYOU4F2XbFwGqtaIdpGPU-i4DCuMaSTuyiOpGBc5SQaAnixj9Ghn0ybCbegKZobuyDSZ2cOw0iRcWcgLYgYYZHm07c0yilexca5YctM5QZp-Ex-opMf-2lqTxelW3hks2aPaGG-GOCGpv9K9gwQTL/https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel
>>>
>>
>>
>> --
>>
>> thanks!
>> -Sarvesh
>>
>> --------------------------------------------
>> Q: Why is this email five sentences or less?
>> A:  
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>
>
> --
> Aditya Bhagwat
> Statistics ∙ Bioinformatics ∙ Data Science
> Translational Proteomics ∙ Philipps-University Marburg
> Karl-von-Frisch-Str 2 ∙ 35043 Marburg ∙ Germany
> Tel.: +49 6421 28 27403
>
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-- 
Aditya Bhagwat
Statistics ∙ Bioinformatics ∙ Data Science
Translational Proteomics ∙ Philipps-University Marburg
Karl-von-Frisch-Str 2 ∙ 35043 Marburg ∙ Germany
Tel.: +49 6421 28 27403