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

Wed Apr 5 15:40:36 CEST 2023

Dear Lori and Sarvesh,

The proxy server at our institute was blocking ssh.
Sorry for bothering you with that, it's working now : )

Thankyou very much for the help!

Aditya

> It looks like it reads /etc/ssh/ssh_config but doesn't actually try  
> a ssh key.  Perhaps try regenerating a ssh key and adding new or  
> check the setting in the ssh_config that it is refrencing.
>
>
> Lori Shepherd - Kern
>
> Bioconductor Core Team
>
> Roswell Park Comprehensive Cancer Center
>
> Department of Biostatistics & Bioinformatics
>
> Elm & Carlton Streets
>
> Buffalo, New York 14263
>
> ________________________________
> From: aditya.bhagwat using uni-marburg.de <aditya.bhagwat using uni-marburg.de>
> Sent: Wednesday, April 5, 2023 8:56 AM
> To: Kern, Lori <Lori.Shepherd using RoswellPark.org>
> Cc: Sarvesh Nikumbh <sarvesh.nikumbh using gmail.com>;  
> 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 Lori,
>
> $ git remote -v
> origin   
> https://secure-web.cisco.com/12mXJ65QixB3NHWkG2clCIt7EuA2ogRSnpCZg2WeBlyKGEe4fCwN92cdYjCXrFEtq8jL9iIpV73weH_1i_U2R1QIgyH1_W4Kb7UGXF3UHvaEuQrElOxLsUMx9R4deNWl0EK9GPJqm2JSSNcjVom1A3ncR7heM9u5_H7hT7FBmKI-zgJm3yhzOBDbhNZraG9LArQLtPzA9WNOZb5ZPbKSGtptjQpk9GncgSkYtYJWMhjOqLQgkOt8PQQrsM96P4Hose38bllGfYhD4bu9M9-MHqRzVI0gY-bK4r0fndo1IA9OAooTEl8_1UG7z8Ec9644p/https%3A%2F%2Fgithub.com%2Fbhagwataditya%2Fautonomics.git  
> (fetch)
> origin   
> https://secure-web.cisco.com/12mXJ65QixB3NHWkG2clCIt7EuA2ogRSnpCZg2WeBlyKGEe4fCwN92cdYjCXrFEtq8jL9iIpV73weH_1i_U2R1QIgyH1_W4Kb7UGXF3UHvaEuQrElOxLsUMx9R4deNWl0EK9GPJqm2JSSNcjVom1A3ncR7heM9u5_H7hT7FBmKI-zgJm3yhzOBDbhNZraG9LArQLtPzA9WNOZb5ZPbKSGtptjQpk9GncgSkYtYJWMhjOqLQgkOt8PQQrsM96P4Hose38bllGfYhD4bu9M9-MHqRzVI0gY-bK4r0fndo1IA9OAooTEl8_1UG7z8Ec9644p/https%3A%2F%2Fgithub.com%2Fbhagwataditya%2Fautonomics.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://secure-web.cisco.com/18MFSeHzZZB_WuIlGDqlzJdFRKETumUZjeCtSgSrANYmR9CyDbS-RMo8AVTsDgJKleT8dp9w9QTrX9eiy0thyU3IL8BCWxDa550ejaMKUoVKvybRr8chTr3WQqgYudsSKXSv-GvtBRgs2YuhV4R5GZGK3qJ34BxkHYk2lPkkYGywLSuMzYSP-MQshj85idbKgtIJ7GSLyNVnPjwm3vA9SpP6T9_6rTWyDbly5cmSvREZISPzhTEBnPX3m5lSozzqjCOWNHqUASmQLoCjJlWGSJZjKNp7gx2pS5lsOGvr2CYtE5TQao2-3h9u0x4FihANR/http%3A%2F%2Fcontributions.bioconductor.org%2Fgit-version-control.html%23faq
>>
>> 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
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>>>>
>>>
>>>
>>> --
>>>
>>> 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
>>
>> _______________________________________________
>> Bioc-devel using r-project.org mailing list
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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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> confidential information.  If you are not the intended recipient(s),  
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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