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

Wed Apr 5 15:03:47 CEST 2023

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
>>> 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:
>> http://secure-web.cisco.com/1LnTiYl4U5aiZv9MUQP8HFGMMtS3dII6KIIXyAig8z_4ahFQ0zUCrVtQOST4Lh8XxFx_GJAQU8xO_Pml_jbz64SSaRt9i30NzqAGq_Fn8b5JHMV8Fj8S2TmKYbAz2K-1-ivKeePv2HupVikTt9AZhVI8QlecwemzZ_o8gUDicwVcdIdyeFKoACKmqNeiCqFeRluTyb16JeQCYOVJF-yOj5ATVrJAS2A7000VwaREP1pyZKLeSkJJeEcV7607ZULhbMBzrYIPjB8lZ00_aupQ_5rhrSh0ETTBFNyO8LEzwq1psweEQErRCNWBO3dOqvBXN/http%3A%2F%2Ffive.sentenc.es
>
>
>
> --
> 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

This email message may contain legally privileged and/or confidential information.  If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited.  If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you.
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