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.bhag...@uni-marburg.de <aditya.bhag...@uni-marburg.de>
Sent: Wednesday, April 5, 2023 8:56 AM
To: Kern, Lori <lori.sheph...@roswellpark.org>
Cc: Sarvesh Nikumbh <sarvesh.niku...@gmail.com>;
bioc-devel@r-project.org <bioc-devel@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 g...@git.bioconductor.org:packages/autonomics.git (fetch)
upstream g...@git.bioconductor.org:packages/autonomics.git (push)
$ ssh -T -v g...@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 g...@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-boun...@r-project.org> on behalf of
Aditya Bhagwat via Bioc-devel <bioc-devel@r-project.org>
Sent: Wednesday, April 5, 2023 7:33 AM
To: Sarvesh Nikumbh <sarvesh.niku...@gmail.com>
Cc: bioc-devel@r-project.org <bioc-devel@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@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
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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
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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
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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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