Re: [Bioc-devel] Fixing autonomics - ssh: connect to host git.bioconductor.org port 22: Connection timed out
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 Sent: Wednesday, April 5, 2023 8:56 AM To: Kern, Lori Cc: Sarvesh Nikumbh ; 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) upstreamg...@git.bioconductor.org:packages/autonomics.git (fetch) upstreamg...@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 on behalf of Aditya Bhagwat via Bioc-devel Sent: Wednesday, April 5, 2023 7:33 AM To: Sarvesh Nikumbh Cc: 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
Re: [Bioc-devel] Fixing autonomics - ssh: connect to host git.bioconductor.org port 22: Connection timed out
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 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 on behalf of Aditya Bhagwat via Bioc-devel Sent: Wednesday, April 5, 2023 7:33 AM To: Sarvesh Nikumbh Cc: 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 >> >> ___ >> Bioc-devel@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@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 This email message ma
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://bioconductor.github.io/biocblog/posts/2023-03-01-transition-to-devel/ 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 ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel -- thanks! -Sarvesh Q: Why is this email five sentences or less? A: http://five.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@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Fixing autonomics - ssh: connect to host git.bioconductor.org port 22: Connection timed out
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://bioconductor.github.io/biocblog/posts/2023-03-01-transition-to-devel/ 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 > > ___ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > -- thanks! -Sarvesh Q: Why is this email five sentences or less? A: http://five.sentenc.es [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] Fixing autonomics - ssh: connect to host git.bioconductor.org port 22: Connection timed out
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@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
