[Bioc-devel] git commit issues

Tue Apr 23 13:30:39 CEST 2024

I might suggest adding a new ssh key to your BiocCredentials account as it seems to be having issues with your key

Lori Shepherd - Kern

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

________________________________
From: Carlotta Meyring <carlotta.meyring using uniklinik-freiburg.de>
Sent: Tuesday, April 23, 2024 7:20 AM
To: Kern, Lori <Lori.Shepherd using RoswellPark.org>; bioc-devel using r-project.org <bioc-devel using r-project.org>
Subject: AW: [Bioc-devel] git commit issues

Thank you very much, but still when I run: git push upstream main:devel, I get the same error message:

error: cannot spawn https://github.com/cmeyring.keys: No such file or directory

error: cannot spawn https://github.com/cmeyring.keys: No such file or directory

fatal: unable to fork

Carlotta Meyring

Methods of Modelling and Bioinformatics in Systems Biomedicine (MSB)

Institute of Medical Biometry and Statistics (IMBI)
Faculty of Medicine and Medical Center - University of Freiburg

Postal Address: Stefan-Meier-Str. 26, 79104 Freiburg
Mail: carlotta.meyring using uniklinik-freiburg.de

Phone: +49 761 270 83805

Homepage: www.uniklinik-freiburg.de/imbi/msb.html<http://secure-web.cisco.com/1BWMZS7l4AGYT32E92dROhhM3cZR0mXRr0rm1mCf3XGpnYegf686-dW6GWNqXodkZufZ7MuVI8tNmBwEiui2N5ayOj6LeFJjP9kNWxaU0vf40kmU-qZORa4j0n8K-eaZnIbS5RJL3xip-X5k_N-R6umsSqpgMTUUb6zW4oPGj60YWSv94Z6Xs7ImwM7fylG8oNAS8tD2g88kN9haoJz6qHT1DGCQzo7c3XaQJeudtvmNFXSFaobH3p3YKjb-nN_Ug5xrRGBfkABQerKGAUJj8x-Q6y-fujr4-sYmxX6Pd_r1cy3IwY0ik4Q0A2YgU52uv/http%3A%2F%2Fwww.uniklinik-freiburg.de%2Fimbi.html>

Von: Kern, Lori <Lori.Shepherd using RoswellPark.org>
Gesendet: Dienstag, 23. April 2024 13:16
An: Carlotta Meyring <carlotta.meyring using uniklinik-freiburg.de>; bioc-devel using r-project.org
Betreff: Re: [Bioc-devel] git commit issues

Bioconductor does not have a main branch.  Please refer to documentation

http://contributions.bioconductor.org/git-version-control.html<http://secure-web.cisco.com/1CWLafUqEUvpL8uB9Kx8Zd4JHV-S4X2hsuGvdXKhtsq4SuDmNFyGmFlkJD3LM1oaayKVUDDUeOqxDtkNbaxjWUM_ufJDDgnuvGLN_mdtqDc2OQvmk0aVFixAOoETsRLf_Y8Y5HZU9t2oH4_sg_phi0iAX096COCbbvisoIqU1Dv9r-l1am76Xtoub40-pAhXv250YMDNKaLGOe-RtEetDvOVQCq66Xs0HG707jRlnH18QJ7-dcmXXFLGaQQKxQuTD_J7o6CUJEsdyT9Rzd9Vk9azRCa4sVpblvfFtfXdHaJEsj3AHFaa2uMS8XxJAA5BI/http%3A%2F%2Fcontributions.bioconductor.org%2Fgit-version-control.html>

Bioconductor default branch is devel.   If you have set up where your default branch is main do to another remote (like github), You can map main to devel with something like the following

git push upstream main:devel

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<mailto:bioc-devel-bounces using r-project.org>> on behalf of Carlotta Meyring <carlotta.meyring using uniklinik-freiburg.de<mailto:carlotta.meyring using uniklinik-freiburg.de>>
Sent: Tuesday, April 23, 2024 7:04 AM
To: bioc-devel using r-project.org<mailto:bioc-devel using r-project.org> <bioc-devel using r-project.org<mailto:bioc-devel using r-project.org>>
Subject: [Bioc-devel] git commit issues

Hello,

I submitted a package named zitools to Bioconductor. Now I want to committ he updatest o Bioconductor.
However, this is not working.

My output of:
$ git remote -v
origin  https://secure-web.cisco.com/1GnPQpRFt9TG8Nx9p4h1Z4s0wSct926b0z1tufMD1WU2mNF0fsogaDXit-OEpae5_TTuayObS0WA6uaEPYzzxlZPnIB32lupQMWF5sIcLl7CYmwdkmLJgZiDCQiJMyfX7r_xVsLaagPMfz30RViw070xq2YaudeE_TWg75Zenet-6p96pTGE-_yF4Ma-aRKX617hS0DXZll2izCm1l4wDG2JcHy5AfQA1DALcetU2mIF5DphPhTJoTLvXYjbyZB3a1x1720-BIxVXG__2vDN1HfVNUrL0krNSJoGhsxtieXA98d124cn_Hvv-7ZJneM5s/https%3A%2F%2Fgithub.com%2Fkreutz-lab%2Fzitools.git (fetch)
origin  https://secure-web.cisco.com/1GnPQpRFt9TG8Nx9p4h1Z4s0wSct926b0z1tufMD1WU2mNF0fsogaDXit-OEpae5_TTuayObS0WA6uaEPYzzxlZPnIB32lupQMWF5sIcLl7CYmwdkmLJgZiDCQiJMyfX7r_xVsLaagPMfz30RViw070xq2YaudeE_TWg75Zenet-6p96pTGE-_yF4Ma-aRKX617hS0DXZll2izCm1l4wDG2JcHy5AfQA1DALcetU2mIF5DphPhTJoTLvXYjbyZB3a1x1720-BIxVXG__2vDN1HfVNUrL0krNSJoGhsxtieXA98d124cn_Hvv-7ZJneM5s/https%3A%2F%2Fgithub.com%2Fkreutz-lab%2Fzitools.git (push)
upstream        git using git.bioconductor.org:zitools/zitools.git<mailto:git using git.bioconductor.org:zitools/zitools.git> (fetch)
upstream        git using git.bioconductor.org:zitools/zitools.git<mailto:git using git.bioconductor.org:zitools/zitools.git> (push)

and if I check ssh -T git using git.bioconductor.org<mailto:git using git.bioconductor.org>
I have both read (R) and write (W) permissions for the package.
However if I run:
git push upstream main

I get the following error.
error: cannot spawn https://secure-web.cisco.com/1bfCTvE0S1JmnGSX6z44y7yimg-nfasTqmfDDXfXVBOI1bpKy7NuEFFLr5w0u3fbJ9lMuxWaPPHwL5RcAaAycGcJ39-zsU3QRgt0PId5_xwPJuh8eTK3aV9wcQdpuDR9NdK2-TTTjc-n23sir6NbYEVOMjLUYduMsu6_hOEDYkRO_UrLZ4CplEWgV9f4wYBcj7KRBoNjZ5KilpXhEL2LF-ifif9meNJnoAMx--FEbEp9PPb5IkLsRLn79Xgp5D-kthzcYQhQbr0iEuYvBDVqKETPtjHhPLG7_1Dt7KgQJBDd-xFyoZHAfvQdgsr-UP01k/https%3A%2F%2Fgithub.com%2Fmyname.keys%3A No such file or directory
error: cannot spawn https://secure-web.cisco.com/1bfCTvE0S1JmnGSX6z44y7yimg-nfasTqmfDDXfXVBOI1bpKy7NuEFFLr5w0u3fbJ9lMuxWaPPHwL5RcAaAycGcJ39-zsU3QRgt0PId5_xwPJuh8eTK3aV9wcQdpuDR9NdK2-TTTjc-n23sir6NbYEVOMjLUYduMsu6_hOEDYkRO_UrLZ4CplEWgV9f4wYBcj7KRBoNjZ5KilpXhEL2LF-ifif9meNJnoAMx--FEbEp9PPb5IkLsRLn79Xgp5D-kthzcYQhQbr0iEuYvBDVqKETPtjHhPLG7_1Dt7KgQJBDd-xFyoZHAfvQdgsr-UP01k/https%3A%2F%2Fgithub.com%2Fmyname.keys%3A No such file or directory
fatal: unable to fork

Any help is highly appreciated. Thanks in advance,

Carlotta

Carlotta Meyring
Methods of Modelling and Bioinformatics in Systems Biomedicine (MSB)
Institute of Medical Biometry and Statistics (IMBI)
Faculty of Medicine and Medical Center - University of Freiburg

Postal Address: Stefan-Meier-Str. 26, 79104 Freiburg
Mail: carlotta.meyring using uniklinik-freiburg.de<mailto:carlotta.meyring using uniklinik-freiburg.de>
Phone: +49 761 270 83805
Homepage: http://secure-web.cisco.com/12cYQm0BZOpBmyHwRDtdk_I-5jlGrvbxv8i3g0J8wNkoKBLPoKY_vPDGfKJ2H8ciFuXBzxpJgVz91isuH_FXfvmi87-balDCB76K63rbbLd51ogmmL68wigw88VF5jw7T9Re-6vIgniPVDUdhX1djUVwDUXrNZ9E1gu6AJDlnCiOaKbyZ4xzGpmu9mEya-E7O4qb1kKFD0pTtpW7HRb3XvOVWxNj-PzVPHSnujHIajweDSmsIc2u8xXNjw7No6uE33fsCFxAWC1rFnOfZT9C11SipQpszJ-A0-pQYSRPp3Qncq0rRBDl38Hem448R4OjR/http%3A%2F%2Fwww.uniklinik-freiburg.de%2Fimbi%2Fmsb.html<http://secure-web.cisco.com/1R4JrM9-sEUVTPnau9d1hcgSzQNSJQofy-Ui6cNGM_9UjoCt9pkicBP7OQMeTKfwuyej7V6VnMWz09h6Ue48_0mRhwHqNvorWrSV_QAIwIItIY4XqrcFBvyxoCWYB3jcYTTf_CKIwywZmkCtIfRaM5igOyLYEAzSQDD_ylAzDYZVTgwANWyCN-aK_sR6Nz3_z04QH1Kuqc1-8Egya16goOdvD5MuDz5rCo5jaDtLnTLInZli_YWN_4EW-ZcKcZwtLXo8BVaybDjaYbt_QBxydHybVIKCb1umlvOWvVwAVWglflmFUjQfN2jWYKS45EfQD/http%3A%2F%2Fwww.uniklinik-freiburg.de%2Fimbi.html><http://secure-web.cisco.com/12cYQm0BZOpBmyHwRDtdk_I-5jlGrvbxv8i3g0J8wNkoKBLPoKY_vPDGfKJ2H8ciFuXBzxpJgVz91isuH_FXfvmi87-balDCB76K63rbbLd51ogmmL68wigw88VF5jw7T9Re-6vIgniPVDUdhX1djUVwDUXrNZ9E1gu6AJDlnCiOaKbyZ4xzGpmu9mEya-E7O4qb1kKFD0pTtpW7HRb3XvOVWxNj-PzVPHSnujHIajweDSmsIc2u8xXNjw7No6uE33fsCFxAWC1rFnOfZT9C11SipQpszJ-A0-pQYSRPp3Qncq0rRBDl38Hem448R4OjR/http%3A%2F%2Fwww.uniklinik-freiburg.de%2Fimbi%2Fmsb.html%3chttp:/secure-web.cisco.com/1R4JrM9-sEUVTPnau9d1hcgSzQNSJQofy-Ui6cNGM_9UjoCt9pkicBP7OQMeTKfwuyej7V6VnMWz09h6Ue48_0mRhwHqNvorWrSV_QAIwIItIY4XqrcFBvyxoCWYB3jcYTTf_CKIwywZmkCtIfRaM5igOyLYEAzSQDD_ylAzDYZVTgwANWyCN-aK_sR6Nz3_z04QH1Kuqc1-8Egya16goOdvD5MuDz5rCo5jaDtLnTLInZli_YWN_4EW-ZcKcZwtLXo8BVaybDjaYbt_QBxydHybVIKCb1umlvOWvVwAVWglflmFUjQfN2jWYKS45EfQD/http%3A%2F%2Fwww.uniklinik-freiburg.de%2Fimbi.html%3e>

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