[Bioc-devel] Push update to an existing remote branch

2023-10-18 Thread Carlotta Meyring 
Hi all,



I have a package in review on 
g...@git.bioconductor.org and I have added a 
remote named upstream pointing to my package there. I want to push an updated 
version and



$ git push origin main



Works well, however



$ git push upstream main


Doesn't work with the error message being:

error: cannot spawn https://github.com/myowngithubname.keys: No such file or 
directory
error: cannot spawn https://github.com/myowngithubname.keys: No such file or 
directory
fatal: unable to fork


I already checked that the key is connected with my github account.
Any help would be appreciated!

Thanks in advance!

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[Bioc-devel] Error on macOS (merida1)

2024-04-26 Thread Carlotta Meyring 
Dear Bioconductor Team,


I pushed my updates for the package zitools a few days ago. However, there is 
an error on macOS merida1: ERROR: this R is version 4.3.3, package 'zitools' 
requires R >= 4.4.0.


On Linux (nebbiolo1) is everything fine. Is that a problem? Because as far as I 
understood, the package should be dependent on R-4.4.

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.meyr...@uniklinik-freiburg.de
Phone: +49 761 270 83805
Homepage: 
www.uniklinik-freiburg.de/imbi/msb.html<http://www.uniklinik-freiburg.de/imbi.html>


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Re: [Bioc-devel] git commit issues

2024-04-23 Thread Carlotta Meyring 
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.meyr...@uniklinik-freiburg.de
Phone: +49 761 270 83805
Homepage: 
www.uniklinik-freiburg.de/imbi/msb.html<http://www.uniklinik-freiburg.de/imbi.html>

Von: Kern, Lori 
Gesendet: Dienstag, 23. April 2024 13:16
An: Carlotta Meyring ; 
bioc-devel@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


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 
mailto:bioc-devel-boun...@r-project.org>> on 
behalf of Carlotta Meyring 
mailto:carlotta.meyr...@uniklinik-freiburg.de>>
Sent: Tuesday, April 23, 2024 7:04 AM
To: bioc-devel@r-project.org<mailto:bioc-devel@r-project.org> 
mailto:bioc-devel@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
g...@git.bioconductor.org:zitools/zitools.git<mailto:g...@git.bioconductor.org:zitools/zitools.git>
 (fetch)
upstream
g...@git.bioconductor.org:zitools/zitools.git<mailto:g...@git.bioconductor.org:zitools/zitools.git>
 (push)


and if I check ssh -T 
g...@git.bioconductor.org<mailto:g...@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.meyr...@uniklinik-freiburg.de<mailto:carlotta.meyr...@uniklinik-freiburg.de>
Phone: +49 761 270 83805
Homepage: 
http://secure-web.cisco.com/12cYQm0BZOpBmyHwRDtdk_I-5jlGrvbxv8i3g0J8wNkoKBLPoKY_vPDGfKJ2H8ciFuXBzxpJgVz91isuH_FXfvmi87-balDCB76K63rbbLd51ogmmL68wigw88VF5jw7T9Re-6vIgniPVDUdhX1djUVwDUXrNZ9E1gu6AJDlnCiOaKbyZ4xzGpmu9mEya-E7O4qb1kKFD0pTtpW7HRb3XvOVWxNj-PzVPHSnujHIajweDSmsIc2u8xXNjw7No6uE33fsCFxAWC1rFnOfZT9C11SipQpszJ-A0-pQYSRPp3Qncq0rR

[Bioc-devel] git commit issues

2024-04-23 Thread Carlotta Meyring 
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://github.com/kreutz-lab/zitools.git (fetch)
origin  https://github.com/kreutz-lab/zitools.git (push)
upstreamg...@git.bioconductor.org:zitools/zitools.git (fetch)
upstreamg...@git.bioconductor.org:zitools/zitools.git (push)


and if I check ssh -T g...@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://github.com/myname.keys: No such file or directory
error: cannot spawn https://github.com/myname.keys: 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.meyr...@uniklinik-freiburg.de
Phone: +49 761 270 83805
Homepage: 
www.uniklinik-freiburg.de/imbi/msb.html<http://www.uniklinik-freiburg.de/imbi.html>


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Re: [Bioc-devel] Error on macOS (merida1)

2024-04-30 Thread Carlotta Meyring 
How can that be changed? How far as I understood the package will not be 
reviewed again when there is an error in the build report.

Thanks in advance,

Carlotta Meyring




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.meyr...@uniklinik-freiburg.de
Phone: +49 761 270 83805
Homepage: 
www.uniklinik-freiburg.de/imbi/msb.html<http://www.uniklinik-freiburg.de/imbi.html>

Von: Kern, Lori 
Gesendet: Freitag, 26. April 2024 13:10
An: Carlotta Meyring ; 
bioc-devel@r-project.org
Betreff: Re: [Bioc-devel] Error on macOS (merida1)

Yes a package in submission should depend on R 4.4.0.  Merida1 was accidently 
started for the package review process but should not have been included yet.


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 
mailto:bioc-devel-boun...@r-project.org>> on 
behalf of Carlotta Meyring 
mailto:carlotta.meyr...@uniklinik-freiburg.de>>
Sent: Friday, April 26, 2024 3:37 AM
To: bioc-devel@r-project.org<mailto:bioc-devel@r-project.org> 
mailto:bioc-devel@r-project.org>>
Subject: [Bioc-devel] Error on macOS (merida1)

Dear Bioconductor Team,


I pushed my updates for the package zitools a few days ago. However, there is 
an error on macOS merida1: ERROR: this R is version 4.3.3, package 'zitools' 
requires R >= 4.4.0.


On Linux (nebbiolo1) is everything fine. Is that a problem? Because as far as I 
understood, the package should be dependent on R-4.4.

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.meyr...@uniklinik-freiburg.de<mailto:carlotta.meyr...@uniklinik-freiburg.de>
Phone: +49 761 270 83805
Homepage: 
http://secure-web.cisco.com/1pfXSDYRNGtlPft0VUNHWCrSQI4uGEi3JdavTMpos07xuzJE5-RsEZVSBCux1LCAmJslAlgoNPfpAb7SInYhepvg8eiGL7EHPsg2qwFhxi8IG_zImJJjnnEKjNA9GpyIEdOKukD-XxwgA5B1iRuTBBC0TrRdwVAzBHpRTPagOfg9WuWCwnIiiFqDFOlSv8De7L49A67HbqBEKVPh3Q_WIHhPrYSYQ4gEiotN6Y8MAZI9_QrFgFml_ylc8q6kTWxz-c0zznOD_YOSiqE9ym4Lmv5aVRn30qAv87bfuzDR-F_LFJjUUA-ldMbCaFwdu4KFU/http%3A%2F%2Fwww.uniklinik-freiburg.de%2Fimbi%2Fmsb.html<http://secure-web.cisco.com/1w8-qOjr_6UBi-5Z2-GP82iR6er-LQU_GO4nv87erfmeHHDjPgASw9uX85y6VzyIejgzZYM_FC5G0CU4yqNGU2mkrM7ExnhEQeiulbcs3ATJdJEEBIvesdmnVf0mtUYxgeDgG2SxHYcGfBUbmrFDhrmKFXlI0kJHA9AKsXIoB5s8GENuoyNBuLsuTJR4hOHwIrPTPeWPzg3OciBg7MttUJYihFY2JuLyzxEZChkhKaJOf-N86QUmBUoYk0JYJtP7p8GdRIPxhNryDbpPnxQ_zUfhNTURfA0ivxQcO9FggecCKQpBz-S38MtX3CR_HaFbu/http%3A%2F%2Fwww.uniklinik-freiburg.de%2Fimbi.html><http://secure-web.cisco.com/1pfXSDYRNGtlPft0VUNHWCrSQI4uGEi3JdavTMpos07xuzJE5-RsEZVSBCux1LCAmJslAlgoNPfpAb7SInYhepvg8eiGL7EHPsg2qwFhxi8IG_zImJJjnnEKjNA9GpyIEdOKukD-XxwgA5B1iRuTBBC
 
0TrRdwVAzBHpRTPagOfg9WuWCwnIiiFqDFOlSv8De7L49A67HbqBEKVPh3Q_WIHhPrYSYQ4gEiotN6Y8MAZI9_QrFgFml_ylc8q6kTWxz-c0zznOD_YOSiqE9ym4Lmv5aVRn30qAv87bfuzDR-F_LFJjUUA-ldMbCaFwdu4KFU/http%3A%2F%2Fwww.uniklinik-freiburg.de%2Fimbi%2Fmsb.html%3chttp:/secure-web.cisco.com/1w8-qOjr_6UBi-5Z2-GP82iR6er-LQU_GO4nv87erfmeHHDjPgASw9uX85y6VzyIejgzZYM_FC5G0CU4yqNGU2mkrM7ExnhEQeiulbcs3ATJdJEEBIvesdmnVf0mtUYxgeDgG2SxHYcGfBUbmrFDhrmKFXlI0kJHA9AKsXIoB5s8GENuoyNBuLsuTJR4hOHwIrPTPeWPzg3OciBg7MttUJYihFY2JuLyzxEZChkhKaJOf-N86QUmBUoYk0JYJtP7p8GdRIPxhNryDbpPnxQ_zUfhNTURfA0ivxQcO9FggecCKQpBz-S38MtX3CR_HaFbu/http%3A%2F%2Fwww.uniklinik-freiburg.de%2Fimbi.html%3e>


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