[Bioc-devel] Bioconductor failing package MEAL

Thu, Sep 14, 2017 9:23 AM

Hi Carlos,

Do you by any chance have 2 separate SVN id?s?

1. c.ruiz
2. c.ruiz-arenas

Best,

Nitesh

On Sep 14, 2017, at 12:17 PM, Carlos Ruiz <carlos.ruiz at isglobal.org> wrote:

Hi, 
Today I definitely was able to fetch from the Bioc git. However, I cannot push. Here, the commands and the error:


C:\Users\cruiz.ISGLOBAL\Documents\MEAL [master =]> git push upstream master
Warning: Permanently added 'git.bioconductor.org,34.192.48.227' (ECDSA) to the l
ist of known hosts.
FATAL: W any packages/MEAL c.ruiz DENIED by fallthru
(or you mis-spelled the reponame)
fatal: Could not read from remote repository.

Please make sure you have the correct access rights
and the repository exists.
C:\Users\cruiz.ISGLOBAL\Documents\MEAL [master =]> git remote -v
origin  https://github.com/isglobal-brge/MEAL.git (fetch)
origin  https://github.com/isglobal-brge/MEAL.git (push)
upstream        git at git.bioconductor.org:packages/MEAL.git (fetch)
upstream        git at git.bioconductor.org:packages/MEAL.git (push)

Can you help me?

Thanks, 

Carlos Ruiz


El 13/09/2017 a las 10:09, Carlos Ruiz escribi?:

Hi to both,

These are the commands that I tried and the error:

$ git remote -v
origin  https://github.com/isglobal-brge/MEAL.git (fetch)
origin  https://github.com/isglobal-brge/MEAL.git (push)
upstream        git at git.bioconductor.org:packages/MEAL (fetch)
upstream        git at git.bioconductor.org:packages/MEAL (push)


$  git fetch --all
Fetching origin
Fetching upstream
Permission denied (publickey).
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 think that there was a similar error in the BiocDevel list that was solved after sending the ssh keys. I resent the form yesterday so I hope tomorrow I'll be able to push. Just in case, my svn user name was c.ruiz-arenas.

Bests,
Carlos Ruiz

El 12/09/2017 a las 18:12, Shepherd, Lori escribi?:

Once you submit the key you should have access.  Please provide the calls you are using and also the results of git remote -v 



Lori Shepherd
Bioconductor Core Team
Roswell Park Cancer Institute
Department of Biostatistics & Bioinformatics
Elm & Carlton Streets
Buffalo, New York 14263
From: Carlos Ruiz <carlos.ruiz at isglobal.org>
Sent: Tuesday, September 12, 2017 12:08:15 PM
To: Shepherd, Lori
Subject: Re: Bioconductor failing package MEAL
 
Hi,

I am experiencing some problems with the git system. I think that i have not properly configured the ssh keys. I have filled again the form with the ssh keys (user name: c.ruiz-arenas). Once you introduced my keys in the system, should I do anything else to update the repo? Should I change the configuration on git?

Thank you,
Carlos Ruiz

El 12/09/2017 a las 17:37, Shepherd, Lori escribi?:

Please update. We have temporarily added your package to the deprecation list as we did not hear from you and there were no updates. If you package builds and checks cleanly we will remove it from the list of deprecated packages. 

Please also be advised we have transitioned to git. There are some useful information here: 
http://bioconductor.org/developers/how-to/git/


Lori Shepherd
Bioconductor Core Team
Roswell Park Cancer Institute
Department of Biostatistics & Bioinformatics
Elm & Carlton Streets
Buffalo, New York 14263
From: Carlos Ruiz <carlos.ruiz at isglobal.org>
Sent: Tuesday, September 12, 2017 11:28:33 AM
To: Shepherd, Lori
Subject: Re: Bioconductor failing package MEAL
 
Hi Lori,

I apologize for not replying you sooner but I have just finished my holidays today. I have finished the vignettes today and I only need to update the tests to have a fully working version again. Therefore, I expect to push my changes during this week.

MEAL contains wrappers to other methods to ease performing methylation and gene expression analyses. I previously created a data package to show MEAL functionalities and I used it in my vignettes. We have created a new data package (BRGEdata) in our group that could be used by different packages. My colleague uploaded it in the submission of omicRexpsome but he is experiencing some problems that are trying to solve with Martin. 

Until this package is not working, the new version of MEAL will fail to build the vignettes. Should I wait until BRGEdata issue is solved or can I update the package without including the vignettes?

Bests,

2017-09-01 14:21 GMT+02:00 Shepherd, Lori <Lori.Shepherd at roswellpark.org>:
Dear MEAL maintainer,

The MEAL package continues to fail to pass 'R CMD build' on all platforms in the devel version of Bioconductor (i.e. BioC 3.6):

http://bioconductor.org/checkResults/3.6/bioc-LATEST/MEAL/malbec1-buildsrc.html

If no action is taken we will begin the deprecation process for your package.  Thank you for your time and effort. 

I understand that you reached out indicating there were big changes to MEAL; As it is getting closer to our next release (end Oct), these changes should be pushed as soon as possible to allow for others who depend on your package to update there packages accordingly 

Thanks for your contribution to Bioconductor.


Lori Shepherd
Bioconductor Core Team
Roswell Park Cancer Institute
Department of Biostatistics & Bioinformatics
Elm & Carlton Streets
Buffalo, New York 14263
From: Carlos Ruiz <carlos.ruiz at isglobal.org>
Sent: Friday, July 21, 2017 9:24:41 AM
To: Shepherd, Lori
Subject: Re: Bioconductor failing package MEAL
 
Hi Lori,

I apology for not answering to you before. I am doing big changes to MEAL package. Currently, I have a working version but I have to redo the vignette and the tests. Once I finish them, I will make a new bump to my package. 

Bests,
Carlos Ruiz


2017-07-21 15:17 GMT+02:00 Shepherd, Lori <Lori.Shepherd at roswellpark.org>:
Dear MEAL maintainer,

The MEAL package continues to fail to pass 'R CMD build' on all platforms in the devel version of Bioconductor (i.e. BioC 3.6):

http://bioconductor.org/checkResults/3.6/bioc-LATEST/MEAL/malbec1-buildsrc.html

Don't hesitate to ask questions on the support site if you are having trouble. 

If no action is taken over the next several weeks we will begin the deprecation process for your package.  Thank you for your time and effort. 


Thanks for your contribution to Bioconductor.



Lori Shepherd
Bioconductor Core Team
Roswell Park Cancer Institute
Department of Biostatistics & Bioinformatics
Elm & Carlton Streets
Buffalo, New York 14263
From: Shepherd, Lori
Sent: Wednesday, July 12, 2017 7:12:35 AM
To: carles.hernandez at isglobal.org; juanr.gonzalez at isglobal.org; carlos.ruiz at isglobal.org
Subject: Bioconductor failing package MEAL
 
Dear MEAL maintainer,

I'd like to bring to your attention that the MAIT package is failing to pass 'R CMD build' on all platforms in the devel version of Bioconductor (i.e. BioC 3.6):

http://bioconductor.org/checkResults/3.6/bioc-LATEST/MEAL/malbec1-buildsrc.html

Would you mind taking a look at this? Don't hesitate to ask on the bioc-devel mailing list if you have any question or need help.

If no action is taken over the next several weeks we will begin the deprecation process for your package.  Thank you for your time and effort. 


Thanks for your contribution to Bioconductor.


Lori Shepherd
Bioconductor Core Team
Roswell Park Cancer Institute
Department of Biostatistics & Bioinformatics
Elm & Carlton Streets
Buffalo, New York 14263

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-- 
Carlos Ruiz
PhD Student
ISGlobal
Instituto de Salud Global de Barcelona - Campus MAR
Barcelona Biomedical Research Park (PRBB) (office 183.01 C)
Doctor Aiguader, 88
08003 Barcelona, Spain
Tel. +34 93 214 73 09
carlos.ruiz at isglobal.org
www.isglobal.org

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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.



-- 
Carlos Ruiz
PhD Student
ISGlobal
Instituto de Salud Global de Barcelona - Campus MAR
Barcelona Biomedical Research Park (PRBB) (office 183.01 C)
Doctor Aiguader, 88
08003 Barcelona, Spain
Tel. +34 93 214 73 09
carlos.ruiz at isglobal.org
www.isglobal.org

This message is intended exclusively for its addressee and may contain information that is CONFIDENTIAL and protected by professional privilege. If you are not the intended recipient you are hereby notified that any dissemination, copy or disclosure of this communication is strictly prohibited by law. If this message has been received in error, please immediately notify us via e-mail and delete it.
DATA PROTECTION. We inform you that your personal data, including your e-mail address and data included in your email correspondence, are included in the ISGlobal Foundation files. Your personal data will be used for the purpose of contacting you and sending information on the activities of the above foundations. You can exercise your rights of access, rectification, cancellation and opposition by contacting the following address: lopd at isglobal.org. ISGlobal Privacy Policy at www.isglobal.org.
-----------------------------------------------------------------------------------------------------------------------------
CONFIDENCIALIDAD. Este mensaje y sus anexos se dirigen exclusivamente a su destinatario y puede contener informaci?n confidencial, por lo que la utilizaci?n, divulgaci?n y/o copia sin autorizaci?n est? prohibida por la legislaci?n vigente. Si ha recibido este mensaje por error, le rogamos lo comunique inmediatamente por esta misma v?a y proceda a su destrucci?n.
PROTECCI?N DE DATOS. Sus datos de car?cter personal utilizados en este env?o, incluida su direcci?n de e-mail, forman parte de ficheros de titularidad de la Fundaci?n ISGlobal  para cualquier finalidades de contacto, relaci?n institucional y/o env?o de informaci?n sobre sus actividades. Los datos que usted nos pueda facilitar contestando este correo quedar?n incorporados en los correspondientes ficheros, autorizando el uso de su direcci?n de e-mail para las finalidades citadas. Puede ejercer los derechos de acceso, rectificaci?n, cancelaci?n y oposici?n dirigi?ndose a lopd at isglobal.org . Pol?tica de privacidad en www.isglobal.org.

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.

--
Carlos Ruiz
PhD Student
ISGlobal
Barcelona Institute for Global Health - Campus MAR
Barcelona Biomedical Research Park (PRBB) (office 001)
Doctor Aiguader, 88
08003 Barcelona, Spain
Tel. +34 93 214 7309

carlos.ruiz at isglobal.org
www.isglobal.org

We are pleased to tell you that after three years of a strategic alliance between ISGlobal and CREAL, both institutions have merged. The resulting institution, which retains the ISGlobal name, will build upon the existing areas of excellence to become a world-class player in research, education and innovation in Global Health. More info at:
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DATA PROTECTION. We inform you that your personal data, including your e-mail address and data included in your email correspondence, are included in the ISGlobal Foundation files. Your personal data will be used for the purpose of contacting you and sending information on the activities of the above foundations. You can exercise your rights of access, rectification, cancellation and opposition by contacting the following address:
lopd at isglobal.org. ISGlobal Privacy Policy at www.isglobal.org
.

This message is intended exclusively for its addressee and may contain information that is CONFIDENTIAL and protected by professional privilege. If you are not the intended recipient you are hereby notified that any dissemination, copy or disclosure of this communication is strictly prohibited by law. If this message has been received in error, please immediately notify us via e-mail and delete it.
DATA PROTECTION. We inform you that your personal data, including your e-mail address and data included in your email correspondence, are included in the ISGlobal Foundation files. Your personal data will be used for the purpose of contacting you and sending information on the activities of the above foundations. You can exercise your rights of access, rectification, cancellation and opposition by contacting the following address: lopd at isglobal.org. ISGlobal Privacy Policy at www.isglobal.org.
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CONFIDENCIALIDAD. Este mensaje y sus anexos se dirigen exclusivamente a su destinatario y puede contener informaci?n confidencial, por lo que la utilizaci?n, divulgaci?n y/o copia sin autorizaci?n est? prohibida por la legislaci?n vigente. Si ha recibido este mensaje por error, le rogamos lo comunique inmediatamente por esta misma v?a y proceda a su destrucci?n.
PROTECCI?N DE DATOS. Sus datos de car?cter personal utilizados en este env?o, incluida su direcci?n de e-mail, forman parte de ficheros de titularidad de la Fundaci?n ISGlobal para cualquier finalidades de contacto, relaci?n institucional y/o env?o de informaci?n sobre sus actividades. Los datos que usted nos pueda facilitar contestando este correo quedar?n incorporados en los correspondientes ficheros, autorizando el uso de su direcci?n de e-mail para las finalidades citadas. Puede ejercer los derechos de acceso, rectificaci?n, cancelaci?n y oposici?n dirigi?ndose a lopd at isglobal.org . Pol?tica de privacidad en www.isglobal.org.

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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[Bioc-devel] Bioconductor failing package MEAL

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