[Bioc-devel] TIMEOUT on package MEAL

Fri Apr 20 17:39:17 CEST 2018

Hi Lori,

I made some changes to the MEAL vignettes and now MEAL successfully 
passes tests on Linux and Windows (build time: 1854 and 1613 seconds 
respectively). However, it still times out in OSX. Should I try to 
reduce the building time in merida2?

Thanks,
Carlos Ruiz

El 13/04/2018 a las 19:39, Shepherd, Lori escribió:
>
> It is by fluke that the windows did not time out... The 
> builders timeout occur at 2400 sec and you are right up against the 
> edge at 2145.4 seconds on windows.
>
>
> The build reports include an EllapsedTime  indication in the summary 
> section for each builder ...
>
>
> Your package does not meet the requirement (<2400 (40min!!)  and your 
> vignette needs to be altered to fit the time constraints of the builders.
>
>
> You should easily be able to test R CMD build on your system and log 
> the time to debug this issue. On linux there is the `time <command>`  
> option.
>
>
>
>
> Lori Shepherd
>
> Bioconductor Core Team
>
> Roswell Park Cancer Institute
>
> Department of Biostatistics & Bioinformatics
>
> Elm & Carlton Streets
>
> Buffalo, New York 14263
>
> ------------------------------------------------------------------------
> *From:* Bioc-devel <bioc-devel-bounces at r-project.org> on behalf of 
> Carlos Ruiz <carlos.ruiz at isglobal.org>
> *Sent:* Friday, April 13, 2018 11:26:03 AM
> *To:* Turaga, Nitesh; Bioc-devel
> *Subject:* Re: [Bioc-devel] TIMEOUT on package MEAL
> Hi BiocDevel,
>
> Could you help me with this issue? The report is not very informative. I
> suspect that the vignettes are taking too long but I have two vignettes
> and I don't know which one is more problematic. I don't understand
> either why I have a timeout in OS and Linux but not in Windows.
>
> When I had to deal with warnings or errors, I was able to reproduce them
> in my computer and solve them. Is there any way to reproduce the timeouts?
>
> Thank you,
>
> Carlos Ruiz
>
>
> El 12/04/2018 a las 18:22, Turaga, Nitesh escribió:
> > Dear maintainer,
> >
> > I'd like to bring to your attention that the  your package is 
> getting a TIMEOUT 'R CMD build' on platforms in the devel version of 
> Bioconductor (i.e. BioC 3.7):
> >
> > 
> http://bioconductor.org/checkResults/devel/bioc-LATEST/MEAL/malbec2-install.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.
> >
> > The package is failing on devel which is very problematic. If it is 
> not fixed in devel in a timely manner we would also consider this 
> package for potential deprecation in the next cycle.  The deadline for 
> passing R CMD build and check in devel is April 25.
> >
> > Thanks for your contribution to Bioconductor.
> >
> > Pleae be advised that Bioconductor has switched from svn to Git. 
> Some helpful
> > links can be found here:
> > https://bioconductor.org/developers/how-to/git/
> >
> > Best,
> >
> > Nitesh Turaga
> > Bioconductor Core Team
> >
> > This email message may contain legally privileged and/or 
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> -- 
> Carlos Ruiz
> PhD Student
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-- 
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

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.

-- 

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 <mailto:lopd at isglobal.org>. ISGlobal
Privacy Policy at 
www.isglobal.org <http://www.isglobal.org/>.

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