Re: [Bioc-devel] TIMEOUT on package MEAL

2018-04-20 Thread Carlos Ruiz 
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 `  
> 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-boun...@r-project.org> on behalf of 
> Carlos Ruiz <carlos.r...@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 
> 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.r...@isglobal.org
> www.isglobal.org <http://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
>

Re: [Bioc-devel] TIMEOUT on package MEAL

2018-04-13 Thread Shepherd, Lori 
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 `  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-boun...@r-project.org> on behalf of Carlos Ruiz 
<carlos.r...@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 escribi�:
> 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 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.r...@isglobal.org
www.isglobal.org<http://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
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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: l...@isglobal.org. ISGlobal Privacy Policy at
www.isglobal.org<http://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

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by law. If this message has been received in error, please
immediately notify
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DATA PROTECTION. We
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included in your email correspondence, are included in
the ISGlobal
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Re: [Bioc-devel] TIMEOUT on package MEAL

2018-04-13 Thread Carlos Ruiz 

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 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.r...@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: l...@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: 
l...@isglobal.org . ISGlobal
Privacy Policy at 
www.isglobal.org .





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