[Bioc-devel] Timeout in check for a new submission

[Bernat Gel Moreno]

Thanks Lori :)

I've already written to my reviewer (Qian Liu) asking if it's possible to proceed with the review in the current situation.

The code in the package is quite fast (and simple) but I'll take a look at that link to see  if I can get a few more seconds out.

Bernat







El 4/5/19 a las 4:43 PM, Shepherd, Lori escribi�:

Also,  the reviewer might be able to glance at the code and help try to make it run more efficiently.  See points on http://bioconductor.org/developers/how-to/efficient-code/  for things like vectorization and pre-allocation.



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 using r-project.org><mailto:bioc-devel-bounces using r-project.org> on behalf of Shepherd, Lori <Lori.Shepherd using RoswellPark.org><mailto:Lori.Shepherd using RoswellPark.org>
Sent: Friday, April 5, 2019 10:40:07 AM
To: Bernat Gel Moreno; bioc-devel using r-project.org<mailto:bioc-devel using r-project.org>
Subject: Re: [Bioc-devel] Timeout in check for a new submission

If the check time is passing on the other platforms,  and the windows check isn't incredibly over the time limit,  you should be okay.  Talk with your reviewer but in general we would make an exception for this warning.

Most of the time subsets of data can be used for examples and vignettes which also help to reduce the check time but still retain usefulness of an application, without knowing your data just an example  instead of running over all chromosomes,  limit to one smaller chromosome, etc...   If this has already been done then you should be able to proceed through the submission process despite this warning.


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 using r-project.org><mailto:bioc-devel-bounces using r-project.org> on behalf of Bernat Gel Moreno <bgel using igtp.cat><mailto:bgel using igtp.cat>
Sent: Friday, April 5, 2019 10:27:21 AM
To: bioc-devel using r-project.org<mailto:bioc-devel using r-project.org>
Subject: [Bioc-devel] Timeout in check for a new submission


Hi all,

I've submitted a new package (CopyNumberPlots, issue 1076) and I have a
problem. It keeps giving me a warning because on windows it takes  more
than 5 minutes to check (in Lunix it works with no problems). I've
reduced the examples, removed part of the vignette... and in my machine
it take 3min 20seconds to check, of which only 30seconds are spent in
the examples and vignette and the other 2min 50 seconds are spent in all
other checks.

Other than reducing the vignette and examples I don't know how to reduce
the cheking time. Any pointers?

Thanks a lot

Bernat

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