From plummerm at iarc.fr  Fri May 15 16:44:59 2015
From: plummerm at iarc.fr (Martyn Plummer)
Date: Fri, 15 May 2015 14:44:59 +0000
Subject: [Rd] example fails during R CMD CHECK but works interactively?
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Message-ID: <1431701098.2753.26.camel@iarc.fr>

The error can be reproduced by running the bigmemory-Ex.R script which
you can find in the bigmemory.Rcheck directory, either in batch mode or
via source() in an interactive session.

It seems that you have underlying memory allocation problems. I can get
the script to running by adding gc() calls when necessary (i.e. when a
failure is reported, add gc() just before this point in the script and
rerun).

Martyn

On Fri, 2015-05-15 at 07:05 -0500, Charles Determan wrote:
> Does anyone else have any thoughts about troubleshooting the R CMD check
> environment?
> 
> Charles
> 
> On Wed, May 13, 2015 at 1:57 PM, Charles Determan <cdetermanjr at gmail.com>
> wrote:
> 
> > Thank you Dan but it isn't my tests that are failing (all of them pass
> > without problem) but one of the examples from the inst/examples directory.
> > I did try, however, to start R with the environmental variables as you
> > suggest but it had no effect on my tests.
> >
> > Charles
> >
> > On Wed, May 13, 2015 at 1:51 PM, Dan Tenenbaum <dtenenba at fredhutch.org>
> > wrote:
> >
> >>
> >>
> >> ----- Original Message -----
> >> > From: "Charles Determan" <cdetermanjr at gmail.com>
> >> > To: r-devel at r-project.org
> >> > Sent: Wednesday, May 13, 2015 11:31:36 AM
> >> > Subject: [Rd] example fails during R CMD CHECK but works interactively?
> >> >
> >> > Greetings,
> >> >
> >> > I am collaborating with developing the bigmemory package and have run
> >> > in to
> >> > a strange problem when we run R CMD CHECK.  For some reason that
> >> > isn't
> >> > clear to us one of the examples crashes stating:
> >> >
> >> > Error:  memory could not be allocated for instance of type big.matrix
> >> >
> >> > You can see the output on the Travis CI page at
> >> > https://travis-ci.org/kaneplusplus/bigmemory where the error starts
> >> > at line
> >> > 1035.  This is completely reproducible when running
> >> > devtools::check(args='--as-cran') locally.  The part that is
> >> > confusing is
> >> > that the calls work perfectly when called interactively.
> >> >
> >> > Hadley comments on the 'check' page of his R packages website (
> >> > http://r-pkgs.had.co.nz/check.html) regarding test failing following
> >> > R CMD
> >> > check:
> >> >
> >> > Occasionally you may have a problem where the tests pass when run
> >> > interactively with devtools::test(), but fail when in R CMD check.
> >> > This
> >> > usually indicates that you?ve made a faulty assumption about the
> >> > testing
> >> > environment, and it?s often hard to figure it out.
> >> >
> >> > Any thoughts on how to troubleshoot this problem?  I have no idea
> >> > what
> >> > assumption we could have made.
> >>
> >> Note that R CMD check runs R with environment variables set as follows
> >> (at least on my system; you can check $R_HOME/bin/check to see what it does
> >> on yours):
> >>
> >>  R_DEFAULT_PACKAGES= LC_COLLATE=C
> >>
> >> So try staring R like this:
> >>
> >>  R_DEFAULT_PACKAGES= LC_COLLATE=C  R
> >>
> >> And see if that reproduces the test failure. The locale setting could
> >> affect tests of sort order, and the default package setting could
> >> potentially affect other things.
> >>
> >> Dan
> >>
> >>
> >>
> >> >
> >> > Regards,
> >> > Charles
> >> >
> >> >       [[alternative HTML version deleted]]
> >> >
> >> > ______________________________________________
> >> > R-devel at r-project.org mailing list
> >> > https://stat.ethz.ch/mailman/listinfo/r-devel
> >> >
> >>
> >
> >
> 
> 	[[alternative HTML version deleted]]
> 
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel



[Rd] example fails during R CMD CHECK but works interactively?
Martyn Plummer