R devel - May 2015 - 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.

Regards,
Charles

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----- 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
>

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
> >
>
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