From cdetermanjr at gmail.com  Wed May 13 20:57:51 2015
From: cdetermanjr at gmail.com (Charles Determan)
Date: Wed, 13 May 2015 13:57:51 -0500
Subject: [Rd] example fails during R CMD CHECK but works interactively?
In-Reply-To: <1612739531.2387533.1431543079541.JavaMail.root@fredhutch.org>
References: <CAKxd1KNtOjyq5DYEVmvw=NQUrnL5LVZYuSt=1cyfE=QQQquCLw@mail.gmail.com>
	<1612739531.2387533.1431543079541.JavaMail.root@fredhutch.org>
Message-ID: <CAKxd1KMgT700+uKmD8v-QJoG5NmpeA+t3rSR-gg1L19=NbpzPw@mail.gmail.com>

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]]



[Rd] example fails during R CMD CHECK but works interactively?
Charles Determan