From cdetermanjr at gmail.com  Fri May 15 14:05:18 2015
From: cdetermanjr at gmail.com (Charles Determan)
Date: Fri, 15 May 2015 07:05:18 -0500
Subject: [Rd] example fails during R CMD CHECK but works interactively?
In-Reply-To: <CAKxd1KMgT700+uKmD8v-QJoG5NmpeA+t3rSR-gg1L19=NbpzPw@mail.gmail.com>
References: <CAKxd1KNtOjyq5DYEVmvw=NQUrnL5LVZYuSt=1cyfE=QQQquCLw@mail.gmail.com>
	<1612739531.2387533.1431543079541.JavaMail.root@fredhutch.org>
	<CAKxd1KMgT700+uKmD8v-QJoG5NmpeA+t3rSR-gg1L19=NbpzPw@mail.gmail.com>
Message-ID: <CAKxd1KMkW6mx9hYdDwtQ6k9R7BnvufZspFs8fJPovYJXXgW75Q@mail.gmail.com>

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]]



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