From dtenenba at fredhutch.org  Wed May 13 20:51:19 2015
From: dtenenba at fredhutch.org (Dan Tenenbaum)
Date: Wed, 13 May 2015 11:51:19 -0700 (PDT)
Subject: [Rd] example fails during R CMD CHECK but works interactively?
In-Reply-To: <CAKxd1KNtOjyq5DYEVmvw=NQUrnL5LVZYuSt=1cyfE=QQQquCLw@mail.gmail.com>
Message-ID: <1612739531.2387533.1431543079541.JavaMail.root@fredhutch.org>



----- 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]]
> 
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>



[Rd] example fails during R CMD CHECK but works interactively?
Dan Tenenbaum