On 05/15/2015 05:05 AM, Charles Determan wrote:
Does anyone else have any thoughts about troubleshooting the R CMD check
environment?
In the pkg.Rcheck directory there is a file pkg-Ex.R.
LANGUAGE=en _R_CHECK_INTERNALS2_=1 $(R_HOME)/bin/R --vanilla pkge-Ex.R
followed by the usual strategy of bisecting the file into smaller chunks that
still reproduce the example.
(this is based on my parsing of the complicated source, most relevant at
https://github.com/wch/r-source/blob/trunk/src/library/tools/R/check.R#L2467
and
https://github.com/wch/r-source/blob/trunk/src/library/tools/R/check.R#L36
)
Martin
Charles
On Wed, May 13, 2015 at 1:57 PM, Charles Determan <cdeterma...@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 <dtene...@fredhutch.org>
wrote:
----- Original Message -----
From: "Charles Determan" <cdeterma...@gmail.com>
To: r-devel@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
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