The error can be reproduced by running the bigmemory-Ex.R script which you can find in the bigmemory.Rcheck directory, either in batch mode or via source() in an interactive session.
It seems that you have underlying memory allocation problems. I can get the script to running by adding gc() calls when necessary (i.e. when a failure is reported, add gc() just before this point in the script and rerun). Martyn On Fri, 2015-05-15 at 07:05 -0500, Charles Determan wrote: > 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 <[email protected]> > 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 <[email protected]> > > wrote: > > > >> > >> > >> ----- Original Message ----- > >> > From: "Charles Determan" <[email protected]> > >> > To: [email protected] > >> > 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]] > >> > > >> > ______________________________________________ > >> > [email protected] mailing list > >> > https://stat.ethz.ch/mailman/listinfo/r-devel > >> > > >> > > > > > > [[alternative HTML version deleted]] > > ______________________________________________ > [email protected] mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel ______________________________________________ [email protected] mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
