Re: 'Cannot allocate memory' during autopkgtest

[Michael Rutter <marutter@gmail.com>]

On 12/1/18 6:13 AM, Graham Inggs wrote:
> Hi R People
>
> Since the upload of R 3.5, the autopkgtests of r-bioc-biovizbase and
> r-bioc-cummerbund have been failing in Ubuntu where the test runners
> have less than ~2GB RAM.

Graham,

What is the source of the binaries?  Are they coming from an Ubuntu 
repository or one of my PPA's?

Thanks,
Michael

> In both cases, the autopkgtest consists of generating the
> documentation from a .rnw file.  The last step in the .rnw file is a
> call to sessionInfo() which seems to run out of memory while trying to
> execute 'uname' to determine the platform, as follows:
>
> > sessionInfo()
> Error in system(paste(which, shQuote(names[i])), intern = TRUE,
> ignore.stderr = TRUE) :
>    cannot popen '/usr/bin/which 'uname' 2>/dev/null', probable reason
> 'Cannot allocate memory'
> Calls: source ... withVisible -> eval -> eval -> sessionInfo -> Sys.which
> Execution halted
> Warning message:
> system call failed: Cannot allocate memory
>
> I don't believe this failure is a reflection of the quality of the
> r-bioc-biovizbase and r-bioc-cummerbund packages, and the following
> workaround does the trick:
>
> --- a/debian/tests/run-unit-test
> +++ b/debian/tests/run-unit-test
> @@ -10,6 +10,7 @@ cp -r /usr/lib/R/site-library/$oname/ext
>   cp /usr/share/doc/$pkg/examples/vignettes/* $ADTTMP
>   find . -name "*.gz" -exec gunzip \{\} \;
>   for rnw in `ls *.[rRS]nw` ; do
> +sed -i '/^sessionInfo\(\)/d' $rnw
>   rfile=`echo $rnw | sed 's/\.[rRS]nw/.R/'`
>   LC_ALL=C R --no-save <<EOT
>     Stangle("$rnw")
>
> Would there be any objections to me making this change in the Debian
> packaging of r-bioc-biovizbase and r-bioc-cummerbund?
> codesearch.debian.net suggests there may be other affected packages,
> but either the documentation is not generated as part of the
> autopkgtest, or the autopkgtest has never passed.
>
> Regards
> Graham