Dear R developers: When i run "make check" in R-patched_2011-02-12 and R-devel_2011-02-22 on a specific machine, the test fails and the file tests/Examples/base-Ex.Rout.fail ends with > txt.xz <- memCompress(txt, "x") Error in memCompress(txt, "x") : internal error 5 in memCompress Execution halted The error may be reproduced using commands txt <- readLines(file.path(R.home("doc"), "COPYING")) txt.xz <- memCompress(txt, "x") in both the above installed versions. The machine is CentOS release 5.4 (Final) under VMware. I did not observe this error on other machines, some of which are also CentOS. For the development version, sessionInfo() is R version 2.13.0 Under development (unstable) (2011-02-22 r54523) Platform: i686-pc-linux-gnu (32-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base gcc --version gcc (GCC) 4.1.2 20080704 (Red Hat 4.1.2-46) Petr Savicky.
So it seems that there is something wrong with the liblzma library used on that machine. Did it use the version supplied with R or an external library (which is the default if one is found)? My first step would be to force the internal version via --with-system-xz=no. That error appears to be LZMA_MEM_ERROR: see xz/api/lzma/base.h . On Tue, 22 Feb 2011, Petr Savicky wrote:> Dear R developers: > > When i run "make check" in R-patched_2011-02-12 and R-devel_2011-02-22 > on a specific machine, the test fails and the file > > tests/Examples/base-Ex.Rout.fail > > ends with > > > txt.xz <- memCompress(txt, "x") > Error in memCompress(txt, "x") : internal error 5 in memCompress > Execution halted > > The error may be reproduced using commands > > txt <- readLines(file.path(R.home("doc"), "COPYING")) > txt.xz <- memCompress(txt, "x") > > in both the above installed versions. The machine is CentOS > release 5.4 (Final) under VMware. > > I did not observe this error on other machines, some of which are > also CentOS. > > For the development version, sessionInfo() is > > R version 2.13.0 Under development (unstable) (2011-02-22 r54523) > Platform: i686-pc-linux-gnu (32-bit) > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=en_US.UTF-8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > gcc --version > > gcc (GCC) 4.1.2 20080704 (Red Hat 4.1.2-46) > > Petr Savicky. > > ______________________________________________ > R-devel at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel >-- Brian D. Ripley, ripley at stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UK Fax: +44 1865 272595
On Tue, Feb 22, 2011 at 11:25:50AM +0000, Prof Brian Ripley wrote:> So it seems that there is something wrong with the liblzma library > used on that machine. Did it use the version supplied with R or an > external library (which is the default if one is found)? My first > step would be to force the internal version via --with-system-xz=no.Thank you for your reply. I tried ./configure --with-x=no --with-system-xz=no in a clean R-devel_2011-02-22 and the result of make check is the same. The commands txt <- readLines(file.path(R.home("doc"), "COPYING")) txt.xz <- memCompress(txt, "x") do not produce an error, if the compiled R runs in the same shell, where "make check" was run. However, they produce the error, if R is started in a new shell. The command find /usr -name "liblzma*" has empty output. Petr Savicky.
On Tue, Feb 22, 2011 at 01:38:07PM +0100, Petr Savicky wrote: ...> The commands > > txt <- readLines(file.path(R.home("doc"), "COPYING")) > txt.xz <- memCompress(txt, "x") > > do not produce an error, if the compiled R runs in the same shell, > where "make check" was run. However, they produce the error, if R is > started in a new shell.Athough i did see the above two lines with no error on my screen, the change of the behavior is not reproducible. I am sorry, i probably mixed up windows or something. According to a repeated test, the above two lines produce the error Error in memCompress(txt, "x") : internal error 5 in memCompress on the machine described in the first email, even if --with-system-xz=no was used for configuration. Petr Savicky.