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.
error in memCompress() in make check
4 messages · Petr Savicky, Brian Ripley
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.