thr3ads.net - R help - [R] glibc detected *** /usr/lib64/R/bin/exec/R: double free or corruption ???? tm package [Jan 2008]

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Jan Wijffels

2008-Jan-07 10:33 UTC

[R] glibc detected *** /usr/lib64/R/bin/exec/R: double free or corruption ???? tm package

Hi,

I have a collection of .txt documents in my working folder for which I want to
do some text mining. If I run TextDocCol from the tm package, R crashes with
some memory issues. Does anyone has any idea if this is related to R itself or
to the tm package?
Below you can find what is happening here.
>
setwd("/home/jan/Work/2008/Profacts/textmining/tryouts/workfolder")
> require(tm)Loading required package: tm
Loading required package: filehash
Simple key-value database (1.0-1 2007-08-13)
Loading required package: Matrix
Loading required package: lattice
Loading required package: Snowball
Loading required package: RWeka
Loading required package: rJava
Loading required package: grid
Loading required package: XML> sessionInfo()R version 2.6.1 (2007-11-26)
x86_64-redhat-linux-gnu

locale:
LC_CTYPE=nl_BE.UTF-8;LC_NUMERIC=C;LC_TIME=nl_BE.UTF-8;LC_COLLATE=nl_BE.UTF-8;LC_MONETARY=nl_BE.UTF-8;LC_MESSAGES=nl_BE.UTF-8;LC_PAPER=nl_BE.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=nl_BE.UTF-8;LC_IDENTIFICATION=C

attached base packages:
[1] grid      stats     graphics  grDevices utils     datasets  methods
[8] base

other attached packages:
[1] tm_0.2-3.7        XML_1.93-2        Snowball_0.0-3    RWeka_0.3-9
[5] rJava_0.5-1       Matrix_0.999375-3 lattice_0.17-2    filehash_1.0-1

loaded via a namespace (and not attached):
[1] proxy_0.3       rcompgen_0.1-17> R.Version()$platform
[1] "x86_64-redhat-linux-gnu"

$arch
[1] "x86_64"

$os
[1] "linux-gnu"

$system
[1] "x86_64, linux-gnu"

$status
[1] ""

$major
[1] "2"

$minor
[1] "6.1"

$year
[1] "2007"

$month
[1] "11"

$day
[1] "26"

$`svn rev`
[1] "43537"

$language
[1] "R"

$version.string
[1] "R version 2.6.1 (2007-11-26)"
> test      <- TextDocCol(DirSource(getwd()), readerControl = list(reader
= readPlain, load = TRUE, language = "nl_BE"))*** glibc detected *** /usr/lib64/R/bin/exec/R: double free or corruption
(!prev): 0x0000000022e20680 ***
======= Backtrace: ========/lib64/libc.so.6[0x359946f4f4]
/lib64/libc.so.6(cfree+0x8c)[0x3599472b1c]
/usr/lib64/R/lib/libR.so[0x305b670a3d]
/usr/lib64/R/lib/libR.so[0x305b6f875e]
/usr/lib64/R/lib/libR.so(Rf_eval+0x436)[0x305b6c39a6]
/usr/lib64/R/lib/libR.so[0x305b6c4ce2]
/usr/lib64/R/lib/libR.so(Rf_eval+0x436)[0x305b6c39a6]
/usr/lib64/R/lib/libR.so(Rf_applyClosure+0x291)[0x305b6c6c01]
/usr/lib64/R/lib/libR.so(Rf_eval+0x303)[0x305b6c3873]
/usr/lib64/R/lib/libR.so[0x305b6c4648]
/usr/lib64/R/lib/libR.so(Rf_eval+0x502)[0x305b6c3a72]
/usr/lib64/R/lib/libR.so[0x305b6c4ce2]
/usr/lib64/R/lib/libR.so(Rf_eval+0x436)[0x305b6c39a6]
/usr/lib64/R/lib/libR.so[0x305b6c6504]
/usr/lib64/R/lib/libR.so(R_execMethod+0x239)[0x305b6c6889]
/usr/lib64/R/library/methods/libs/methods.so[0x2aaaae4367e9]
/usr/lib64/R/lib/libR.so[0x305b6f9cf7]
/usr/lib64/R/lib/libR.so(Rf_eval+0x55d)[0x305b6c3acd]
/usr/lib64/R/lib/libR.so(Rf_applyClosure+0x291)[0x305b6c6c01]
/usr/lib64/R/lib/libR.so(Rf_eval+0x303)[0x305b6c3873]
/usr/lib64/R/lib/libR.so[0x305b6c638e]
/usr/lib64/R/lib/libR.so(Rf_eval+0x436)[0x305b6c39a6]
/usr/lib64/R/lib/libR.so[0x305b6c4ce2]
/usr/lib64/R/lib/libR.so(Rf_eval+0x436)[0x305b6c39a6]
/usr/lib64/R/lib/libR.so[0x305b6c5009]
/usr/lib64/R/lib/libR.so(Rf_eval+0x436)[0x305b6c39a6]
/usr/lib64/R/lib/libR.so[0x305b6c4ce2]
/usr/lib64/R/lib/libR.so(Rf_eval+0x436)[0x305b6c39a6]
/usr/lib64/R/lib/libR.so[0x305b6c6504]
/usr/lib64/R/lib/libR.so(R_execMethod+0x239)[0x305b6c6889]
/usr/lib64/R/library/methods/libs/methods.so[0x2aaaae4367e9]
/usr/lib64/R/lib/libR.so[0x305b6f9cf7]
/usr/lib64/R/lib/libR.so(Rf_eval+0x55d)[0x305b6c3acd]
/usr/lib64/R/lib/libR.so(Rf_applyClosure+0x291)[0x305b6c6c01]
/usr/lib64/R/lib/libR.so(Rf_eval+0x303)[0x305b6c3873]
/usr/lib64/R/lib/libR.so[0x305b6c638e]
/usr/lib64/R/lib/libR.so(Rf_eval+0x436)[0x305b6c39a6]
/usr/lib64/R/lib/libR.so(Rf_ReplIteration+0x183)[0x305b6e7893]
/usr/lib64/R/lib/libR.so(run_Rmainloop+0xc2)[0x305b6e7bc2]
/usr/lib64/R/bin/exec/R(main+0x1b)[0x40080b]
/lib64/libc.so.6(__libc_start_main+0xf4)[0x359941d8a4]
/usr/lib64/R/bin/exec/R[0x400709]
======= Memory map: =======00400000-00401000 r-xp 00000000 fd:00 12868864       
/usr/lib64/R/bin/exec/R
00600000-00602000 rw-p 00000000 fd:00 12868864                          
/usr/lib64/R/bin/exec/R
1de8b000-2305b000 rw-p 1de8b000 00:00 0
40000000-40001000 ---p 40000000 00:00 0
40001000-40101000 rwxp 40001000 00:00 0
40101000-40102000 ---p 40101000 00:00 0
40102000-40202000 rwxp 40102000 00:00 0
40202000-40203000 ---p 40202000 00:00 0
40203000-40303000 rwxp 40203000 00:00 0
40303000-40306000 ---p 40303000 00:00 0
40306000-40404000 rwxp 40306000 00:00 0
40404000-40407000 ---p 40404000 00:00 0
40407000-40505000 rwxp 40407000 00:00 0
40505000-40508000 ---p 40505000 00:00 0
40508000-40606000 rwxp 40508000 00:00 0
40606000-40609000 ---p 40606000 00:00 0
40609000-40707000 rwxp 40609000 00:00 0
40707000-4070a000 ---p 40707000 00:00 0
4070a000-40808000 rwxp 4070a000 00:00 0
40808000-4080b000 ---p 40808000 00:00 0
4080b000-40909000 rwxp 4080b000 00:00 0
40909000-4090a000 ---p 40909000 00:00 0
4090a000-40a0a000 rwxp 4090a000 00:00 0
305b200000-305b22c000 r-xp 00000000 fd:00 12996246                      
/usr/lib64/R/lib/libRblas.so
305b22c000-305b42b000 ---p 0002c000 fd:00 12996246                      
/usr/lib64/R/lib/libRblas.so
305b42b000-305b42c000 rw-p 0002b000 fd:00 12996246                      
/usr/lib64/R/lib/libRblas.so
305b600000-305b88e000 r-xp 00000000 fd:00 12996244                      
/usr/lib64/R/lib/libR.so
305b88e000-305ba8d000 ---p 0028e000 fd:00 12996244                      
/usr/lib64/R/lib/libR.so
305ba8d000-305baa2000 rw-p 0028d000 fd:00 12996244                      
/usr/lib64/R/lib/libR.so
305baa2000-305bb3c000 rw-p 305baa2000 00:00 0
3599000000-359901a000 r-xp 00000000 fd:00 16433498                      
/lib64/ld-2.5.so
3599219000-359921a000 r--p 00019000 fd:00 16433498                      
/lib64/ld-2.5.so
359921a000-359921b000 rw-p 0001a000 fd:00 16433498                      
/lib64/ld-2.5.so
3599400000-3599546000 r-xp 00000000 fd:00 16433500                      
/lib64/libc-2.5.so
3599546000-3599746000 ---p 00146000 fd:00 16433500                      
/lib64/libc-2.5.so
3599746000-359974a000 r--p 00146000 fd:00 16433500                      
/lib64/libc-2.5.so
359974a000-359974b000 rw-p 0014a000 fd:00 16433500                      
/lib64/libc-2.5.so
359974b000-3599750000 rw-p 359974b000 00:00 0
3599800000-3599882000 r-xp 00000000 fd:00 16433654                      
/lib64/libm-2.5.so
3599882000-3599a81000 ---p 00082000 fd:00 16433654                      
/lib64/libm-2.5.so
3599a81000-3599a82000 r--p 00081000 fd:00 16433654                      
/lib64/libm-2.5.so
3599a82000-3599a83000 rw-p 00082000 fd:00 16433654                      
/lib64/libm-2.5.so
3599c00000-3599c02000 r-xp 00000000 fd:00 16433675                      
/lib64/libdl-2.5.so
3599c02000-3599e02000 ---p 00002000 fd:00 16433675                      
/lib64/libdl-2.5.so
3599e02000-3599e03000 r--p 00002000 fd:00 16433675                      
/lib64/libdl-2.5.so
3599e03000-3599e04000 rw-p 00003000 fd:00 16433675                      
/lib64/libdl-2.5.so
359a000000-359a096000 r-xp 00000000 fd:00 11008745                      
/usr/lib64/libgfortran.so.1.0.0
359a096000-359a295000 ---p 00096000 fd:00 11008745                      
/usr/lib64/libgfortran.so.1.0.0
359a295000-359a297000 rw-p 00095000 fd:00 11008745                      
/usr/lib64/libgfortran.so.1.0.0
359a400000-359a414000 r-xp 00000000 fd:00 11017340                      
/usr/lib64/libz.so.1.2.3
359a414000-359a613000 ---p 00014000 fd:00 11017340                      
/usr/lib64/libz.so.1.2.3
359a613000-359a614000 rw-p 00013000 fd:00 11017340                      
/usr/lib64/libz.so.1.2.3
359a800000-359a835000 r-xp 00000000 fd:00 11015184                      
/usr/lib64/libreadline.so.5.1
359a835000-359aa34000 ---p 00035000 fd:00 11015184                      
/usr/lib64/libreadline.so.5.1
359aa34000-359aa3c000 rw-p 00034000 fd:00 11015184                      
/usr/lib64/libreadline.so.5.1
359aa3c000-359aa3d000 rw-p 359aa3c000 00:00 0
359cc00000-359cc03000 r-xp 00000000 fd:00 16433785                      
/lib64/libtermcap.so.2.0.8
359cc03000-359ce02000 ---p 00003000 fd:00 16433785                      
/lib64/libtermcap.so.2.0.8
359ce02000-359ce03000 rw-p 00002000 fd:00 16433785                      
/lib64/libtermcap.so.2.0.8
359dc00000-359dc07000 r-xp 00000000 fd:00 16433693                      
/lib64/librt-2.5.so
359dc07000-359de07000 ---p 00007000 fd:00 16433693                      
/lib64/librt-2.5.so
359de07000-359de08000 r--p 00007000 fd:00 16433693                      
/lib64/librt-2.5.so
359de08000-359de09000 rw-p 00008000 fd:00 16433693                      
/lib64/librt-2.5.so
359f400000-359f40d000 r-xp 00000000 fd:00 16433680                      
/lib64/libgcc_s-4.1.2-20070626.so.1
359f40d000-359f60d000 ---p 0000d000 fd:00 16433680                      
/lib64/libgcc_s-4.1.2-20070626.so.1
359f60d000-359f60e000 rw-p 0000d000 fd:00 16433680                     
Afgebroken
[jan at cable-213 tryouts]$


thanks,
Jan
_________________________________________________________________
Share life as it happens with the new Windows Live.

08

Prof Brian Ripley

2008-Jan-07 12:50 UTC

head link

[R] glibc detected *** /usr/lib64/R/bin/exec/R: double free or corruption ???? tm package

On Mon, 7 Jan 2008, Jan Wijffels wrote:
> I have a collection of .txt documents in my working folder for which I 
> want to do some text mining. If I run TextDocCol from the tm package, R 
> crashes with some memory issues. Does anyone has any idea if this is 
> related to R itself or to the tm package?
Given that R runs many, many other things without doing this, it is almost 
certainly a bug in one of those packages. The way to find the original 
problem is to run under valgrind (possibly using an R build set up for 
it): the report is probably on a result of previous memory corruption.

See 'Writing R Extensions' for how to debug such issues.
> Below you can find what is happening here.
>
>>
setwd("/home/jan/Work/2008/Profacts/textmining/tryouts/workfolder")
>> require(tm)
> Loading required package: tm
> Loading required package: filehash
> Simple key-value database (1.0-1 2007-08-13)
> Loading required package: Matrix
> Loading required package: lattice
> Loading required package: Snowball
> Loading required package: RWeka
> Loading required package: rJava
> Loading required package: grid
> Loading required package: XML
[...]

-- 
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

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