2.10.0 Under development (unstable) (2009-09-15 r49711) just built segfaults on Debian Squeeze
On 16/09/2009 8:46 PM, Mark Kimpel wrote:
Okay, now that I knew what to look at, I've narrowed to the problem down
to the line
'source("~/R.functions/General_Functions/my.update.packages.func.R")'
Never mind my other request, I've got it now. I'm not sure what's going wrong, but I can reproduce the crash, so I should be able to track it down and fix it. Thanks for all the info! Duncan Murdoch
if just this line is commented out, R loads fine. If not, it crashes
reliably. Interestingly, if commented out, once R is loaded, the
function loads into R just fine and in facts runs as intended. So,
perhaps there is something in the way R is sourcing the file or with the
source command itself?
Thanks for helping me to figure this out, let me know if there is
anything specific you want me to try.
Mark
Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry
Indiana University School of Medicine
15032 Hunter Court, Westfield, IN 46074
(317) 490-5129 Work, & Mobile & VoiceMail
(317) 399-1219 Skype No Voicemail please
On Wed, Sep 16, 2009 at 8:07 PM, Duncan Murdoch <murdoch at stats.uwo.ca
<mailto:murdoch at stats.uwo.ca>> wrote:
On 16/09/2009 7:48 PM, Mark Kimpel wrote:
Peter,
I have not yet tried Simon's suggestion of using gcc 4.3 (just
got back from
a meeting), but running your commands produces the output below.
As you can
see, R --vanilla works, but just plain "R" doesn't. See the
results of gdb
far below.
That's helpful. It died in the parser while trying to read your
user profile. I can't tell what file it was trying to read, but the
order it tries them is as follows:
If you have R_PROFILE_USER set, it tries to read the file named there.
It tries to read .Rprofile in the current directory.
If you have HOME set, it tries to read .Rprofile in that directory.
It appears that you found a bug in the parser while trying to read
that file: you shouldn't be able to get a segfault, at worst you
should get a syntax error.
Can you work out what file it read, and send me a copy? I'd like to
track this down.
Duncan Murdoch
I do not have a saved workspace in my R_HOME or any of its
subdirectories.
Will report back on what I get with gcc 4.3 just as soon as I
read the
R-admin manual and figure out how to get configure configured....
Mark
mkimpel-XPS ~/sshfs: R --vanilla
R version 2.10.0 Under development (unstable) (2009-09-15 r49711)
Copyright (C) 2009 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
Natural language support but running in an English locale
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
q()
mkimpel-XPS ~/sshfs: R
R version 2.10.0 Under development (unstable) (2009-09-15 r49711)
Copyright (C) 2009 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
Natural language support but running in an English locale
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
*** caught segfault ***
address (nil), cause 'memory not mapped'
Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace
Selection: 4
mkimpel-XPS ~/sshfs: R -d gdb
GNU gdb (GDB) 6.8.50.20090628-cvs-debian
Copyright (C) 2009 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later
<http://gnu.org/licenses/gpl.html
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law. Type
"show copying"
and "show warranty" for details.
This GDB was configured as "x86_64-linux-gnu".
For bug reporting instructions, please see:
<http://www.gnu.org/software/gdb/bugs/>...
(gdb) run
Starting program:
/home/mkimpel/R_HOME/R-devel/R-build/lib64/R/bin/exec/R
R version 2.10.0 Under development (unstable) (2009-09-15 r49711)
Copyright (C) 2009 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
Natural language support but running in an English locale
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
Program received signal SIGSEGV, Segmentation fault.
Rf_setAttrib (vec=0x12e3d68, name=0x94d450, val=0x0) at
../../../src/main/attrib.c:226
226 if (NAMED(val)) val = duplicate(val);
(gdb) bt
#0 Rf_setAttrib (vec=0x12e3d68, name=0x94d450, val=0x0) at
../../../src/main/attrib.c:226
#1 0x000000000056264f in xxexprlist1 () at gram.y:574
#2 Rf_yyparse () at gram.y:337
#3 0x0000000000563469 in R_Parse1 (status=0x94d450) at gram.y:1126
#4 0x0000000000563cfb in R_Parse1File (fp=0x1200920, gencode=1,
status=0x7fffffffcd94, first=<value optimized out>) at gram.y:1164
#5 0x0000000000416cb2 in R_ReplFile (fp=0x1200920, rho=0x973338,
savestack=0, browselevel=<value optimized out>) at
../../../src/main/main.c:87
#6 0x0000000000416e08 in R_LoadProfile (fparg=<value optimized
out>,
env=0x973338) at ../../../src/main/main.c:651
#7 0x00000000004172c2 in setup_Rmainloop () at
../../../src/main/main.c:875
#8 0x00000000004185c9 in Rf_mainloop () at
../../../src/main/main.c:967
#9 0x0000000000415c38 in main (ac=<value optimized out>, av=<value
optimized out>) at ../../../src/main/Rmain.c:33
#10 0x00007ffff6ed05c6 in __libc_start_main () from /lib/libc.so.6
#11 0x0000000000415b29 in _start () at
../sysdeps/x86_64/elf/start.S:113
(gdb)
Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry
Indiana University School of Medicine
15032 Hunter Court, Westfield, IN 46074
(317) 490-5129 Work, & Mobile & VoiceMail
(317) 399-1219 Skype No Voicemail please
On Wed, Sep 16, 2009 at 4:45 PM, Peter Dalgaard
<p.dalgaard at biostat.ku.dk <mailto:p.dalgaard at biostat.ku.dk>>wrote:
Mark Kimpel wrote:
I just downloaded R-devel and when loaded it immediately
segfaults. I'm
not
sure how much or what sort of diagnostic info and can
provide, but below
is
my build script, my console output, and the output of
uname -r. I am
currently dependent on the development version of a
package, so I'd like
to
get R-devel up and running if possible. I am sure there
is more info I can
provide, but before deluging the list with unnecessary
output, I thought I
would ask first what would be helpfu. Mark
Not happening for me with 49727 (SUSE 64bit).
Do you have a saved workspace in that dir by any chance?
Could you try
R --vanilla
and
R -d gdb
followed by "run" and "bt" on the segfault
#Make R
cd ~/R_HOME
wget ftp://ftp.stat.math.ethz.ch/Software/R/R-devel.tar.gz
tar -xzf R-devel.tar.gz
cd ~/R_HOME/R-devel
mkdir R-build
cd R-build
../configure --prefix=/home/mkimpel/R_HOME/R-devel/R-build
make all
make install
#####################################33
# console output
mkimpel-XPS ~/R_HOME/R-devel/R-build/bin: ./R
R version 2.10.0 Under development (unstable)
(2009-09-15 r49711)
Copyright (C) 2009 The R Foundation for Statistical
Computing
ISBN 3-900051-07-0
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
Natural language support but running in an English locale
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
*** caught segfault ***
address (nil), cause 'memory not mapped'
Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace
Selection: 2
Save workspace image? [y/n/c]: n
######################################
# kernel version
mkimpel-XPS ~/R_HOME/R-devel/R-build/bin: uname -r
2.6.30-1-amd64
mkimpel-XPS ~/R_HOME/R-devel/R-build/bin:
Mark W. Kimpel MD ** Neuroinformatics ** Dept. of
Psychiatry
Indiana University School of Medicine
15032 Hunter Court, Westfield, IN 46074
(317) 490-5129 Work, & Mobile & VoiceMail
(317) 399-1219 Skype No Voicemail please
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c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K
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~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk
<mailto:p.dalgaard at biostat.ku.dk>) FAX: (+45)
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