[Rd] 2.10.0 Under development (unstable) (2009-09-15 r49711) just built segfaults on Debian Squeeze
Duncan Murdoch
murdoch at stats.uwo.ca
Thu Sep 17 03:14:13 CEST 2009
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
>
> [[alternative HTML version deleted]]
>
> ______________________________________________
> R-devel at r-project.org <mailto:R-devel at r-project.org>
> mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>
>
> --
> O__ ---- Peter Dalgaard Øster Farimagsgade 5,
> Entr.B
> c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K
> (*) \(*) -- University of Copenhagen Denmark Ph:
> (+45) 35327918
> ~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk
> <mailto:p.dalgaard at biostat.ku.dk>) FAX: (+45)
> 35327907
>
>
> [[alternative HTML version deleted]]
>
>
>
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