From murdoch at stats.uwo.ca  Thu Sep 17 03:14:13 2009
From: murdoch at stats.uwo.ca (Duncan Murdoch)
Date: Wed, 16 Sep 2009 21:14:13 -0400
Subject: [Rd] 2.10.0 Under development (unstable) (2009-09-15 r49711)
 just built segfaults on Debian Squeeze
In-Reply-To: <6b93d1830909161746v110d7bf5ued79c024c3c7ee26@mail.gmail.com>
References: <6b93d1830909161251w2148379bg963a66dbbb931487@mail.gmail.com>	
	<4AB14E87.6080608@biostat.ku.dk>	
	<6b93d1830909161648p66b194ffm1a54eda946a17f24@mail.gmail.com>	
	<4AB17DD5.3030809@stats.uwo.ca>
	<6b93d1830909161746v110d7bf5ued79c024c3c7ee26@mail.gmail.com>
Message-ID: <4AB18D65.1050307@stats.uwo.ca>

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             ?ster 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]]
> 
> 
> 
>         ------------------------------------------------------------------------
> 
>         ______________________________________________
>         R-devel at r-project.org <mailto:R-devel at r-project.org> mailing list
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> 
> 
>



[Rd] 2.10.0 Under development (unstable) (2009-09-15 r49711) just built segfaults on Debian Squeeze
Duncan Murdoch