From murdoch at stats.uwo.ca  Thu Sep 17 02:07:49 2009
From: murdoch at stats.uwo.ca (Duncan Murdoch)
Date: Wed, 16 Sep 2009 20:07:49 -0400
Subject: [Rd] 2.10.0 Under development (unstable) (2009-09-15 r49711)
 just built segfaults on Debian Squeeze
In-Reply-To: <6b93d1830909161648p66b194ffm1a54eda946a17f24@mail.gmail.com>
References: <6b93d1830909161251w2148379bg963a66dbbb931487@mail.gmail.com>	<4AB14E87.6080608@biostat.ku.dk>
	<6b93d1830909161648p66b194ffm1a54eda946a17f24@mail.gmail.com>
Message-ID: <4AB17DD5.3030809@stats.uwo.ca>

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>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 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)              FAX: (+45) 35327907
>>
> 
> 	[[alternative HTML version deleted]]
> 
> 
> 
> ------------------------------------------------------------------------
> 
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel



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