From bolker at ufl.edu  Wed May 13 04:58:54 2009
From: bolker at ufl.edu (Ben Bolker)
Date: Tue, 12 May 2009 22:58:54 -0400
Subject: [Rd] View() crashy on Ubuntu 9.04
In-Reply-To: <556e90a80905121943o85a6d7et8862c940fafda773@mail.gmail.com>
References: <4A0A0A64.6030706@ufl.edu>	
	<18954.10612.51851.692033@ron.nulle.part>
	<556e90a80905121943o85a6d7et8862c940fafda773@mail.gmail.com>
Message-ID: <4A0A376E.8020305@ufl.edu>

  Actually, gdb seems not to want to debug this -- in either the
Debian-magic version or the one I configured/made on my own system, I
get to the View() command and get

>> View(v)
> [Thread debugging using libthread_db enabled]
> Error while reading shared library symbols:
> Cannot find new threads: generic error
> Cannot find new threads: generic error

  ??

  cheers
   Ben Bolker


Kjetil Halvorsen wrote:
> I can reproduce this too.
> Run  from within emacs:
> 
>> v <- data.frame(1:3,2:4)
>> sessionInfo()
> R version 2.9.0 (2009-04-17)
> i686-pc-linux-gnu
> 
> locale:
> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
> 
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>> View(v)
>>
>  *** caught segfault ***
> address 0x4, 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: 3
> 
> Process R exited abnormally with code 70 at Tue May 12 22:41:55 2009
> 
> Kjetil
> 
> 
> On Tue, May 12, 2009 at 9:59 PM, Dirk Eddelbuettel <edd at debian.org<mailto:edd at debian.org>> wrote:
> 
> On 12 May 2009 at 19:46, Ben Bolker wrote:
> |   It's my vague impression that View() is workable on Windows and maybe
> | on MacOS, but on Ubuntu Linux 9.04 (intrepid) it seems completely
> | unstable.  I can reliably crash R by trying to look  at a very small,
> | simple data frame ...
> |
> |    I was going to try to run with debug turned on, but my installed
> | version (2.9.0) doesn't have debugging symbols, and I'm having trouble
> 
> Good news: just run
> 
>     sudo apt-get install r-base-core-dbg
> 
> Most (library) packages (lib)foo now also ship (lib)foo-dbg which is provide
> something close to pure magic -- just by installing these the already
> instrumented gdb knows where to look for them.  See, no more recompiling.
> Debug symbols appear out of thin air.  (I have used it only on Debian at home
> when debugging R stuff, but it should really work the same for you there on
> Ubuntu.)
> 
> | building the latest SVN version (./configure gives "checking for
> | recommended packages... ls: cannot access
> | ./src/library/Recommended/boot_*.tar.gz: No such file or directory")
> 
> It's moot as per the above but you need to either run the script to rsync
> those in, or configure using
> 
>                    --without-recommended-packages
> 
> As for x11 instability, I happen to spend my daytime hours in from of
> Cygwin/X connected to a few Ubuntu machines running R, and of late the
> display has been unstable.  I tend to blame the other software first, but
> indeed, the most recent change was probably R.  Did anybody experience that?
> 
> |    Can anyone confirm?
> |
> |   cheers
> |     Ben Bolker
> |
> |
> | R --vanilla
> |
> | > v <- data.frame(1:3,2:4)
> | > sessionInfo()
> | R version 2.9.0 (2009-04-17)
> | i486-pc-linux-gnu
> |
> | locale:
> | LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
> |
> | attached base packages:
> | [1] stats     graphics  grDevices utils     datasets  methods   base
> |
> | > View(v)
> |
> |   [change focus to the view window, hit "down arrow"]
> |
> | >
> |  *** caught segfault ***
> | address 0x4, 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: 3
> 
> Confirmed. Dies for me too, but from Debian and Ubuntu connected to the same
> display (Ubuntu 9.04).
> 
> Dirk
> 
> --
> Three out of two people have difficulties with fractions.
> 
> ______________________________________________
> R-devel at r-project.org<mailto:R-devel at r-project.org> mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
> 


-- 
Ben Bolker
Associate professor, Biology Dep't, Univ. of Florida
bolker at ufl.edu / www.zoology.ufl.edu/bolker
GPG key: www.zoology.ufl.edu/bolker/benbolker-publickey.asc

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[Rd] View() crashy on Ubuntu 9.04
Ben Bolker