R crash

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R crash

Nick Guenther
I just installed 4.8 and the R statistical language from packages, but
it keeps crashing whenever I try to use plot().


$ R

R version 2.8.1 (2008-12-22)
Copyright (C) 2008 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.

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.

> plot(1:10)
/usr/local/lib/R/bin/exec/R:/usr/local/lib/libgthread-2.0.so.1803.0:
undefined symbol 'pthread_attr_destroy'
/usr/local/lib/R/bin/exec/R:/usr/local/lib/libgthread-2.0.so.1803.0:
undefined symbol 'pthread_create'
/usr/local/lib/R/bin/exec/R:/usr/local/lib/libgthread-2.0.so.1803.0:
undefined symbol 'pthread_attr_init'
/usr/local/lib/R/bin/exec/R:/usr/local/lib/libgthread-2.0.so.1803.0:
undefined symbol 'pthread_exit'
/usr/local/lib/R/bin/exec/R:/usr/local/lib/libgthread-2.0.so.1803.0:
undefined symbol 'pthread_attr_setscope'
/usr/local/lib/R/bin/exec/R:/usr/local/lib/libgthread-2.0.so.1803.0:
undefined symbol 'pthread_attr_setstacksize'
/usr/local/lib/R/bin/exec/R:/usr/local/lib/libgthread-2.0.so.1803.0:
undefined symbol 'pthread_mutex_trylock'
/usr/local/lib/R/bin/exec/R:/usr/local/lib/libgthread-2.0.so.1803.0:
undefined symbol 'pthread_attr_setdetachstate'
/usr/local/lib/R/bin/exec/R:/usr/local/lib/libgthread-2.0.so.1803.0:
undefined symbol 'pthread_join'
/usr/local/lib/R/bin/exec/R:/usr/local/lib/libgthread-2.0.so.1803.0:
undefined symbol 'pthread_cond_timedwait'

 *** caught segfault ***
address 0xf5e, cause 'memory not mapped'

Traceback:
 1: axis(side = side, at = at, labels = labels, ...)
 2: Axis.default(...)
 3: Axis(...)
 4: localAxis(if (is.null(y)) xy$x else x, side = 1, ...)
 5: plot.default(1:10)
 6: plot(1:10)

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:



Non-plotting commands seem to work fine:

> sin(seq(-202, 23, 2))
  [1] -0.80641841  0.87329730  0.07957859 -0.93953006  0.70238633  0.35493836
  [7] -0.99779928  0.47552367  0.60202394 -0.97658438  0.21078107  0.80115264
 [13] -0.87757534 -0.07075224  0.93646197 -0.70865914 -0.34664946  0.99717329
 [19] -0.48329156 -0.59493278  0.97845035 -0.21942526 -0.79582410  0.88178462
 [25]  0.06192034 -0.93332052  0.71487643  0.33833339 -0.99646917  0.49102159
 [31]  0.58779501 -0.98023966  0.22805226  0.79043321 -0.88592482 -0.05308359
 [37]  0.93010595 -0.72103771 -0.32999083  0.99568699 -0.49871315 -0.58061118
 [43]  0.98195217 -0.23666139 -0.78498039  0.88999560  0.04424268 -0.92681851
 [49]  0.72714250  0.32162240 -0.99482679  0.50636564  0.57338187 -0.98358775
 [55]  0.24525199  0.77946607 -0.89399666 -0.03539830  0.92345845 -0.73319032
 [61] -0.31322878  0.99388865 -0.51397846 -0.56610764  0.98514626 -0.25382336
 [67] -0.77389068  0.89792768  0.02655115 -0.92002604  0.73918070  0.30481062
 [73] -0.99287265  0.52155100  0.55878905 -0.98662759  0.26237485  0.76825466
 [79] -0.90178835 -0.01770193  0.91652155 -0.74511316 -0.29636858  0.99177885
 [85] -0.52908269 -0.55142668  0.98803162 -0.27090579 -0.76255845  0.90557836
 [91]  0.00885131 -0.91294525  0.75098725  0.28790332 -0.99060736  0.53657292
 [97]  0.54402111 -0.98935825  0.27941550  0.75680250 -0.90929743  0.00000000
[103]  0.90929743 -0.75680250 -0.27941550  0.98935825 -0.54402111 -0.53657292
[109]  0.99060736 -0.28790332 -0.75098725  0.91294525 -0.00885131




I also compiled from ports and
===>  Building package for R-2.8.1p3
Create /usr/ports/packages/i386/all/R-2.8.1p3.tgz
Link to /usr/ports/packages/i386/ftp/R-2.8.1p3.tgz
Link to /usr/ports/packages/i386/cdrom/R-2.8.1p3.tgz
$ ls /usr/ports/pa
packages/  palm/
$ sudo pkg_delete R
Password:
R-2.8.1p3: ok
Read shared items: ok
r/ports/packages/i386/all/R-2.8.1p3.tgz                                        <
No pkgname in packing-list for gvfs-1.6.3p0
R-2.8.1p3: ok
$ R
... same output



Any clues?

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Re: R crash

Stuart Henderson
On 2010/11/09 00:27, Nick Guenther wrote:
> I just installed 4.8 and the R statistical language from packages, but
> it keeps crashing whenever I try to use plot().

this problem will have started when threads were enabled in glib2,
there is still some fallout from this change. the R binary will now
need to be linked with -pthread (see graphviz patch-cmd_dot_Makefile_in
for an example).. for now as a quick hack you could try setting
LD_PRELOAD=libpthread.so before starting R, this may work but may
cause other problems.

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Re: R crash

Nick Guenther
On Tue, Nov 9, 2010 at 3:41 AM, Stuart Henderson <[hidden email]> wrote:
> On 2010/11/09 00:27, Nick Guenther wrote:
>> I just installed 4.8 and the R statistical language from packages, but
>> it keeps crashing whenever I try to use plot().
>
> for now as a quick hack you could try setting
> LD_PRELOAD=libpthread.so before starting R, this may work but may
> cause other problems.

Thanks, that made plotting work, which is good enough to do what I
want! I was worried it was a hopeless cause at this point, but that
was quick of you. I'll report any weirdness I run into for the
archives.

-Nick