[R-SIG-Mac] help difficulties on

Simon Urbanek simon.urbanek at r-project.org
Wed Feb 10 23:22:24 CET 2010

On Feb 10, 2010, at 4:44 PM, Ben Bolker wrote:

>  Dear R-sig-Mac'ers:
>  I'm posting on behalf of a student who is having trouble with
> accessing the help files in R.app (I think) on MacOS X.4 (I think
> X.4.11?) .  The basic symptom is that in a clean R session she gets
> results like this:
>> ?plot
> Error in file(out, "wt") : cannot open the connection

It seems likely a problem in your system setup -- possibly your temporary directory has wrong permission and/or TMP/TEMP settings are wrong. That is a long shot though, please use something like options(error=recover) to dump the call stack and look at the "out" value to see where is the problem on the machine.

>  This is generic (i.e. happens with any help request).  After a bit
> more poking around we triggered

That is completely unrelated - do you have a way to reproduce that?


> 2010-02-09 15:20:21.010 R[16728] *** Exception handlers were not
> properly removed. Some code has jumped or returned out of an
> NS_DURING...NS_HANDLER region without using the NS_VOIDRETURN or
> R(16728,0xa000ed88) malloc: *** error for object 0x3b610038:
> Non-aligned pointer being freed
> R(16728,0xa000ed88) malloc: *** set a breakpoint in szone_error to
> debug
> R(16728,0xa000ed88) malloc: ***  Deallocation of a pointer not
> malloced: 0x41d60; This could be a double free(), or free() called
> with the middle of an allocated block; Try setting environment
> variable MallocHelp to see tools to help debug
>  We have both tried searching/googling for this particular problem,
> without success -- found a fair amount about issues with help.start()
> when running firewalls, but nothing that seemed to match our situation.
>  * Does this ring any bells for anyone? Have we missed something
> obvious (I hope)?  What are the next steps in the
> diagnostic/troubleshooting pathway?


enter the last frame and have a look at the value of out -- that will tell you where on the machine is R trying to create a file that fails. Also the frame stack may be useful in case it's a deeper error.

>  * Is there a searchable version of the R-sig-mac archives?


In your case I doubt you'll find much as this seems likely a peculiarity of your machine.

> Rsitesearch doesn't seem to offer it, and the R-sig-mac archives seem to
> be available only month-by-month (& not searchable), as far as I can tell.
>  thanks,
>    Ben Bolker
>> sessionInfo()
> R version 2.10.1 (2009-12-14)
> powerpc-apple-darwin8.11.1
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods
> [7] base
> loaded via a namespace (and not attached):
> [1] tools_2.10.1
> -- 
> Ben Bolker
> Associate professor, Biology Dep't, Univ. of Florida
> bolker at ufl.edu / people.biology.ufl.edu/bolker
> GPG key: people.biology.ufl.edu/bolker/benbolker-publickey.asc
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