help difficulties on
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? Thanks, Simon
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 NS_VALUERETURN macros. 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?
options(error=recover) 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?
http://blog.gmane.org/gmane.comp.lang.r.mac 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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