[R-sig-Geo] spgrass6 and R 2.9

[Dylan Beaudette]

On Friday 29 May 2009, Torleif Markussen Lunde wrote:
> Hi
>
> First try updating glibc, and install spgrass6 again. If this does not work
> you could try
>
> export MALLOC_CHECK_=0
>
> before you start R. The error might be related to "somewhere something" is
> trying to free memory that has already been unallocated. I don't know the
> details here, but it could be worth a try?
>
> Best wishes
> Torleif

Hi Torleif, thanks for the tips.

I just updated my libc, and tried the MALLOC_CHECK trick-- neither fixed the 
problem. Still get the same error... Very strange, as I did not encounter 
this problem on a very similar machine.

Could this have anything to do with configure arguments such as -march ?

Cheers,
Dylan


> On Friday 29 May 2009 11:26:56 pm Dylan Beaudette wrote:
> > Hi,
> >
> > Just upgraded to R 2.9.0 this morning, and tried to update all of my
> > packages. Everyhing seemed to work, except spgrass6. Manually removing
> > the old packing and installing fresh resulted in:
> >
> > install.packages('spgrass6', dep=TRUE)
> > trying URL
> > 'http://cran.cnr.Berkeley.edu/src/contrib/spgrass6_0.6-6.tar.gz' Content
> > type 'application/x-gzip' length 332298 bytes (324 Kb)
> > opened URL
> > ==================================================
> > downloaded 324 Kb
> >
> > * Installing *source* package 'spgrass6' ...
> > ** R
> > ** inst
> > ** preparing package for lazy loading
> > Geospatial Data Abstraction Library extensions to R successfully loaded
> > Loaded GDAL runtime: GDAL 1.7.0dev, released 2008/11/26
> > Path to GDAL shared files: /usr/local/share/gdal
> > Loaded PROJ.4 runtime: Rel. 4.6.0, 21 Dec 2007
> > Path to PROJ.4 shared files: (autodetected)
> > ** help
> > *** installing help indices
> >
> >  >>> Building/Updating help pages for package 'spgrass6'
> >
> >      Formats: text html latex example
> >   execGRASS                         text    html    latex   example
> >   gmeta6                            text    html    latex   example
> >   initGRASS                         text    html    latex   example
> >   readRAST6                         text    html    latex   example
> >   readVECT6                         text    html    latex   example
> >   spgrass6                          text    html    latex   example
> > ** building package indices ...
> > * DONE (spgrass6)
> > *** glibc detected *** /usr/local/lib/R/bin/exec/R: double free or
> > corruption (fasttop): 0x096ac2b0 ***
> >
> >
> > At this point R stops responding, and I have to issue a `kill -9` to make
> > regain control of the shell.
> >
> > Any ideas?
> >
> > Dylan



-- 
Dylan Beaudette
Soil Resource Laboratory
http://casoilresource.lawr.ucdavis.edu/
University of California at Davis
530.754.7341