[R-sig-Geo] spgrass6 and R 2.9

[Dylan Beaudette]

On Monday 01 June 2009, Roger Bivand wrote:
> On Mon, 1 Jun 2009, Dylan Beaudette wrote:
> > 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 ?
>
> You haven't told us what your underlying system is, or how you installed
> R. If you built R from source, did you run "make check"? Does the problem
> arise installing other packages? It most likely is something on your
> system, otherwise there would be lots of reports of the same.
>
> Roger

Right. Should have been a little less hasty about posting to the list. R has 
been built from source, spgrass6 was accessed from CRAN via 
install.packages(). This problems has not occurred at anyother time while 
updating packages that were installed under R 2.7. 

1. make check (R 2.9.0): OK

2. sessionInfo()
R version 2.9.0 (2009-04-17) 
i686-pc-linux-gnu 

locale:
LC_CTYPE=en_US;LC_NUMERIC=C;LC_TIME=en_US;LC_COLLATE=en_US;LC_MONETARY=C;LC_MESSAGES=en_US;LC_PAPER=en_US;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US;LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base 

Is there any way that I can do a 'make check' type of operation with the 
latest spgrass6 from CRAN?

Note that trying to manually install the package, like this:
sudo R CMD INSTALL spgrass6_0.6-6.tar.gz

results in:
* Installing to library '/usr/local/lib/R/library'
* 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): 0x0857d880 ***

hope that is enough information.

Cheers,
Dylan


> > 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