spgrass6 and R 2.9

Fri, Jun 5, 2009 1:55 AM

On Thu, 4 Jun 2009, Dylan Beaudette wrote:

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?

Yes, do R CMD check spgrass6_0.6-6.tar.gz. When building R, are you 
setting the architecture flags manually? Have you tried letting R sort 
things out for itself? Could you try R CMD check rgdal (from the source 
tarball)? Could you try:

R -d gbd

and then a traceback after install fails? Otherwise we are left with 
non-random cosmic rays as the explanation?

Roger

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

Roger Bivand
Economic Geography Section, Department of Economics, Norwegian School of
Economics and Business Administration, Helleveien 30, N-5045 Bergen,
Norway. voice: +47 55 95 93 55; fax +47 55 95 95 43
e-mail: Roger.Bivand at nhh.no

spgrass6 and R 2.9

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