[R-sig-Geo] spgrass6 and R 2.9

[Roger Bivand]

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

>
> 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