[R-sig-Geo] spgrass6 and R 2.9

[Roger Bivand]

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