[GRASS-stats] readRAST6 and readVECT6 errors with grass70
Eric Momsen
eric.momsen at gmail.com
Thu Mar 8 11:46:01 EST 2012
On Thu, Mar 8, 2012 at 4:42 AM, Roger Bivand <Roger.Bivand at nhh.no> wrote:
> I've committed changes to spgrass6 on R-forge, project rspatial as revision
> 1224, which address the r.info flag issue, and another issue related to my
> using GDAL 1.9.0, which is less forgiving about overwriting vector files in
> the temporary directory (but not the cause of your vector problem). I always
> compile GDAL, GEOS, etc. from source, and do not see any issues with
> spearfish vector files converted to GRASS 7 (but had to enable sqlite in
> GRASS to avoid problems). I am always sceptical about Linux binary builds,
> and cannot replicate this issue (but which may mean that rgdal is broken in
> some odd way if it was also installed using binary dependencies). Can you
> run:
>
> wget http://cran.r-project.org/src/contrib/rgdal_0.7-8.tar.gz
> R CMD check rgdal_0.7-8.tar.gz
>
> to test the package on your platform?
It seemed OK, ( http://pastebin.com/gykPF4EX ), the only problems were
with the manual:
* checking PDF version of manual ... WARNING
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
* checking PDF version of manual without hyperrefs or index ... ERROR
Re-running with no redirection of stdout/stderr.
Hmm ... looks like a package
Error in texi2dvi("Rd2.tex", pdf = (out_ext == "pdf"), quiet = FALSE, :
pdflatex is not available
Error in running tools::texi2dvi
You may want to clean up by 'rm -rf /tmp/RtmpqvwW8e/Rd2pdf69b337d4f332'
>
> If you check out rspatial, you will be able to do R CMD check on spgrass6
> too in its current development revision:
>
> svn checkout svn://scm.r-forge.r-project.org/svnroot/rspatial/
> cd rspatial/pkg
> (start GRASS7 in spearfish)
> R CMD check spgrass6
full output at: http://pastebin.com/n6a7SGXh
Everything was OK until:
* checking examples ... ERROR
Running examples in ‘spgrass6-Ex.R’ failed
The error most likely occurred in:
> ### Name: readRAST6
I did not (yet) move anything or install as packages in R, just ran R
CMD where the downloaded file was at.
Thanks for your help so far, any suggestion for what to try next?
Eric
>
> Roger
>
>
>
>
> On Tue, 6 Mar 2012, Eric Momsen wrote:
>
>> Thank you for the quick response! I've added follow up after the points
>> below.
>>
>> On Tue, Mar 6, 2012 at 2:25 PM, Roger Bivand <Roger.Bivand at nhh.no> wrote:
>>>
>>> On Tue, 6 Mar 2012, Eric Momsen wrote:
>>>
>>>> Hello!
>>>>
>>>> I have been trying to get spgrass6 working in a Debian environment,
>>>> and have started from scratch with both GRASS 6.4.3 and GRASS 7.0. I
>>>> previously had the same errors in "old" installations of both 6 and 7,
>>>> after following the advice in the listserve archive I am half way
>>>> there. Since the behavior had been the same for both, I was suprised
>>>> it didn't resolve the issue completely! Any suggestions would be
>>>> appreciated.
>>>>
>>>> I hope it is OK to include all 3 questions here, since they all relate
>>>> to spgrass6. Here is a listing of sessionInfo and various Debian
>>>> package versions: http://pastebin.com/68XST1vK
>>>>
>>>>
>>>> My installation of spgrass6 is working now with GRASS 6.4.3, I can
>>>> read and write vectors and rasters.
>>>>
>>>> 1. I am getting one warning message, is this OK, or am I missing some
>>>> dependency still?
>>>>
>>>>> spear <- readRAST6(c("elevation.dem", "geology"), cat = c(FALSE, TRUE))
>>>>
>>>>
>>>> Warning message:
>>>> statistics not supported by this driver
>>>>
>>>> The program does continue to successfully import the data.
>>>
>>>
>>>
>>> Not a problem - an artefact of calling GDALinfo() on the temporary file.
>>
>>
>> Great. After all the real errors I've caused, it is nice to have
>> reached a point where I can ignore the warnings.
>>
>>>
>>>
>>>>
>>>>
>>>> Moving onto GRASS 7:
>>>>
>>>> 2. readRAST6 gives an error in grass70, output as follows:
>>>>
>>>>> spear <- readRAST6(c("geology", "elevation.dem"), cat=c(TRUE, FALSE),
>>>>
>>>>
>>>> + useGDAL=FALSE)
>>>
>>>
>>>
>>> r.info is called twice, once with -t, once with -r. In GRASS 7, all of
>>> have
>>> been collected in -g, which simply breaks compatibility - arguably, -t
>>> could
>>> have been left in place. When I find time to build a GRASS 7, I'll try to
>>> accommodate the broken flag. -r is retained, so it is only on line 48 in
>>> R/bin_link.R that any change is required.
>>>
>>
>> I changed the flag as suggested and readRAST6 now works for my
>> installation.
>>
>>>> Command: r.info
>>>> Description: Outputs basic information about a raster map.
>>>> Keywords: raster, metadata, history
>>>> Parameters:
>>>> name: map, type: string, required: yes, multiple: no
>>>> keydesc: name, keydesc_count: 1
>>>> [Name of raster map]
>>>> Flags:
>>>> name: g [Print raster array information only] {FALSE}
>>>> name: r [Print range only] {FALSE}
>>>> name: e [Print extended metadata information only] {FALSE}
>>>> name: h [Print raster history instead of info] {FALSE}
>>>> name: verbose [Verbose module output] {FALSE}
>>>> name: quiet [Quiet module output] {FALSE}
>>>> Error in doGRASS(cmd, flags = flags, ..., parameters = parameters,
>>>> echoCmd = echoCmd) :
>>>> Invalid flag value: t
>>>>
>>>> I checked that r.info works:
>>>>>
>>>>>
>>>>> system("r.info geology")
>>>>
>>>>
>>>>
>>>>
>>>> +----------------------------------------------------------------------------+
>>>> | Layer: geology Date: Mon May 4 10:00:14
>>>> 1987
>>>> : |
>>>> | Mapset: PERMANENT Login of Creator: grass
>>>> |
>>>> | Location: spearfish70
>>>> .
>>>> .
>>>> .
>>>>
>>>>
>>>> I see that -t is in the GRASS6.4.3 version of r.info, but not in the
>>>> GRASS7.0 version of r.info.
>>>>
>>>> I'm not sure what to do next here.
>>>>
>>>>
>>>> 3. readVECT6 causes R to exit.
>>>>
>>>>> bugsDF <- readVECT6("bugsites")
>>>>
>>>>
>>>> GRASS 7.0.svn (spearfish70):~ >
>>>>
>>>> I went back to check that the bugsites map was available:
>>>>>
>>>>>
>>>>> system("v.info bugsites")
>>>>
>>>>
>>>>
>>>>
>>>> +----------------------------------------------------------------------------+
>>>> | Name: bugsites
>>>> |
>>>> | Mapset: PERMANENT
>>>> |
>>>> | Location: spearfish70
>>>> |
>>>> | Database: /home/shared/research/GRASSDATA
>>>> |
>>>> .
>>>> .
>>>> .
>>>>
>>>> And then tried the debug tool to see where things went wrong...
>>>>
>>>> complete output at: http://pastebin.com/dJFsRSBC with the final lines
>>>> as:
>>>>
>>>> debug: res <- readOGR(dsn, layer = as.character(layer), verbose =
>>>> !ignore.stderr,
>>>> pointDropZ = pointDropZ)
>>>> Browse[2]>
>>>
>>>
>>>
>>> I'll look at this later, looks like a broken shapefile.
>>
>>
>> I wasn't sure if you meant my local shapefile was broken? So I
>> checked the function on my real data as well as a fresh download of
>> spearfish. Neither worked. I also tried it in a spearfish60
>> location.
>>
>> My spearfish70 is simply spearfish60 after `v.build all` has been run.
>>
>>>
>>> Roger
>>>
>>>> GRASS 7.0.svn (spearfish70):~ >
>>>>
>>>>
>>>> I found a 2009 post regarding readOGR / readVECT6 and some versioning
>>>> issues: https://stat.ethz.ch/pipermail/r-sig-geo/2009-April/005553.html
>>>> but I installed both rgdal and spgrass6 inside of R as packages. So
>>>> I'm not sure if this older post is still applicable, especially since
>>>> it works in GRASS 6.4.3. Any suggestions for what to try next?
>>>>
>>>>
>>>> Thanks in advance for any help provided.
>>>>
>>>> Eric
>>>> _______________________________________________
>>>> grass-stats mailing list
>>>> grass-stats at lists.osgeo.org
>>>> http://lists.osgeo.org/mailman/listinfo/grass-stats
>>>>
>>>
>>> --
>>> Roger Bivand
>>> Department of Economics, NHH Norwegian School of Economics,
>>> 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
>>>
>>
>
> --
> Roger Bivand
> Department of Economics, NHH Norwegian School of Economics,
> 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
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