[GRASS-stats] readRAST6 and readVECT6 errors with grass70

Eric Momsen eric.momsen at gmail.com
Fri Mar 9 16:20:58 EST 2012 

Roger,

Thanks for your help and guidance.  I have tried to sort out the
dependencies and get the gdal-grass plugin to look at grass7.  I can't
get it to configure, details in line with your previous email.

This is the plugin I have downloaded:
http://download.osgeo.org/gdal/
"Get the GDAL/OGR-GRASS plugin - file: gdal-grass-1.4.3.tar.gz (or later)"

I've seen this closed ticket about the plugin not working with grass7
( http://trac.osgeo.org/gdal/ticket/2953  ) but it sounds like you
don't have any problems with it.  So I assume it should work.   I was
able to get this same plugin to configure against grass 6.4.

I am trying to configure it directly from what was downloaded, without
any patches.

Am I using the right plug in?
Are there some extra/different steps for grass7?
I assume I need this plugin to use spgrass6 (and v.krige from in
grass), or is there something else I should try?

It feels like I'm missing just one key point to get everything to work
beautifully!

Regards,
Eric


On Thu, Mar 8, 2012 at 1:39 PM, Roger Bivand <Roger.Bivand at nhh.no> wrote:
> Eric,
>
> The check of spgrass6 gets through readRAST6() with two rasters, which sets
> plugin=FALSE (twice, once not using GDAL, once using GDAL). It fails either
> in readRAST6(elevation.dem", plugin=TRUE, mapset="PERMANENT") if "GRASS"
> %in% gdalDrivers()$name or at writeRAST6(spear, "sqdemSP", zcol="sqdem").
>
> My prejudice is to suspect the plugin. Can you do:
>
> library(rgdal)
> "GRASS" %in% gdalDrivers()$name
> "GRASS" %in% ogrDrivers()$name
>

Both were TRUE.

> If they are TRUE, then the smoking gun is some dependency mixup in the GDAL
> GRASS plugin drivers, possibly pointing to a stale plugin, a stale GRASS
> version linked to GRASS, or something like that. Managing plugins across
> multiple versions of GRASS and/or GDAL is for very off-piste people who like
> excitement, I'm afraid.

The plug in wasn't even something I was aware of (The system admin had
installed grass 6.4, I was adding grass 7.0 later when the admin was
busy.)  My understanding is that for the GDAL-GRASS plug in he had
used a Debian package, and based on your comments now, it makes sense
that this is tied to GRASS 6.4 when it was first installed.

I didn't review the GDAL installation procedure, since it was already
installed.  !  Seems that was a mistake.  I downloaded the source code
for the plug in and attempted to compile it.  I had added grass to the
.conf , which didn't work, then tried LD_LIBRARY_PATH to go directly
to my new grass installation, and still it doesn't seem to find the
libraries:

root at gisdev:/opt/gdal-grass-1.4.3# ./configure
--with-gdal=/usr/local/bin/gdal-config
--with-grass=/usr/local/grass-7.0.svn
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ANSI C... none needed
checking for g++... g++
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking for ranlib... ranlib
checking for g++ -shared ... yes
user supplied gdal-config (/usr/local/bin/gdal-config)
using /usr/local/lib/gdalplugins as GDAL shared library autoload directory
checking for G_asprintf in -lgrass_gis... no
configure: error: --with-grass=/usr/local/grass-7.0.svn requested, but
libraries not found!  Perhaps you need to set LD_LIBRARY_PATH to
include /usr/local/grass-7.0.svn/lib?

double checking to answer the output's question:
root at gisdev:/opt/gdal-grass-1.4.3# $LD_LIBRARY_PATH
bash: /usr/local/grass-7.0.svn/lib: Is a directory

I tried this:
./configure --with-gdal=/usr/local/bin/gdal-config
--with-grass=/usr/local/grass-6.4.3svn/
and it configured successfully (without any changes to LD_LIBRARY_PATH
or the .conf files).

>
> The rgdal check suggests that the standard GDAL and OGR drivers work when
> GRASS is not in the picture.
>
> Roger
>
>
> On Thu, 8 Mar 2012, Eric Momsen wrote:
>
>> 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
>>
>>
>
> --
> 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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