[GRASS-stats] readRAST6 and readVECT6 errors with grass70

Eric Momsen eric.momsen at gmail.com
Thu Mar 15 12:46:24 EDT 2012 

Success!  Thank you!!

I tried last weekend to remove the gdal-grass plug in and to sort out
the gdal reinstallation, I found at least 3 versions of gdal from
debian repositories and from source on our server.  I was not able to
get gdal to compile with grass, so this week we set up a new virtual
machine to start over with a clean install and without multiple
versions of grass and gdal.

I installed gdal (w/o grass) then grass (w/ gdal).  I successfully
configuring gdal w/ grass.  But the make failed.  I went ahead with
testing in R/spgrass6 just to see what would happen... and it worked
for loading both vector and rasters from grass into R.  I don't have
the gdal-grass plugin OR gdal installed w/ grass support.  The check
of spgrass6 worked (except for the documentation.)

Should I be concerned that some other features won't work later on?

Since it is running, I don't know if it is worth the time to track
down the make error, or if a different place would be better to start
a new discussion.  But just in case, here is the configure results and
make error  http://pastebin.com/34kgysxz

It seems there is are many different (sometimes conflicting)
procedures for installing gdal/grass/spgrass6.  For example
http://trac.osgeo.org/gdal/wiki/GRASS recommends the plug in.

a.  Is my confusion due to my lack of experience with unix/open
source/Debian/etc
or
b.  Could/should I help update any of this documentation and/or post
the installation procedure I followed somewhere?

Regards,
Eric


On Sat, Mar 10, 2012 at 9:33 AM, Roger Bivand <Roger.Bivand at nhh.no> wrote:
> On Fri, 9 Mar 2012, Eric Momsen wrote:
>
>> 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 never use the plugin at all, I only install and uninstall to check that it
> works for GRASS 6. It causes a great deal of trouble for Debian/Ubuntu users
> installing binary GDAL. I advise against its use unless the user builds it
> for a specific GRASS version. The separate gdal-grass plugin is deprecated -
> one adds the path to the GRASS installation in ./configure to GDAL when
> installing from source. The problem is the round tour:
>
> install GDAL without the GRASS plugin,
> install GRASS linking against that GDAL,
> re-install GDAL with the path to GRASS given in ./configure.
>
> However, any GDAL or GRASS upgrade will break the plugin.
>
> Try to get rid of the plugin altogether, and try again, please. It may live
> under /usr/local somewhere.
>
> Roger
>
>
>>
>> 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
>>
>>
>
> --
> 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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