[GRASS-user] Re: Installing spgrass6 package - Errors and warnings

Sun Sep 12 06:16:46 EDT 2010

Please see comments inline below. Please also consider the list for GRASS and
statistics, which specifically handles the GRASS-R interface. Also always
explain how you install software - assuming that software is installed
binary is not safe, as it leads (especially for Ubuntu/Debian users) to
dependency hell - dependencies undeclared by packages that intermediate
users may not know that they need when using interfaces between systems.
Installing everything from source always exposes missing dependencies, but
installing binaries doesn't show them, because the installed software is not
expected to interface with other software.

Chethan S. wrote:
> 
> Hello everybody!
> 
> I am using GRASS 6.4.0 RC6 in ubuntu 10.04. I installed R version 2.11.1
> (2010-05-31) just today. As I need GRASS and R interface for my work, I
> went
> ahead as per instructions in
> http://www.osgeo.org/files/journal/final_pdfs/OSGeo_vol1_GRASS-R.pdf.
> 
> Initially when I started R from within GRASS and tried the command I got
> the
> following errors:
>> install.packages("spgrass6", dependencies = TRUE)
> Warning in install.packages("spgrass6", dependencies = TRUE) :
>   argument 'lib' is missing: using '/usr/local/lib/R/site-library'
> Warning in install.packages("spgrass6", dependencies = TRUE) :
>   'lib = "/usr/local/lib/R/site-library"' is not writable
> Would you like to create a personal library
> '~/R/i486-pc-linux-gnu-library/2.11'
> to install packages into?  (y/n) n
> Error in install.packages("spgrass6", dependencies = TRUE) :
>   unable to install packages
>> q()
> 
> <COMMENT> You need to understand how your binary install of R handles the
> installation of additional contributed packages. Your choice of "no" to
> the question:
> 
> Would you like to create a personal library?
> 
> is the wrong answer. You should NEVER run anything sudo, ever, unless
> doing system work - adding contributed packages is NOT system work. Read
> the explanation that comes with your R distribution about personal
> libraries, and allow one to be created. I'm not familiar with this
> distribution, so I don't know if it adds the path to any created personal
> library to the library search path, but if things work from then on, we
> can assume that they do work.
> 
> Try install.packages("XML") first, and get that working - you have missing
> dependencies that you need to provide. Then install.packages("rgdal")
> using Micha's good advice to add at least the Ubuntu development package -
> probably also for proj, not just libgdal, by the way, there are some
> comments in the rgdal README file (under inst/ in the source package).
> From there, spgrass6 will install.
> 
> </COMMENT>
> 
> Later I started R using "sudo R" and then the following errors and
> warnings
> occurred.
> 
>> install.packages("spgrass6", dependencies = TRUE)
> Warning in install.packages("spgrass6", dependencies = TRUE) :
>   argument 'lib' is missing: using '/usr/local/lib/R/site-library'
> --- Please select a CRAN mirror for use in this session ---
> Loading Tcl/Tk interface ... done
> also installing the dependencies ‘rgdal’, ‘XML’
> 
> trying URL 'http://mirror.kapook.com/cran/src/contrib/rgdal_0.6-28.tar.gz'
> Content type 'application/x-gzip' length 1416605 bytes (1.4 Mb)
> opened URL
> ==================================================
> downloaded 1.4 Mb
> 
> trying URL 'http://mirror.kapook.com/cran/src/contrib/XML_3.1-1.tar.gz'
> Content type 'application/x-gzip' length 779143 bytes (760 Kb)
> opened URL
> ==================================================
> downloaded 760 Kb
> 
> trying URL
> 'http://mirror.kapook.com/cran/src/contrib/spgrass6_0.6-20.tar.gz
> '
> Content type 'application/x-gzip' length 334459 bytes (326 Kb)
> opened URL
> ==================================================
> downloaded 326 Kb
> 
> * installing *source* package ‘rgdal’ ...
> gdal-config: gdal-config
> ./configure: line 1311: gdal-config: command not found
> Error: gdal-config not found
> The gdal-config script distributed with GDAL could not be found.
> If you have not installed the GDAL libraries, you can
> download the source from  http://www.gdal.org/
> If you have installed the GDAL libraries, then make sure that
> gdal-config is in your path. Try typing gdal-config at a
> shell prompt and see if it runs. If not, use:
>  --configure-args='--with-gdal-config=/usr/local/bin/gdal-config' echo
> with
> appropriate values for your installation.
> 
> ERROR: configuration failed for package ‘rgdal’
> * removing ‘/usr/local/lib/R/site-library/rgdal’
> * installing *source* package ‘XML’ ...
> 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 ISO C89... none needed
> checking how to run the C preprocessor... gcc -E
> checking for sed... /bin/sed
> checking for pkg-config... /usr/bin/pkg-config
> checking for xml2-config... no
> Cannot find xml2-config
> ERROR: configuration failed for package ‘XML’
> * removing ‘/usr/local/lib/R/site-library/XML’
> ERROR: dependencies ‘rgdal’, ‘XML’ are not available for package
> ‘spgrass6’
> * removing ‘/usr/local/lib/R/site-library/spgrass6’
> 
> The downloaded packages are in
>     ‘/tmp/RtmpP2fUan/downloaded_packages’
> Warning messages:
> 1: In install.packages("spgrass6", dependencies = TRUE) :
>   installation of package 'rgdal' had non-zero exit status
> 2: In install.packages("spgrass6", dependencies = TRUE) :
>   installation of package 'XML' had non-zero exit status
> 3: In install.packages("spgrass6", dependencies = TRUE) :
>   installation of package 'spgrass6' had non-zero exit status
> 
> The result is I am not able to use spgrass.
>> library(spgrass6)
> Error in library(spgrass6) : there is no package called 'spgrass6'
> 
> As an intermediate level user in terms of commands and also regarding R
> and
> GRASS packages I am not able to decide what went wrong. Can you please
> help
> me out.
> 
> Regards,
> 
> Chethan S.
> 
> _______________________________________________
> grass-user mailing list
> grass-user at lists.osgeo.org
> http://lists.osgeo.org/mailman/listinfo/grass-user
> 
> 

-----
Roger Bivand
Economic Geography Section
Department of Economics
Norwegian School of Economics and Business Administration
Helleveien 30
N-5045 Bergen, Norway

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