[R] sharing experience - installing R Spatial Views

From: Hendro Wibowo <hendrohwibowo_at_gmail.com>
Date: Sat, 12 Jun 2010 07:37:54 +0700


Hi Guys,

I would like to share my experience when installing the Spatial views packages for R. I could not install 32 packages which are parts of the Spatial views, and I use google-search and search to solve ALL those problems for about 2 days. I hope maybe somebody would benefit from my experience.

I admitted that I do not have excellent programming skills at all. So, perhaps some of steps I did are not necessary to solve the problem at hands. But it works and I am happy.

I was lucky if the problem I have was already solved by someone else, or if the problem is just a matter of installing another R packages that depends on other packages. Sometimes it has something to do not with R package but with a package that has to be installed in my operating system (in my case LinuxMint 8, based on ubuntu karmic). so I just guessed the nature of the problem, and try to solve it via already solved similar problem.

i found many problems solved direct or indirect from Nabble - OSGeo FOSS4G websites. of course many problem are also solved from other website other than Nabble, but I forgot their address, as I google search again and again for all those problems. But I do appreciate everyone who post their problems, solved or not solved, so I can solved my own problem, either directly or indirectly (by using the idea and guessing from already solved problem).

I found that we need to change from gcc version 4 to 3, in order to some packages to be installed (I forgot which one). The script i used to achieve that, taken from the internet, is placed at the bottom of this message.

and finally below here are lists of problems and solutions of installing Spatial Views.



install-R views Spatial in linuxmint 8 (ubuntu karmic based)

requirement: update for latest R (> 2.11.1)

# install package ctv
# install.packages("ctv",dependencies=TRUE)
# problems:

package: XML
error: cannot find xml2-config
solved: apt-get install libxml2-dev

# install views Spatial
# install.views("Spatial",dependencies=TRUE)
# problems:

The downloaded packages are in
	‘/tmp/Rtmpb0gy50/downloaded_packages’

There were 32 warnings (use warnings() to see them)  > warnings()
Warning messages:
  1. In install.packages(pkgs, repos = views[[i]]$repository, ... : installation of package 'RODBC' had non-zero exit status

message error:
configure error: "ODBC headers sql.h and sqlext.h not found" solved: apt-get install unixodbc unixodbc-dev



2: In install.packages(pkgs, repos = views[[i]]$repository, ... :

   installation of package 'Rmpi' had non-zero exit status

message error:
configure error: "Cannot find mpi.h header file" solved:
- first add debian source repository -> copy paste existing main restricted, add -src

	deb http://...... karmic main restricted.....
	deb http://...... karmic-updates main restricted.....
become
	deb-src http://...... karmic main restricted.....
	deb-src http://...... karmic-updates main restricted.....
- apt-get update

- apt-get build-dep r-cran-rmpi
- R CMD INSTALL Rmpi --configure-args="--with-mpi=/usr/lib/openmpi"

3: In install.packages(pkgs, repos = views[[i]]$repository, ... :

   installation of package 'rpvm' had non-zero exit status

message error:
Try to guess if pvm is installed somewhere ...   Cannot find pvm.
  If pvm is installed, set PVM_ROOT to where pvm is.   Otherwise, please install pvm first.
ERROR: configuration failed for package ‘rpvm’

solved:
- apt-get install pvm pvm-dev



4: In install.packages(pkgs, repos = views[[i]]$repository, ... :

   installation of package 'rsprng' had non-zero exit status

message error:
Cannot find sprng 2.0 header file.

solved:
- install libsprng2-dev



5: In install.packages(pkgs, repos = views[[i]]$repository, ... :

   installation of package 'tkrplot' had non-zero exit status

message error:

tcltkimg.c:2:16: tk.h: No such file or directory
............
tcltkimg.c:469: error: expected declaration specifiers before ‘Tcl_Interp’
tcltkimg.c:468: warning: type of ‘interp’ defaults to ‘int’
make: *** [tcltkimg.o] Error 1

solved:
apt-get install tk8.5-dev



6: In install.packages(pkgs, repos = views[[i]]$repository, ... :

   installation of package 'rJava' had non-zero exit status

problems: no java compiler javac and javah check with R CMD java reconf

hendro-linux R-packages # R CMD javareconf

Java interpreter : /usr/bin/java
Java version     : 1.6.0_20
Java home path   : /usr/lib/jvm/java-6-sun-1.6.0.20/jre
Java compiler    : not present
Java headers gen.:
Java archive tool:
Java library path: 

$(JAVA_HOME)/lib/i386/client:$(JAVA_HOME)/lib/i386:$(JAVA_HOME)/../lib/i386::/usr/java/packages/lib/i386:/lib:/usr/lib JNI linker flags : -L$(JAVA_HOME)/lib/i386/client -L$(JAVA_HOME)/lib/i386 -L$(JAVA_HOME)/../lib/i386

solved:
apt-get install sun-java6-jdk

check again with R CMD java reconf

hendro-linux R-packages # R CMD javareconf

Java interpreter : /usr/bin/java
Java version     : 1.6.0_20
Java home path   : /usr/lib/jvm/java-6-sun-1.6.0.20/jre
Java compiler    : /usr/bin/javac
Java headers gen.: /usr/bin/javah
Java archive tool: /usr/bin/jar
Java library path: 

$(JAVA_HOME)/lib/i386/client:$(JAVA_HOME)/lib/i386:$(JAVA_HOME)/../lib/i386::/usr/java/packages/lib/i386:/lib:/usr/lib JNI linker flags : -L$(JAVA_HOME)/lib/i386/client -L$(JAVA_HOME)/lib/i386 -L$(JAVA_HOME)/../lib/i386 -L -L/usr/java/packages/lib/i386 -L/lib -L/usr/lib -ljvm JNI cpp flags : -I$(JAVA_HOME)/../include -I$(JAVA_HOME)/../include/linux

7: In install.packages(pkgs, repos = views[[i]]$repository, ... :

   installation of package 'rgl' had non-zero exit status

message error:
configure: error: missing required header GL/gl.h

solved:
apt-get install libglu1-mesa-dev



8: In install.packages(pkgs, repos = views[[i]]$repository, ... :

   installation of package 'fields' had non-zero exit status

message error:
ERROR: dependencies ‘spam’ are not available for package ‘fields’

solved:
cd /usr/lib
ln -s libgfortran.so.3 libgfortran.so
install.packages("fields",dependencies=TRUE)



9: In install.packages(pkgs, repos = views[[i]]$repository, ... :

   installation of package 'ncdf' had non-zero exit status

message error:
Fatal error: I cannot find the directory that holds the netcdf include file netcdf.h!

solved:
apt-get install libnetcdf-dev


  1. In install.packages(pkgs, repos = views[[i]]$repository, ... : installation of package 'spatialsegregation' had non-zero exit status

message error:
make: *** [tcltkimg.o] Error 1
ERROR: compilation failed for package ‘tkrplot’

.
.
.

/usr/bin/ld: cannot find -lgfortran

solved:
package ‘tkrplot’ installed


  1. In install.packages(pkgs, repos = views[[i]]$repository, ... : installation of package 'snowFT' had non-zero exit status

solved:
install.packages("snowFT",dependencies=TRUE)


  1. In install.packages(pkgs, repos = views[[i]]$repository, ... : installation of package 'shapes' had non-zero exit status

solved:
install.packages("shapes",dependencies=TRUE)


  1. In install.packages(pkgs, repos = views[[i]]$repository, ... : installation of package 'compositions' had non-zero exit status

solved:
install.packages("compositions",dependencies=TRUE)


  1. In install.packages(pkgs, repos = views[[i]]$repository, ... : installation of package 'DSpat' had non-zero exit status

message error:
ERROR: dependencies ‘spatstat’ are not available for package ‘DSpat’

solved:
spatstat need tkrplot
package ‘tkrplot’ installed


  1. In install.packages(pkgs, repos = views[[i]]$repository, ... : installation of package 'FieldSim' had non-zero exit status

solved:
R CMD INSTALL FieldSim_3.1.tar.gz


  1. In install.packages(pkgs, repos = views[[i]]$repository, ... : installation of package 'MBA' had non-zero exit status

message error:
configure: error: Boost header files not found. Under linux/Unix try R CMD INSTALL MBA_0.0-0.tar.gz
--configure-args='--with-boost-include=INCLUDE_PATH' ERROR: configuration failed for package ‘MBA’

solved:
apt-get install libboost-dev


  1. In install.packages(pkgs, repos = views[[i]]$repository, ... : installation of package 'ramps' had non-zero exit status

message error:

dependencies:
spam (spam need fields)
fields

solved:
by installing spam and fields


  1. In install.packages(pkgs, repos = views[[i]]$repository, ... : installation of package 'rgdal' had non-zero exit status

message error:
./configure: line 1311: gdal-config: command not found

solved:
The program 'gdal-config' is currently not installed apt-get install libgdal1-dev


  1. In install.packages(pkgs, repos = views[[i]]$repository, ... : installation of package 'latentnet' had non-zero exit status

solved:
as the above problems are solved (not sure which one), this one is solved automatically



20: In install.packages(pkgs, repos = views[[i]]$repository, ... :

   installation of package 'VIM' had non-zero exit status

message error:
ERROR: dependencies ‘tkrplot’ are not available for package ‘VIM’



21: In install.packages(pkgs, repos = views[[i]]$repository, ... :

   installation of package 'CircSpatial' had non-zero exit status

solved:
as the above problems are solved (not sure which one), this one is solved automatically



22: In install.packages(pkgs, repos = views[[i]]$repository, ... :

   installation of package 'clustTool' had non-zero exit status

solved:
as the above problems are solved (not sure which one), this one is solved automatically



23: In install.packages(pkgs, repos = views[[i]]$repository, ... :

   installation of package 'cshapes' had non-zero exit status

solved:
as the above problems are solved (not sure which one), this one is solved automatically



24: In install.packages(pkgs, repos = views[[i]]$repository, ... :

   installation of package 'ecespa' had non-zero exit status

solved:
as the above problems are solved (not sure which one), this one is solved automatically



25: In install.packages(pkgs, repos = views[[i]]$repository, ... :

   installation of package 'ModelMap' had non-zero exit status

solved:
as the above problems are solved (not sure which one), this one is solved automatically



26: In install.packages(pkgs, repos = views[[i]]$repository, ... :

   installation of package 'RSurvey' had non-zero exit status

solved:
as the above problems are solved (not sure which one), this one is solved automatically



27: In install.packages(pkgs, repos = views[[i]]$repository, ... :

   installation of package 'spgrass6' had non-zero exit status

solved:
as the above problems are solved (not sure which one), this one is solved automatically



28: In install.packages(pkgs, repos = views[[i]]$repository, ... :

   installation of package 'statnet' had non-zero exit status

solved:
as the above problems are solved (not sure which one), this one is solved automatically



29: In install.packages(pkgs, repos = views[[i]]$repository, ... :

   installation of package 'GeoXp' had non-zero exit status

solved:
as the above problems are solved (not sure which one, definitely one of them is 'spam' package), this one is solved automatically



30: In install.packages(pkgs, repos = views[[i]]$repository, ... :

   installation of package 'intamap' had non-zero exit status

solved:
as the above problems are solved (not sure which one), this one is solved automatically



31: In install.packages(pkgs, repos = views[[i]]$repository, ... :

   installation of package 'spcosa' had non-zero exit status

solved:
as the above problems are solved (not sure which one), this one is solved automatically



32: In install.packages(pkgs, repos = views[[i]]$repository, ... :

   installation of package 'psgp' had non-zero exit status

message error:
In file included from optimisation/SCGModelTrainer.h:38,

                  from astonGeostats.h:16,
                  from astonGeostats.cpp:1:
optimisation/ModelTrainer.h:43: error: `eps' was not declared in this scope optimisation/ModelTrainer.h:47: error: `itpp' is not a namespace-name
..
..
..

make: *** [astonGeostats.o] Error 1
ERROR: compilation failed for package ‘psgp’

solved:
apt-get install libblas-dev libblas3gf liblapack-dev liblapack3gf libfftw3-3 libfftw3-dev
apt-get install libitpp-dev libitpp6gf



gcc34 script:
#/bin/sh
mkdir DELEME &&
cd DELEME &&
wget
http://ge.archive.ubuntu.com/ubuntu/pool/universe/g/gcc-3.4/libstdc++6-dev_3.4.6-6ubuntu3_i386.deb &&
wget
http://ge.archive.ubuntu.com/ubuntu/pool/universe/g/gcc-3.4/cpp-3.4_3.4.6-6ubuntu3_i386.deb &&
wget
http://ge.archive.ubuntu.com/ubuntu/pool/universe/g/gcc-3.4/gcc-3.4_3.4.6-6ubuntu3_i386.deb &&
wget
http://ge.archive.ubuntu.com/ubuntu/pool/universe/g/gcc-3.4/gcc-3.4-base_3.4.6-6ubuntu3_i386.deb &&
wget
http://ge.archive.ubuntu.com/ubuntu/pool/universe/g/gcc-3.4/g++-3.4_3.4.6-6ubuntu3_i386.deb &&
sudo dpkg -i *.deb &&
cd .. &&
rm -rf DELEME

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