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]]$repository, ... :
installation of package 'ncdf' had non-zero exit status
message error:
Fatal error: I cannot find the directory that holds the netcdf include
file netcdf.h!
solved:
apt-get install libnetcdf-dev
===============================================================================================10:
In install.packages(pkgs, repos = views[[i]]$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
===============================================================================================11:
In install.packages(pkgs, repos = views[[i]]$repository, ... :
installation of package 'snowFT' had non-zero exit status
solved:
install.packages("snowFT",dependencies=TRUE)
===============================================================================================12:
In install.packages(pkgs, repos = views[[i]]$repository, ... :
installation of package 'shapes' had non-zero exit status
solved:
install.packages("shapes",dependencies=TRUE)
===============================================================================================13:
In install.packages(pkgs, repos = views[[i]]$repository, ... :
installation of package 'compositions' had non-zero exit status
solved:
install.packages("compositions",dependencies=TRUE)
===============================================================================================14:
In install.packages(pkgs, repos = views[[i]]$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
===============================================================================================15:
In install.packages(pkgs, repos = views[[i]]$repository, ... :
installation of package 'FieldSim' had non-zero exit status
solved:
R CMD INSTALL FieldSim_3.1.tar.gz
===============================================================================================16:
In install.packages(pkgs, repos = views[[i]]$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
===============================================================================================17:
In install.packages(pkgs, repos = views[[i]]$repository, ... :
installation of package 'ramps' had non-zero exit status
message error:
dependencies:
spam (spam need fields)
fields
solved:
by installing spam and fields
===============================================================================================18:
In install.packages(pkgs, repos = views[[i]]$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
===============================================================================================19:
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