lmramba at gmail.com
2009-Oct-10 03:40 UTC
[Rd] rJava downloads but cannot load, when I run R as root (PR#13994)
> library(rJava)Error in library(rJava) : there is no package called 'rJava'> install.packages("rJava")Warning in install.packages("rJava") : 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 trying URL 'http://cran.uk.r-project.org/src/contrib/rJava_0.7-0.tar.gz' Content type 'application/x-gzip' length 249486 bytes (243 Kb) opened URL =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D downloaded 243 Kb * Installing *source* package =91rJava=92 ... checking for gcc... gcc -std=3Dgnu99 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 -std=3Dgnu99 accepts -g... yes checking for gcc -std=3Dgnu99 option to accept ISO C89... none needed checking how to run the C preprocessor... gcc -std=3Dgnu99 -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... yes checking for sys/wait.h that is POSIX.1 compatible... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for string.h... (cached) yes checking sys/time.h usability... yes checking sys/time.h presence... yes checking for sys/time.h... yes checking for unistd.h... (cached) yes checking for an ANSI C-conforming const... yes checking whether time.h and sys/time.h may both be included... yes configure: checking whether gcc -std=3Dgnu99 supports static inline... yes checking Java support in R... present: interpreter : '/usr/bin/java' archiver : '/usr/bin/jar' compiler : '/usr/bin/javac' header prep.: '/usr/bin/javah' cpp flags : '' java libs : '-L/usr/lib/jvm/java-6-openjdk/jre/lib/i386/server -L/usr/lib/jvm/java-6-openjdk/jre/lib/i386 -L/usr/lib/jvm/java-6-openjdk/jre/../lib/i386 -L -L/usr/java/packages/lib/i386 -L/lib -L/usr/lib -ljvm' configure: error: One or more Java configuration variables are not set. Make sure R is configured with full Java support (including JDK). Run R CMD javareconf as root to add Java support to R. If you don't have root privileges, run R CMD javareconf -e to set all Java-related variables and then install rJava. ERROR: configuration failed for package =91rJava=92 * Removing =91/usr/local/lib/R/site-library/rJava=92 The downloaded packages are in =91/tmp/RtmpOjM9hY/downloaded_packages=92 Warning message: In install.packages("rJava") : installation of package 'rJava' had non-zero exit status>I went ahead and did this: root at lmramba-laptop:/home/lmramba# R CMD javareconf Java interpreter : /usr/bin/java Java version : 1.6.0_0 Java home path : /usr/lib/jvm/java-6-openjdk/jre Java compiler : /usr/bin/javac Java headers gen.: /usr/bin/javah Java archive tool: /usr/bin/jar Java library path: $(JAVA_HOME)/lib/i386/server:$(JAVA_HOME)/lib/i386:$(JAVA_HOME)/../lib/i386::/usr/java/packages/lib/i386:/lib:/usr/lib JNI linker flags : -L$(JAVA_HOME)/lib/i386/server -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 : Updating Java configuration in /etc/R Done. But still installing rJava fails Plz help Regards, Lazarus [[alternative HTML version deleted]]
Dirk Eddelbuettel
2009-Oct-10 13:49 UTC
[Rd] rJava downloads but cannot load, when I run R as root (PR#13994)
On 10 October 2009 at 05:40, lmramba at gmail.com wrote:
| > library(rJava)
| Error in library(rJava) : there is no package called 'rJava'
| > install.packages("rJava")
| Warning in install.packages("rJava") :
| 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
| trying URL
'http://cran.uk.r-project.org/src/contrib/rJava_0.7-0.tar.gz'
| Content type 'application/x-gzip' length 249486 bytes (243 Kb)
| opened URL
| =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D|
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
| downloaded 243 Kb
|
| * Installing *source* package =91rJava=92 ...
| checking for gcc... gcc -std=3Dgnu99
| checking for C compiler default output file name... a.out
[...]
| configure: checking whether gcc -std=3Dgnu99 supports static inline...
| yes
| checking Java support in R... present:
| interpreter : '/usr/bin/java'
| archiver : '/usr/bin/jar'
| compiler : '/usr/bin/javac'
| header prep.: '/usr/bin/javah'
| cpp flags : ''
| java libs : '-L/usr/lib/jvm/java-6-openjdk/jre/lib/i386/server
| -L/usr/lib/jvm/java-6-openjdk/jre/lib/i386
| -L/usr/lib/jvm/java-6-openjdk/jre/../lib/i386 -L
| -L/usr/java/packages/lib/i386 -L/lib -L/usr/lib -ljvm'
| configure: error: One or more Java configuration variables are not set.
| Make sure R is configured with full Java support (including JDK). Run
| R CMD javareconf
| as root to add Java support to R.
R tells you your Java setup is not right. This *is* difficult, which is why I
have offered to maintain and provide the rJava in Debian / Ubuntu as
r-cran-rjava.
As demonstrated to you two emails ago, it also works. I would use that.
Otherwise, fix your Java setup first as R told you to here.
|
| If you don't have root privileges, run
| R CMD javareconf -e
| to set all Java-related variables and then install rJava.
|
| ERROR: configuration failed for package =91rJava=92
| * Removing =91/usr/local/lib/R/site-library/rJava=92
|
| The downloaded packages are in
| =91/tmp/RtmpOjM9hY/downloaded_packages=92
| Warning message:
| In install.packages("rJava") :
| installation of package 'rJava' had non-zero exit status
| >
|
|
| I went ahead and did this:
|
| root at lmramba-laptop:/home/lmramba# R CMD javareconf
| Java interpreter : /usr/bin/java
| Java version : 1.6.0_0
| Java home path : /usr/lib/jvm/java-6-openjdk/jre
| Java compiler : /usr/bin/javac
| Java headers gen.: /usr/bin/javah
| Java archive tool: /usr/bin/jar
| Java library path:
| $(JAVA_HOME)/lib/i386/server:$(JAVA_HOME)/lib/i386:$(JAVA_HOME)/../lib/i386|
::/usr/java/packages/lib/i386:/lib:/usr/lib
| JNI linker flags : -L$(JAVA_HOME)/lib/i386/server -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 :
| Updating Java configuration in /etc/R
| Done.
|
|
| But still installing rJava fails
As before: not a bug in R and you just created extra work for R Core to
maintain the bug database.
Dirk
| Plz help
|
| Regards,
| Lazarus
|
| [[alternative HTML version deleted]]
|
| ______________________________________________
| R-devel at r-project.org mailing list
| https://stat.ethz.ch/mailman/listinfo/r-devel
--
Three out of two people have difficulties with fractions.