I remember JGR installation on SuSE 10.3 as a nightmare that eventually I
overcame with JGR designers' help.
I have installed SuSE 11.1, latest R version and am trying to install JGR
again.
It is still a nightmare.
I have followed the guidelines on
http://jgr.markushelbig.org/JGR_on_Linux.html
I have made sure I have the so R libraries.
I have installed java-1.6.0-sun and its development environment. Following the
on-line guidelines for JGR installation,
the process fails on trying to install "rJava" ... please see all the
messages in the following.
I get the same error if I try to install "rJava" in advance of JGR.
Thank you very much,
Maura
As root:
linux-326k:/home/mauede # sudo R CMD javareconf
Java interpreter : /usr/bin/java
Java version : 1.6.0_0
Java home path : /usr/lib64/jvm/java-1.6.0-openjdk-1.6.0/jre
Java compiler : /usr/bin/javac
Java headers gen.: /usr/bin/javah
Java archive tool: /usr/bin/jar
Java library path:
$(JAVA_HOME)/lib/amd64/server:$(JAVA_HOME)/lib/amd64:$(JAVA_HOME)/../lib/amd64::/usr/java/packages/lib/amd64:/usr/lib64:/lib64:/lib:/usr/lib
JNI linker flags : -L$(JAVA_HOME)/lib/amd64/server -L$(JAVA_HOME)/lib/amd64
-L$(JAVA_HOME)/../lib/amd64 -L -L/usr/java/packages/lib/amd64 -L/usr/lib64
-L/lib64 -L/lib -L/usr/lib -ljvm
JNI cpp flags :
Updating Java configuration in /usr/lib64/R
Done.
linux-326k:/home/mauede # sudo R
> install.packages('JGR')
--- Please select a CRAN mirror for use in this session ---
CRAN mirror
Selection: 24
also installing the dependencies rJava, JavaGD, iplots
trying URL 'http://cran.stat.unipd.it/src/contrib/rJava_0.6-3.tar.gz'
Content type 'application/octet-stream' length 240527 bytes (234 Kb)
opened URL
==================================================
downloaded 234 Kb
trying URL 'http://cran.stat.unipd.it/src/contrib/JavaGD_0.5-2.tar.gz'
Content type 'application/octet-stream' length 87076 bytes (85 Kb)
opened URL
==================================================
downloaded 85 Kb
trying URL 'http://cran.stat.unipd.it/src/contrib/iplots_1.1-3.tar.gz'
Content type 'application/octet-stream' length 331100 bytes (323 Kb)
opened URL
==================================================
downloaded 323 Kb
trying URL 'http://cran.stat.unipd.it/src/contrib/JGR_1.6-7.tar.gz'
Content type 'application/octet-stream' length 506759 bytes (494 Kb)
opened URL
==================================================
downloaded 494 Kb
* Installing *source* package rJava ...
checking for gcc... gcc -std=gnu99
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=gnu99 accepts -g... yes
checking for gcc -std=gnu99 option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -std=gnu99 -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=gnu99 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/lib64/jvm/java-1.6.0-openjdk-1.6.0/jre/lib/amd64/server
-L/usr/lib64/jvm/java-1.6.0-openjdk-1.6.0/jre/lib/amd64
-L/usr/lib64/jvm/java-1.6.0-openjdk-1.6.0/jre/../lib/amd64 -L
-L/usr/java/packages/lib/amd64 -L/usr/lib64 -L/lib64 -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 rJava
* Removing /usr/lib64/R/library/rJava
* Installing *source* package JavaGD ...
checking for gcc... gcc -std=gnu99
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=gnu99 accepts -g... yes
checking for gcc -std=gnu99 option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -std=gnu99 -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
checking for stdlib.h... (cached) yes
checking for GNU libc compatible malloc... yes
checking return type of signal handlers... void
checking for memset... yes
checking for mkdir... yes
checking for rmdir... yes
checking for select... yes
checking for socket... yes
checking Java support in R... present:
interpreter : '/usr/bin/java'
cpp flags : ''
java libs : '-L/usr/lib64/jvm/java-1.6.0-openjdk-1.6.0/jre/lib/amd64/server
-L/usr/lib64/jvm/java-1.6.0-openjdk-1.6.0/jre/lib/amd64
-L/usr/lib64/jvm/java-1.6.0-openjdk-1.6.0/jre/../lib/amd64 -L
-L/usr/java/packages/lib/amd64 -L/usr/lib64 -L/lib64 -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 JavaGD
* Removing /usr/lib64/R/library/JavaGD
* Installing *source* package iplots ...
** R
** inst
** preparing package for lazy loading
Error : package 'rJava' required by 'iplots' could not be found
ERROR: lazy loading failed for package iplots
* Removing /usr/lib64/R/library/iplots
* Installing *source* package JGR ...
** R
** inst
** preparing package for lazy loading
Error : package 'rJava' required by 'JGR' could not be found
ERROR: lazy loading failed for package JGR
* Removing /usr/lib64/R/library/JGR
The downloaded packages are in
/tmp/Rtmpf6sSE6/downloaded_packages
Updating HTML index of packages in '.Library'
Warning messages:
1: In install.packages("JGR") :
installation of package 'rJava' had non-zero exit status
2: In install.packages("JGR") :
installation of package 'JavaGD' had non-zero exit status
3: In install.packages("JGR") :
installation of package 'iplots' had non-zero exit status
4: In install.packages("JGR") :
installation of package 'JGR' had non-zero exit status
>
tutti i telefonini TIM!
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