No se puede instalar rJava 0.9 en Ubuntu 10.04

Uso R 2.13 del repositorio CRAN apt para Ubuntu 10.04, y estoy tratando de instalar Deducer, que requiere JGR/rJava, pero rJava se niega a compilar/instalar, quejándose de no pudiendo construir una aplicación JNI Intenté sudo R CMD javareconf como se sugirió, pero eso solo dio lugar a un error diferente sobre la configuración que se está desarmando. Encontré R: rJava package install failing, así que probé las sugerencias de instalar r-cran-rjava (pero eso es 0.8 y Deducer/JGR parecen insistir en instalar 0.9) y jugar con mi $JAVA_HOME, todo fue en vano. ¿Algunas ideas?No se puede instalar rJava 0.9 en Ubuntu 10.04

He aquí una transcripción más completa de lo sucedido:

$ sudo aptitude install r-cran-rjava 
... 
$ R 

R version 2.13.1 (2011-07-08) 
Copyright (C) 2011 The R Foundation for Statistical Computing 
ISBN 3-900051-07-0 
Platform: x86_64-pc-linux-gnu (64-bit) 

R is free software and comes with ABSOLUTELY NO WARRANTY. 
You are welcome to redistribute it under certain conditions. 
Type 'license()' or 'licence()' for distribution details. 

    Natural language support but running in an English locale 

R is a collaborative project with many contributors. 
Type 'contributors()' for more information and 
'citation()' on how to cite R or R packages in publications. 

Type 'demo()' for some demos, 'help()' for on-line help, or 
'help.start()' for an HTML browser interface to help. 
Type 'q()' to quit R. 

> install.packages(c('JGR','Deducer')) 
Installing package(s) into ‘/home/yang/R/x86_64-pc-linux-gnu-library/2.13’ 
(as ‘lib’ is unspecified) 
also installing the dependencies ‘rJava’, ‘JavaGD’, ‘iplots’ 

trying URL 'http://cran.cnr.Berkeley.edu/src/contrib/rJava_0.9-1.tar.gz' 
Content type 'application/x-gzip' length 527197 bytes (514 Kb) 
opened URL 
================================================== 
downloaded 514 Kb 

trying URL 'http://cran.cnr.Berkeley.edu/src/contrib/JavaGD_0.5-4.tar.gz' 
Content type 'application/x-gzip' length 102242 bytes (99 Kb) 
opened URL 
================================================== 
downloaded 99 Kb 

trying URL 'http://cran.cnr.Berkeley.edu/src/contrib/iplots_1.1-4.tar.gz' 
Content type 'application/x-gzip' length 330323 bytes (322 Kb) 
opened URL 
================================================== 
downloaded 322 Kb 

trying URL 'http://cran.cnr.Berkeley.edu/src/contrib/JGR_1.7-7.tar.gz' 
Content type 'application/x-gzip' length 536564 bytes (523 Kb) 
opened URL 
================================================== 
downloaded 523 Kb 

trying URL 'http://cran.cnr.Berkeley.edu/src/contrib/Deducer_0.4-4.tar.gz' 
Content type 'application/x-gzip' length 5325794 bytes (5.1 Mb) 
opened URL 
================================================== 
downloaded 5.1 Mb 

* installing *source* package ‘rJava’ ... 
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 
c hecking 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 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 supports static inline... 
yes 
checking whether setjmp.h is POSIX.1 compatible... yes 
checking whether sigsetjmp is declared... yes 
checking whether siglongjmp is declared... 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 : '-I/usr/lib/jvm/java-6-openjdk/jre/../include' 
java libs : '-L/usr/lib/jvm/java-6-openjdk/jre/lib/amd64/server -L/usr/lib/jvm/java-6-openjdk/jre/lib/amd64 -L/usr/lib/jvm/java-6-openjdk/jre/../lib/amd64 -L/usr/java/packages/lib/amd64 -L/usr/lib/jni -L/lib -L/usr/lib -ljvm' 
checking whether JNI programs can be compiled... configure: error: Cannot compile a simple JNI program. See config.log for details. 

Make sure you have Java Development Kit installed and correctly registered in R. 
If in doubt, re-run "R CMD javareconf" as root. 

ERROR: configuration failed for package ‘rJava’ 
* removing ‘/home/yang/R/x86_64-pc-linux-gnu-library/2.13/rJava’ 
* installing *source* package ‘JavaGD’ ... 
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 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 : '-I/usr/lib/jvm/java-6-openjdk/jre/../include' 
java libs : '-L/usr/lib/jvm/java-6-openjdk/jre/lib/amd64/server -L/usr/lib/jvm/java-6-openjdk/jre/lib/amd64 -L/usr/lib/jvm/java-6-openjdk/jre/../lib/amd64 -L/usr/java/packages/lib/amd64 -L/usr/lib/jni -L/lib -L/usr/lib -ljvm' 
checking whether JNI programs can be compiled... configure: error: Cannot compile a simple JNI program. See config.log for details. 
ERROR: configuration failed for package ‘JavaGD’ 
* removing ‘/home/yang/R/x86_64-pc-linux-gnu-library/2.13/JavaGD’ 
ERROR: dependency ‘rJava’ is not available for package ‘iplots’ 
* removing ‘/home/yang/R/x86_64-pc-linux-gnu-library/2.13/iplots’ 
ERROR: dependencies ‘rJava’, ‘JavaGD’, ‘iplots’ are not available for package ‘JGR’ 
* removing ‘/home/yang/R/x86_64-pc-linux-gnu-library/2.13/JGR’ 
ERROR: dependencies ‘rJava’, ‘JGR’ are not available for package ‘Deducer’ 
* removing ‘/home/yang/R/x86_64-pc-linux-gnu-library/2.13/Deducer’ 

The downloaded packages are in 
     ‘/tmp/RtmpCSITmm/downloaded_packages’ 
Warning messages: 
1: In install.packages(c("JGR", "Deducer")) : 
    installation of package 'rJava' had non-zero exit status 
2: In install.packages(c("JGR", "Deducer")) : 
    installation of package 'JavaGD' had non-zero exit status 
3: In install.packages(c("JGR", "Deducer")) : 
    installation of package 'iplots' had non-zero exit status 
4: In install.packages(c("JGR", "Deducer")) : 
    installation of package 'JGR' had non-zero exit status 
5: In install.packages(c("JGR", "Deducer")) : 
    installation of package 'Deducer' had non-zero exit status 
> 


R version 2.13.1 (2011-07-08) 
Copyright (C) 2011 The R Foundation for Statistical Computing 
ISBN 3-900051-07-0 
Platform: x86_64-pc-linux-gnu (64-bit) 

R is free software and comes with ABSOLUTELY NO WARRANTY. 
You are welcome to redistribute it under certain conditions. 
Type 'license()' or 'licence()' for distribution details. 

    Natural language support but running in an English locale 

R is a collaborative project with many contributors. 
Type 'contributors()' for more information and 
'citation()' on how to cite R or R packages in publications. 

Type 'demo()' for some demos, 'help()' for on-line help, or 
'help.start()' for an HTML browser interface to help. 
Type 'q()' to quit R. 

> install.packages('rJava') 
Installing package(s) into ‘/home/yang/R/x86_64-pc-linux-gnu-library/2.13’ 
(as ‘lib’ is unspecified) 
trying URL 'http://cran.cnr.Berkeley.edu/src/contrib/rJava_0.9-1.tar.gz' 
Content type 'application/x-gzip' length 527197 bytes (514 Kb) 
opened URL 
================================================== 
downloaded 514 Kb 

* installing *source* package ‘rJava’ ... 
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 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 supports static inline... 
yes 
checking whether setjmp.h is POSIX.1 compatible... yes 
checking whether sigsetjmp is declared... yes 
checking whether siglongjmp is declared... 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 : '-I/usr/lib/jvm/java-6-openjdk/jre/../include' 
java libs : '-L/usr/lib/jvm/java-6-openjdk/jre/lib/amd64/server -L/usr/lib/jvm/java-6-openjdk/jre/lib/amd64 -L/usr/lib/jvm/java-6-openjdk/jre/../lib/amd64 -L/usr/java/packages/lib/amd64 -L/usr/lib/jni -L/lib -L/usr/lib -ljvm' 
checking whether JNI programs can be compiled... configure: error: Cannot compile a simple JNI program. See config.log for details. 

Make sure you have Java Development Kit installed and correctly registered in R. 
If in doubt, re-run "R CMD javareconf" as root. 

ERROR: configuration failed for package ‘rJava’ 
* removing ‘/home/yang/R/x86_64-pc-linux-gnu-library/2.13/rJava’ 

The downloaded packages are in 
     ‘/tmp/RtmpTk0ftk/downloaded_packages’ 
Warning message: 
In install.packages("rJava") : 
    installation of package 'rJava' had non-zero exit status 
> 
$ sudo R CMD javareconf 
Java interpreter : /usr/bin/java 
Java version  : 1.6.0_20 
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: $(JAVA_HOME)/lib/amd64/server:$(JAVA_HOME)/lib/amd64:$(JAVA_HOME)/../lib/amd64:/usr/java/packages/lib/amd64:/usr/lib/jni:/lib:/usr/lib 
JNI linker flags : -L$(JAVA_HOME)/lib/amd64/server -L$(JAVA_HOME)/lib/amd64 -L$(JAVA_HOME)/../lib/amd64 -L/usr/java/packages/lib/amd64 -L/usr/lib/jni -L/lib -L/usr/lib -ljvm 
JNI cpp flags : 

Updating Java configuration in /etc/R 
Done. 

$ R 

R version 2.13.1 (2011-07-08) 
Copyright (C) 2011 The R Foundation for Statistical Computing 
ISBN 3-900051-07-0 
Platform: x86_64-pc-linux-gnu (64-bit) 

R is free software and comes with ABSOLUTELY NO WARRANTY. 
You are welcome to redistribute it under certain conditions. 
Type 'license()' or 'licence()' for distribution details. 

    Natural language support but running in an English locale 

R is a collaborative project with many contributors. 
Type 'contributors()' for more information and 
'citation()' on how to cite R or R packages in publications. 

Type 'demo()' for some demos, 'help()' for on-line help, or 
'help.start()' for an HTML browser interface to help. 
Type 'q()' to quit R. 

> install.packages('rJava') 
Installing package(s) into ‘/home/yang/R/x86_64-pc-linux-gnu-library/2.13’ 
(as ‘lib’ is unspecified) 
trying URL 'http://cran.cnr.Berkeley.edu/src/contrib/rJava_0.9-1.tar.gz' 
Content type 'application/x-gzip' length 527197 bytes (514 Kb) 
opened URL 
================================================== 
downloaded 514 Kb 

* installing *source* package ‘rJava’ ... 
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 grep that handles long lines and -e... /bin/grep 
checking for egrep... /bin/grep -E 
checking for ANSI C header files... yes 
c hecking 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 supports static inline... 
yes 
checking whether setjmp.h is POSIX.1 compatible... yes 
checking whether sigsetjmp is declared... yes 
checking whether siglongjmp is declared... 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/amd64/server -L/usr/lib/jvm/java-6-openjdk/jre/lib/amd64 -L/usr/lib/jvm/java-6-openjdk/jre/../lib/amd64 -L/usr/java/packages/lib/amd64 -L/usr/lib/jni -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 ‘/home/yang/R/x86_64-pc-linux-gnu-library/2.13/rJava’ 

The downloaded packages are in 
     ‘/tmp/RtmpsJBxfe/downloaded_packages’ 
Warning message: 
In install.packages("rJava") : 
    installation of package 'rJava' had non-zero exit status 
>

Fuente

2011-08-20 Yang

Le dio el mismo consejo varias veces. ¿Hay alguna buena razón para no prestarle atención? Aquí está de nuevo si te lo perdiste: "Si tienes dudas, vuelve a ejecutar" R CMD javareconf "como root". –

¿Eh? Expliqué explícitamente que lo hice en mi pregunta original, y también está en la transcripción ... – Yang

Lo siento. Lo que vi fue que hizo referencia a una pregunta y luego procedió a la instalación antes de realizar las correcciones sugeridas. –

Dah, no mucho después de la publicación encontré la respuesta aquí:

http://r-interface.blogspot.com/2012/04/install-r-jgr-and-deducer-in-ubuntu.html

Aunque ya había instalado Sun Java, el La clave era ejecutar update-java-alternatives para realmente cambiar a Sun Java primero antes de ejecutar javareconf:

sudo update-java-alternatives -s java-6-sun 
sudo R CMD javareconf

Fuente

2011-08-20 03:05:12 Yang

Todo debería funcionar como se envió en Debian/Ubuntu con la opción de Java configurada en compilación para los paquetes R y rJava, utilizando el SDK de Java en Ubuntu. Si decides cambiar a un backend Java diferente, debes reconfigurarlo. –

Aquí hay otra opción:

antes de ejecutar R, hacer esto

export LD_LIBRARY_PATH=/usr/lib/jvm/java-1.6.0-openjdk/jre/lib/amd64/server

(por ruta anterior, la ubicación de su sustituto libjvm.so en particular, si usted tiene una configuración diferente). Para encontrar libjvm.so, puede hacerlo

sudo updatedb && locate libjvm.so

Fuente

2011-12-27 05:01:26 DWright

Otra advertencia (relativamente obvio): no hacer lo que hice e instalar tanto java6 y Java7. Eso condujo a un conflicto que no pude 'arreglar' mediante la especificación de rutas y variables de entorno. La eliminación de ambos y la reinstalación de Java condujeron a la instalación exitosa de JGR. (Este bajo Ubuntu precisa, en un PowerBook G4 de Apple)

Fuente

2013-02-06 02:41:06

DWright es alternativa right..an lugar exportar cada vez que se inicia R es localizar su camino java

sudo locate libjvm.so

y añadir ir a ldpaths

sudo gedit /etc/R/ldpaths 

i.e 
${JAVA_HOME=/usr/java/jdk1.7.0_07/jre}

Fuente

2013-07-22 02:58:09 CocoOS

No se puede instalar rJava 0.9 en Ubuntu 10.04

Respuesta

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