[R-es] Help: rJava ubuntu 12.04

Dom Feb 24 16:30:01 CET 2013

Hola, ¿qué tal?

¿Has probado a ejecutar "R CMD javareconf" después de instalar Java?

Un saludo,

Carlos J. Gil Bellosta
http://www.datanalytics.com

2013/2/24 Javier Villacampa González <javier.villacampa.gonzalez en gmail.com>:
> Hola buenas,
>
> utlimamente estoy teniendo más problemas con mi equipo de los que debería.
> Bajo windows no me funciona bien Rstudio y bajo linux soy incapaz de
> instalar rJava. ¿Alguien que sepa de Linux me podría ayudar?
>
> He probado a instalar los openJDK y nada.
>
> También he probado, para instalar Java, a hacer un:
>
> sudo add-apt-repository ppa:webupd8team/java
>
> sudo apt-get update && sudo apt-get install oracle-java7-installer
>
> Y luego cuando le digo a R (vamos que no me lo instala):
>
>> install.packages("rJava")
> Installing package(s) into
> ‘/home/hermesh/R/x86_64-pc-linux-gnu-library/2.15’
> (as ‘lib’ is unspecified)
> probando la URL 'http://cran.rstudio.com/src/contrib/rJava_0.9-3.tar.gz'
> Content type 'application/x-gzip' length 537153 bytes (524 Kb)
> URL abierta
> ==================================================
> downloaded 524 Kb
>
> * installing *source* package ‘rJava’ ...
> ** package ‘rJava’ successfully unpacked and MD5 sums checked
> 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 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-7-openjdk-amd64/jre/../include'
> java libs   : '-L/usr/lib/jvm/java-7-openjdk-amd64/jre/lib/amd64
> -L/usr/lib/jvm/java-7-openjdk-amd64/jre/lib/amd64/server -ljvm'
> checking whether JNI programs can be compiled... yes
> checking JNI data types... ok
> checking whether JRI should be compiled (autodetect)... yes
> checking whether debugging output should be enabled... no
> checking whether memory profiling is desired... no
> checking whether threads support is requested... no
> checking whether callbacks support is requested... no
> checking whether JNI cache support is requested... no
> checking whether JRI is requested... yes
> configure: creating ./config.status
> config.status: creating src/Makevars
> config.status: creating R/zzz.R
> config.status: creating src/config.h
> === configuring in jri (/tmp/RtmpCErgmn/R.INSTALL57e71df9a069/rJava/jri)
> configure: running /bin/bash ./configure '--prefix=/usr/local'
> --cache-file=/dev/null --srcdir=.
> checking build system type... x86_64-unknown-linux-gnu
> checking host system type... x86_64-unknown-linux-gnu
> 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 whether Java interpreter works... checking whether JNI programs
> can be compiled... yes
> checking whether JNI programs can be run... yes
> checking JNI data types... ok
> checking whether Rinterface.h exports R_CStackXXX variables... yes
> checking whether Rinterface.h exports R_SignalHandlers... yes
> configure: creating ./config.status
> config.status: creating src/Makefile
> config.status: creating Makefile
> config.status: creating run
> config.status: creating src/config.h
> ** libs
> gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I.
> -I/usr/lib/jvm/java-7-openjdk-amd64/jre/../include     -fpic  -O2 -pipe -g
> -c Rglue.c -o Rglue.o
> gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I.
> -I/usr/lib/jvm/java-7-openjdk-amd64/jre/../include     -fpic  -O2 -pipe -g
> -c arrayc.c -o arrayc.o
> gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I.
> -I/usr/lib/jvm/java-7-openjdk-amd64/jre/../include     -fpic  -O2 -pipe -g
> -c callJNI.c -o callJNI.o
> gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I.
> -I/usr/lib/jvm/java-7-openjdk-amd64/jre/../include     -fpic  -O2 -pipe -g
> -c callback.c -o callback.o
> gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I.
> -I/usr/lib/jvm/java-7-openjdk-amd64/jre/../include     -fpic  -O2 -pipe -g
> -c fields.c -o fields.o
> gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I.
> -I/usr/lib/jvm/java-7-openjdk-amd64/jre/../include     -fpic  -O2 -pipe -g
> -c init.c -o init.o
> gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I.
> -I/usr/lib/jvm/java-7-openjdk-amd64/jre/../include     -fpic  -O2 -pipe -g
> -c jri_glue.c -o jri_glue.o
> gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I.
> -I/usr/lib/jvm/java-7-openjdk-amd64/jre/../include     -fpic  -O2 -pipe -g
> -c loader.c -o loader.o
> gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I.
> -I/usr/lib/jvm/java-7-openjdk-amd64/jre/../include     -fpic  -O2 -pipe -g
> -c otables.c -o otables.o
> gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I.
> -I/usr/lib/jvm/java-7-openjdk-amd64/jre/../include     -fpic  -O2 -pipe -g
> -c rJava.c -o rJava.o
> gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I.
> -I/usr/lib/jvm/java-7-openjdk-amd64/jre/../include     -fpic  -O2 -pipe -g
> -c tools.c -o tools.o
> gcc -std=gnu99 -shared -o rJava.so Rglue.o arrayc.o callJNI.o callback.o
> fields.o init.o jri_glue.o loader.o otables.o rJava.o tools.o
> -L/usr/lib/jvm/java-7-openjdk-amd64/jre/lib/amd64
> -L/usr/lib/jvm/java-7-openjdk-amd64/jre/lib/amd64/server -ljvm
> -L/usr/lib/R/lib -lR
> (cd ../jri && make)
> make[1]: se ingresa al directorio
> «/tmp/RtmpCErgmn/R.INSTALL57e71df9a069/rJava/jri»
> make -C src JRI.jar
> make[2]: se ingresa al directorio
> «/tmp/RtmpCErgmn/R.INSTALL57e71df9a069/rJava/jri/src»
> /usr/bin/javac -target 1.4 -source 1.4 -d . ../Mutex.java ../RBool.java
> ../RConsoleOutputStream.java ../REXP.java ../RFactor.java ../RList.java
> ../RMainLoopCallbacks.java ../RVector.java ../Rengine.java
> ../package-info.java
> warning: [options] bootstrap class path not set in conjunction with -source
> 1.4
> 1 warning
> /usr/bin/javah -d . -classpath . org.rosuda.JRI.Rengine
> gcc -std=gnu99 -c -o Rengine.o Rengine.c -g -Iinclude  -DRIF_HAS_CSTACK
> -DRIF_HAS_RSIGHAND -O2 -pipe -g
> -I/usr/lib/jvm/java-7-openjdk-amd64/jre/../include  -fpic
> -I/usr/lib/jvm/java-7-openjdk-amd64/jre/../include -I/usr/share/R/include
> -I/usr/share/R/include
> gcc -std=gnu99 -c -o jri.o jri.c -g -Iinclude  -DRIF_HAS_CSTACK
> -DRIF_HAS_RSIGHAND -O2 -pipe -g
> -I/usr/lib/jvm/java-7-openjdk-amd64/jre/../include  -fpic
> -I/usr/lib/jvm/java-7-openjdk-amd64/jre/../include -I/usr/share/R/include
> -I/usr/share/R/include
> gcc -std=gnu99 -c -o Rcallbacks.o Rcallbacks.c -g -Iinclude
> -DRIF_HAS_CSTACK -DRIF_HAS_RSIGHAND -O2 -pipe -g
> -I/usr/lib/jvm/java-7-openjdk-amd64/jre/../include  -fpic
> -I/usr/lib/jvm/java-7-openjdk-amd64/jre/../include -I/usr/share/R/include
> -I/usr/share/R/include
> gcc -std=gnu99 -c -o Rinit.o Rinit.c -g -Iinclude  -DRIF_HAS_CSTACK
> -DRIF_HAS_RSIGHAND -O2 -pipe -g
> -I/usr/lib/jvm/java-7-openjdk-amd64/jre/../include  -fpic
> -I/usr/share/R/include -I/usr/share/R/include
> gcc -std=gnu99 -c -o globals.o globals.c -g -Iinclude  -DRIF_HAS_CSTACK
> -DRIF_HAS_RSIGHAND -O2 -pipe -g
> -I/usr/lib/jvm/java-7-openjdk-amd64/jre/../include  -fpic
> -I/usr/lib/jvm/java-7-openjdk-amd64/jre/../include
> gcc -std=gnu99 -c -o rjava.o rjava.c -g -Iinclude  -DRIF_HAS_CSTACK
> -DRIF_HAS_RSIGHAND -O2 -pipe -g
> -I/usr/lib/jvm/java-7-openjdk-amd64/jre/../include  -fpic
> -I/usr/lib/jvm/java-7-openjdk-amd64/jre/../include
> rjava.c: En la función ‘RJava_init_ctrl’:
> rjava.c:51:8: aviso: se descarta el valor de devolución de ‘write’, se
> declaró con el atributo warn_unused_result [-Wunused-result]
> rjava.c:52:7: aviso: se descarta el valor de devolución de ‘read’, se
> declaró con el atributo warn_unused_result [-Wunused-result]
> rjava.c: En la función ‘RJava_request_callback’:
> rjava.c:39:8: aviso: se descarta el valor de devolución de ‘write’, se
> declaró con el atributo warn_unused_result [-Wunused-result]
> rjava.c: En la función ‘RJava_clear_lock’:
> rjava.c:30:8: aviso: se descarta el valor de devolución de ‘write’, se
> declaró con el atributo warn_unused_result [-Wunused-result]
> rjava.c: En la función ‘RJava_request_lock’:
> rjava.c:22:8: aviso: se descarta el valor de devolución de ‘write’, se
> declaró con el atributo warn_unused_result [-Wunused-result]
> gcc -std=gnu99 -o libjri.so Rengine.o jri.o Rcallbacks.o Rinit.o globals.o
> rjava.o  -shared -L/usr/lib/jvm/java-7-openjdk-amd64/jre/lib/amd64
> -L/usr/lib/jvm/java-7-openjdk-amd64/jre/lib/amd64/server -ljvm
> -L/usr/lib/R/lib -lR
> /usr/bin/javac -target 1.4 -source 1.4 -d . ../Mutex.java ../RBool.java
> ../RConsoleOutputStream.java ../REXP.java ../RFactor.java ../RList.java
> ../RMainLoopCallbacks.java ../RVector.java ../Rengine.java
> ../package-info.java
> warning: [options] bootstrap class path not set in conjunction with -source
> 1.4
> 1 warning
> /usr/bin/jar fc JRI.jar org libjri.so
> make[2]: se sale del directorio
> «/tmp/RtmpCErgmn/R.INSTALL57e71df9a069/rJava/jri/src»
> rm -f libjri.so
> cp src/libjri.so libjri.so
> /usr/bin/javac -target 1.4 -source 1.4 -classpath src/JRI.jar -d examples
> examples/rtest.java
> warning: [options] bootstrap class path not set in conjunction with -source
> 1.4
> Note: examples/rtest.java uses or overrides a deprecated API.
> Note: Recompile with -Xlint:deprecation for details.
> 1 warning
> /usr/bin/javac -target 1.4 -source 1.4 -classpath src/JRI.jar -d examples
> examples/rtest2.java
> warning: [options] bootstrap class path not set in conjunction with -source
> 1.4
> Note: examples/rtest2.java uses or overrides a deprecated API.
> Note: Recompile with -Xlint:deprecation for details.
> 1 warning
> make[1]: se sale del directorio
> «/tmp/RtmpCErgmn/R.INSTALL57e71df9a069/rJava/jri»
> installing via 'install.libs.R' to
> /home/hermesh/R/x86_64-pc-linux-gnu-library/2.15/rJava
> ** R
> ** inst
> ** preparing package for lazy loading
> ** help
> *** installing help indices
> ** building package indices
> ** testing if installed package can be loaded
>
> * DONE (rJava)
>
> The downloaded source packages are in
>     ‘/tmp/RtmpRQzD0x/downloaded_packages’
>
>         [[alternative HTML version deleted]]
>
>
> _______________________________________________
> R-help-es mailing list
> R-help-es en r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-help-es
>