with problems namespace loadnamespace instalar for failed error r rjava

problems - No se puede instalar rJava 0.9 en Ubuntu 10.04



rjava error (4)

Aquí hay otra opción:

antes de ejecutar R, haz esto

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

(para la ruta anterior, sustituya la ubicación de su libjvm.so en particular, si tiene una configuración diferente). Para encontrar libjvm.so, puedes hacer

sudo updatedb && locate libjvm.so

Uso R 2.13 del repositorio CRAN apt para Ubuntu 10.04, y trato de instalar Deducer, que requiere JGR / rJava, pero rJava se niega a compilar / instalar, quejándose de no poder construir una aplicación JNI. Intenté sudo R CMD javareconf como se sugirió, pero eso solo llevó a un error diferente sobre la configuración de la configuración. Descubrí que la instalación del paquete R: rJava está fallando , así que probé las sugerencias de instalar r-cran-rjava (pero eso es 0.8 y Deducer / JGR parece insistir en instalar 0.9) y jugar con mi $JAVA_HOME , todo en vano. ¿Algunas ideas?

Aquí hay una transcripción más completa de lo que sucedió:

$ 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 >

DWright tiene razón ... una alternativa en lugar de exportarlo cada vez que comiences R es ubicar tu ruta java

sudo locate libjvm.so

y agregue ir a ldpaths

sudo gedit /etc/R/ldpaths i.e ${JAVA_HOME=/usr/java/jdk1.7.0_07/jre}

Otra advertencia (relativamente obvia): no haga lo que hice e instale java6 y java7. Eso llevó a un conflicto que no pude "arreglar" al especificar rutas y variables de entorno. La eliminación de ambos y la reinstalación de java6 llevaron a la instalación exitosa de JGR. (Esto debajo de ubuntu precisa, en un Powerbook de Apple G4)