r - 为什么RJava无法安装

Question

我正在尝试安装RJava，但无法安装。以下是我认为可用于排除错误的文件和输出。我检查了类似的问题，但我的错误与发布的其他问题不同

这是错误的输出，一些冗余行已被删除

install.packages("rJava")
installing *source* package ‘rJava’ ...
package ‘rJava’ successfully unpacked and MD5 sums checked
checking for gcc... gcc -std=gnu99
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
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-6-openjdk-   amd64/jre/../include     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c Rglue.c -o Rglue.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -I/usr/lib/jvm/java-6-openjdk-amd64/jre/../include     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c arrayc.c -o arrayc.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -I/usr/lib/jvm/java-6-openjdk-amd64/jre/../include     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c callJNI.c -o callJNI.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -I/usr/lib/jvm/java-6-openjdk-amd64/jre/../include     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c callback.c -o callback.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -I/usr/lib/jvm/java-6-openjdk-amd64/jre/../include     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c fields.c -o fields.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -I/usr/lib/jvm/java-6-openjdk-amd64/jre/../include     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c init.c -o init.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -I/usr/lib/jvm/java-6-openjdk-amd64/jre/../include     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c jri_glue.c -o jri_glue.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -I/usr/lib/jvm/java-6-openjdk-amd64/jre/../include     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c loader.c -o loader.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -I/usr/lib/jvm/java-6-openjdk-amd64/jre/../include     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c otables.c -o otables.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -I/usr/lib/jvm/java-6-openjdk-amd64/jre/../include     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c rJava.c -o rJava.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -I/usr/lib/jvm/java-6-openjdk-amd64/jre/../include     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c tools.c -o tools.o
gcc -std=gnu99 -shared -Wl,-Bsymbolic-functions -Wl,-z,relro -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-6-openjdk-amd64/jre/lib/amd64/server -ljvm -L/usr/lib/R/lib -lR
(cd ../jri && make)
make[1]: Entering directory `/tmp/RtmpyveV0g/R.INSTALL38bc46246ade/rJava/jri`
make -C src JRI.jar
make[2]: Entering directory `/tmp/RtmpyveV0g/R.INSTALL38bc46246ade/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
warning: [options] source value 1.4 is obsolete and will be removed in a future release
warning: [options] target value 1.4 is obsolete and will be removed in a future release
warning: [options] To suppress warnings about obsolete options, use -Xlint:-options.
 4 warnings
/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 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -I/usr/lib/jvm/java-6-openjdk-amd64/jre/../include  -fpic -I/usr/lib/jvm/java-6-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 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -I/usr/lib/jvm/java-6-openjdk-amd64/jre/../include  -fpic -I/usr/lib/jvm/java-6-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 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -I/usr/lib/jvm/java-6-openjdk-amd64/jre/../include  -fpic -I/usr/lib/jvm/java-6-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 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -I/usr/lib/jvm/java-6-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 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -I/usr/lib/jvm/java-6-openjdk-amd64/jre/../include  -fpic -I/usr/lib/jvm/java-6-openjdk-amd64/jre/../include
gcc -std=gnu99 -c -o rjava.o rjava.c -g -Iinclude  -DRIF_HAS_CSTACK -DRIF_HAS_RSIGHAND -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -I/usr/lib/jvm/java-6-openjdk-amd64/jre/../include  -fpic -I/usr/lib/jvm/java-6-openjdk-amd64/jre/../include
rjava.c: In function ‘RJava_init_ctrl’:
rjava.c:51:8: warning: ignoring return value of ‘write’, declared with attribute   warn_unused_result [-Wunused-result]
rjava.c:52:7: warning: ignoring return value of ‘read’, declared with attribute   warn_unused_result [-Wunused-result]
rjava.c: In function ‘RJava_request_callback’:
rjava.c:39:8: warning: ignoring return value of ‘write’, declared with attribute  warn_unused_result [-Wunused-result]
rjava.c: In function ‘RJava_clear_lock’:
rjava.c:30:8: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
rjava.c: In function ‘RJava_request_lock’:
rjava.c:22:8: warning: ignoring return value of ‘write’, declared with attribute 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-6-openjdk-amd64/jre/lib/amd64/server -ljvm -Wl,--export-dynamic -fopenmp  -L/usr/lib/R/lib -lR -lpcre -llzma -lbz2 -lrt -ldl -lm
/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
warning: [options] source value 1.4 is obsolete and will be removed in a future release
warning: [options] target value 1.4 is obsolete and will be removed in a future release
warning: [options] To suppress warnings about obsolete options, use -Xlint:-options.
4 warnings
/usr/bin/jar fc JRI.jar org libjri.so
make[2]: Leaving directory `/tmp/RtmpyveV0g/R.INSTALL38bc46246ade/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
warning: [options] source value 1.4 is obsolete and will be removed in a future release
warning: [options] target value 1.4 is obsolete and will be removed in a future release
warning: [options] To suppress warnings about obsolete options, use -Xlint:-options.
Note: examples/rtest.java uses or overrides a deprecated API.
Note: Recompile with -Xlint:deprecation for details.
4 warnings
/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
warning: [options] source value 1.4 is obsolete and will be removed in a future release
warning: [options] target value 1.4 is obsolete and will be removed in a future release
warning: [options] To suppress warnings about obsolete options, use -Xlint:-options.
Note: examples/rtest2.java uses or overrides a deprecated API.
Note: Recompile with -Xlint:deprecation for details.
4 warnings
make[1]: Leaving directory `/tmp/RtmpyveV0g/R.INSTALL38bc46246ade/rJava/jri`
installing via 'install.libs.R' to /home/waheeb/R/x86_64-pc-linux-gnu-library/3.1/rJava
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Error : .onLoad failed in loadNamespace() for 'rJava', details:
call: dyn.load(file, DLLpath = DLLpath, ...)
error: unable to load shared object '/home/waheeb/R/x86_64-pc-linux-gnu-library /3.1/rJava/libs/rJava.so':
libjvm.so: cannot open shared object file: No such file or directory
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/home/waheeb/R/x86_64-pc-linux-gnu-library/3.1/rJava’
Warning in install.packages :
installation of package ‘rJava’ had non-zero exit status

这是我系统中的 Java 替代方案:

*0            /usr/lib/jvm/java-6-openjdk-amd64/jre/bin/java    1061      auto mode.   
1            /usr/lib/jvm/java-6-openjdk-amd64/jre/bin/java    1061      manual mode.   
2            /usr/lib/jvm/java-7-openjdk-amd64/jre/bin/java    1051      manual mode.   
3            /usr/local/java/jdk1.8.0/bin/java                 1         manual mode.   

这是 /etc/R/ldpaths 文件:仅显示两行。

  ${JAVA_HOME=/usr/lib/jvm/java-6-openjdk/jre}.  
 :${R_JAVA_LD_LIBRARY_PATH=${JAVA_HOME}/lib/amd64/server}

这是libjvm.so文件的位置:

/usr/local/java/jdk1.8.0/jre/lib/amd64/server/libjvm.so

感谢任何帮助

Answer 1

你尝试过吗

sudo apt-get install r-cran-rjava 

还没有？

我们确实维护了一个包，这样您就不必手动进行配置。