我正在尝试安装,RJava但我不能.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
这是错误输出,已删除一些冗余行
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:只显示两行.
${JAVA_HOME=/usr/lib/jvm/java-6-openjdk/jre}.
:${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
任何帮助表示赞赏
你试过了吗
sudo apt-get install r-cran-rjava
然而？
我们确实维护一个包,这样您就不必手动对抗配置.