Supported by Dr. Osamu Ogasawara and  providing  . |
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Last data update: 2014.03.03 |
rJava
Package: rJava
● Cran Task View: HighPerformanceComputing
● 0 images, 36 functions, 0 datasets ● Reverse Depends: 51 Install log
* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'rJava' ...
** package 'rJava' successfully unpacked and MD5 sums checked
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
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-8-oracle/jre/../include -I/usr/lib/jvm/java-8-oracle/jre/../include/linux'
java libs : '-L/usr/lib/jvm/java-8-oracle/jre/lib/amd64/server -ljvm'
checking whether Java run-time works... yes
checking whether -Xrs is supported... yes
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 headless init is enabled... 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/RtmpQuoItK/R.INSTALL13808bd1c44/rJava/jri)
configure: running /bin/bash ./configure --disable-option-checking '--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
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
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 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 -I/home/ddbj/local/lib64/R/include -DNDEBUG -I. -I/usr/lib/jvm/java-8-oracle/jre/../include -I/usr/lib/jvm/java-8-oracle/jre/../include/linux -I/usr/local/include -fpic -g -O2 -c Rglue.c -o Rglue.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I. -I/usr/lib/jvm/java-8-oracle/jre/../include -I/usr/lib/jvm/java-8-oracle/jre/../include/linux -I/usr/local/include -fpic -g -O2 -c arrayc.c -o arrayc.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I. -I/usr/lib/jvm/java-8-oracle/jre/../include -I/usr/lib/jvm/java-8-oracle/jre/../include/linux -I/usr/local/include -fpic -g -O2 -c callJNI.c -o callJNI.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I. -I/usr/lib/jvm/java-8-oracle/jre/../include -I/usr/lib/jvm/java-8-oracle/jre/../include/linux -I/usr/local/include -fpic -g -O2 -c callback.c -o callback.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I. -I/usr/lib/jvm/java-8-oracle/jre/../include -I/usr/lib/jvm/java-8-oracle/jre/../include/linux -I/usr/local/include -fpic -g -O2 -c fields.c -o fields.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I. -I/usr/lib/jvm/java-8-oracle/jre/../include -I/usr/lib/jvm/java-8-oracle/jre/../include/linux -I/usr/local/include -fpic -g -O2 -c init.c -o init.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I. -I/usr/lib/jvm/java-8-oracle/jre/../include -I/usr/lib/jvm/java-8-oracle/jre/../include/linux -I/usr/local/include -fpic -g -O2 -c jri_glue.c -o jri_glue.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I. -I/usr/lib/jvm/java-8-oracle/jre/../include -I/usr/lib/jvm/java-8-oracle/jre/../include/linux -I/usr/local/include -fpic -g -O2 -c loader.c -o loader.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I. -I/usr/lib/jvm/java-8-oracle/jre/../include -I/usr/lib/jvm/java-8-oracle/jre/../include/linux -I/usr/local/include -fpic -g -O2 -c otables.c -o otables.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I. -I/usr/lib/jvm/java-8-oracle/jre/../include -I/usr/lib/jvm/java-8-oracle/jre/../include/linux -I/usr/local/include -fpic -g -O2 -c rJava.c -o rJava.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I. -I/usr/lib/jvm/java-8-oracle/jre/../include -I/usr/lib/jvm/java-8-oracle/jre/../include/linux -I/usr/local/include -fpic -g -O2 -c tools.c -o tools.o
gcc -shared -L/home/ddbj/local/lib64/R/lib -L/usr/local/lib64 -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-8-oracle/jre/lib/amd64/server -ljvm -L/home/ddbj/local/lib64/R/lib -lR
(cd ../jri && make)
make[1]: Entering directory '/tmp/RtmpQuoItK/R.INSTALL13808bd1c44/rJava/jri'
make -C src JRI.jar
make[2]: Entering directory '/tmp/RtmpQuoItK/R.INSTALL13808bd1c44/rJava/jri/src'
/usr/bin/javac -target 1.4 -source 1.4 -d . ../package-info.java ../REXP.java ../RFactor.java ../Mutex.java ../RConsoleOutputStream.java ../RMainLoopCallbacks.java ../RVector.java ../RBool.java ../RList.java ../Rengine.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 -c -o Rengine.o Rengine.c -g -Iinclude -DRIF_HAS_CSTACK -DRIF_HAS_RSIGHAND -g -O2 -I/usr/lib/jvm/java-8-oracle/jre/../include -I/usr/lib/jvm/java-8-oracle/jre/../include/linux -fpic -I/usr/lib/jvm/java-8-oracle/jre/../include -I/usr/lib/jvm/java-8-oracle/jre/../include/linux -I/home/ddbj/local/lib64/R/include -I/home/ddbj/local/lib64/R/include
gcc -c -o jri.o jri.c -g -Iinclude -DRIF_HAS_CSTACK -DRIF_HAS_RSIGHAND -g -O2 -I/usr/lib/jvm/java-8-oracle/jre/../include -I/usr/lib/jvm/java-8-oracle/jre/../include/linux -fpic -I/usr/lib/jvm/java-8-oracle/jre/../include -I/usr/lib/jvm/java-8-oracle/jre/../include/linux -I/home/ddbj/local/lib64/R/include -I/home/ddbj/local/lib64/R/include
gcc -c -o Rcallbacks.o Rcallbacks.c -g -Iinclude -DRIF_HAS_CSTACK -DRIF_HAS_RSIGHAND -g -O2 -I/usr/lib/jvm/java-8-oracle/jre/../include -I/usr/lib/jvm/java-8-oracle/jre/../include/linux -fpic -I/usr/lib/jvm/java-8-oracle/jre/../include -I/usr/lib/jvm/java-8-oracle/jre/../include/linux -I/home/ddbj/local/lib64/R/include -I/home/ddbj/local/lib64/R/include
gcc -c -o Rinit.o Rinit.c -g -Iinclude -DRIF_HAS_CSTACK -DRIF_HAS_RSIGHAND -g -O2 -I/usr/lib/jvm/java-8-oracle/jre/../include -I/usr/lib/jvm/java-8-oracle/jre/../include/linux -fpic -I/home/ddbj/local/lib64/R/include -I/home/ddbj/local/lib64/R/include
gcc -c -o globals.o globals.c -g -Iinclude -DRIF_HAS_CSTACK -DRIF_HAS_RSIGHAND -g -O2 -I/usr/lib/jvm/java-8-oracle/jre/../include -I/usr/lib/jvm/java-8-oracle/jre/../include/linux -fpic -I/usr/lib/jvm/java-8-oracle/jre/../include -I/usr/lib/jvm/java-8-oracle/jre/../include/linux
gcc -c -o rjava.o rjava.c -g -Iinclude -DRIF_HAS_CSTACK -DRIF_HAS_RSIGHAND -g -O2 -I/usr/lib/jvm/java-8-oracle/jre/../include -I/usr/lib/jvm/java-8-oracle/jre/../include/linux -fpic -I/usr/lib/jvm/java-8-oracle/jre/../include -I/usr/lib/jvm/java-8-oracle/jre/../include/linux
rjava.c: In function 'RJava_request_lock':
rjava.c:22:3: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
write(ipcout, buf, sizeof(ptrlong));
^
rjava.c: In function 'RJava_clear_lock':
rjava.c:30:3: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
write(ipcout, buf, sizeof(ptrlong));
^
rjava.c: In function 'RJava_request_callback':
rjava.c:39:3: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
write(ipcout, buf, sizeof(ptrlong) * 3);
^
rjava.c: In function 'RJava_init_ctrl':
rjava.c:51:3: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
write(ipcout, buf, sizeof(ptrlong));
^
rjava.c:52:3: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result]
read(resin, buf, sizeof(ptrlong) * 2);
^
gcc -o libjri.so Rengine.o jri.o Rcallbacks.o Rinit.o globals.o rjava.o -shared -L/usr/lib/jvm/java-8-oracle/jre/lib/amd64/server -ljvm -Wl,--export-dynamic -fopenmp -L/home/ddbj/local/lib64/R/lib -lR -lpcre -llzma -lbz2 -lz -lrt -ldl -lm -licuuc -licui18n
/usr/bin/javac -target 1.4 -source 1.4 -d . ../package-info.java ../RFactor.java ../REXP.java ../RList.java ../Mutex.java ../RVector.java ../RBool.java ../RConsoleOutputStream.java ../Rengine.java ../RMainLoopCallbacks.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/RtmpQuoItK/R.INSTALL13808bd1c44/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/RtmpQuoItK/R.INSTALL13808bd1c44/rJava/jri'
installing via 'install.libs.R' to /home/ddbj/local/lib64/R/library/rJava
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
converting help for package 'rJava'
finding HTML links ... done
Exceptions html
J html
accessOp html
aslist html
clone html
instanceof html
jarray html
jarrayRef-class html
java-tools html
javaImport html
jcall html
jcast html
jcastToArray html
jcheck html
jclassName html
jengine html
jequals html
jfield html
jfloat-class html
jfloat html
jinit html
jmemprof html
jnew html
jnull html
jobjRef-class html
jpackage html
jrectRef-class html
jreflection html
jserialize html
jsimplify html
loader html
new html
rep html
show html
toJava html
with html
** building package indices
** testing if installed package can be loaded
* DONE (rJava)
Making 'packages.html' ... done
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Created & Maintained by Osamu Ogasawara (osamu.ogasawara@gmail.com) and