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@luispuerto luispuerto/rJava-build.log
Last active Mar 27, 2019

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Installing package into ‘/Users/lpuerto/Library/R/3.x/library’
(as ‘lib’ is unspecified)
trying URL 'http://rforge.net/src/contrib/rJava_0.9-11.tar.gz'
Content type 'application/x-gzip' length 656573 bytes (641 KB)
==================================================
downloaded 641 KB
* installing *source* package ‘rJava’ ...
checking for gcc... /usr/local/opt/llvm/bin/clang
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 /usr/local/opt/llvm/bin/clang accepts -g... yes
checking for /usr/local/opt/llvm/bin/clang option to accept ISO C89... none needed
checking how to run the C preprocessor... /usr/local/opt/llvm/bin/clang -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... rm: conftest.dSYM: is a directory
rm: conftest.dSYM: is a directory
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 /usr/local/opt/llvm/bin/clang 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 : '/Library/Java/JavaVirtualMachines/openjdk-11.0.2.jdk/Contents/Home/bin/java'
archiver : '/Library/Java/JavaVirtualMachines/openjdk-11.0.2.jdk/Contents/Home/bin/jar'
compiler : '/Library/Java/JavaVirtualMachines/openjdk-11.0.2.jdk/Contents/Home/bin/javac'
header prep.: '/usr/bin/javah'
cpp flags : '-I/Library/Java/JavaVirtualMachines/openjdk-11.0.2.jdk/Contents/Home/include -I/Library/Java/JavaVirtualMachines/openjdk-11.0.2.jdk/Contents/Home/include/darwin'
java libs : '-L/Library/Java/JavaVirtualMachines/openjdk-11.0.2.jdk/Contents/Home/lib/server -ljvm'
checking whether Java run-time works... yes
checking whether -Xrs is supported... yes
checking whether -Xrs will be used... yes
checking whether JNI programs can be compiled... yes
checking whether JNI programs run... 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... yes
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 (/private/var/folders/wf/41gjf2mx7m7fmvfd8dr22_5h0000gn/T/RtmpvjeO4G/R.INSTALL182339fe17d2/rJava/jri)
configure: running /bin/sh ./configure --disable-option-checking '--prefix=/usr/local' --cache-file=/dev/null --srcdir=.
checking build system type... x86_64-apple-darwin17.7.0
checking host system type... x86_64-apple-darwin17.7.0
checking for gcc... /usr/local/opt/llvm/bin/clang
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 /usr/local/opt/llvm/bin/clang accepts -g... yes
checking for /usr/local/opt/llvm/bin/clang option to accept ISO C89... none needed
checking how to run the C preprocessor... /usr/local/opt/llvm/bin/clang -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... rm: conftest.dSYM: is a directory
rm: conftest.dSYM: is a directory
yes
checking Java version... 11.0.2
checking Java compatibility version (integer)... 11
checking whether /usr/bin/javah actually works... no
checking whether javah was replaced by javac -h... yes
checking for target flags... -h . -target 1.6 -source 1.6
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
/usr/local/opt/llvm/bin/clang -I"/usr/local/Cellar/r/3.5.3/lib/R/include" -DNDEBUG -I. -I/Library/Java/JavaVirtualMachines/openjdk-11.0.2.jdk/Contents/Home/include -I/Library/Java/JavaVirtualMachines/openjdk-11.0.2.jdk/Contents/Home/include/darwin -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c Rglue.c -o Rglue.o
Rglue.c:860:13: warning: unused function 'new_jrectRef' [-Wunused-function]
static SEXP new_jrectRef(JNIEnv *env, jobject a, const char *sig, SEXP dim ) {
^
1 warning generated.
/usr/local/opt/llvm/bin/clang -I"/usr/local/Cellar/r/3.5.3/lib/R/include" -DNDEBUG -I. -I/Library/Java/JavaVirtualMachines/openjdk-11.0.2.jdk/Contents/Home/include -I/Library/Java/JavaVirtualMachines/openjdk-11.0.2.jdk/Contents/Home/include/darwin -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c arrayc.c -o arrayc.o
/usr/local/opt/llvm/bin/clang -I"/usr/local/Cellar/r/3.5.3/lib/R/include" -DNDEBUG -I. -I/Library/Java/JavaVirtualMachines/openjdk-11.0.2.jdk/Contents/Home/include -I/Library/Java/JavaVirtualMachines/openjdk-11.0.2.jdk/Contents/Home/include/darwin -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c callJNI.c -o callJNI.o
/usr/local/opt/llvm/bin/clang -I"/usr/local/Cellar/r/3.5.3/lib/R/include" -DNDEBUG -I. -I/Library/Java/JavaVirtualMachines/openjdk-11.0.2.jdk/Contents/Home/include -I/Library/Java/JavaVirtualMachines/openjdk-11.0.2.jdk/Contents/Home/include/darwin -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c callback.c -o callback.o
/usr/local/opt/llvm/bin/clang -I"/usr/local/Cellar/r/3.5.3/lib/R/include" -DNDEBUG -I. -I/Library/Java/JavaVirtualMachines/openjdk-11.0.2.jdk/Contents/Home/include -I/Library/Java/JavaVirtualMachines/openjdk-11.0.2.jdk/Contents/Home/include/darwin -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c fields.c -o fields.o
/usr/local/opt/llvm/bin/clang -I"/usr/local/Cellar/r/3.5.3/lib/R/include" -DNDEBUG -I. -I/Library/Java/JavaVirtualMachines/openjdk-11.0.2.jdk/Contents/Home/include -I/Library/Java/JavaVirtualMachines/openjdk-11.0.2.jdk/Contents/Home/include/darwin -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c init.c -o init.o
init.c:157:38: warning: assigning to 'void *' from 'int (FILE *, const char *, struct __va_list_tag *)' (aka 'int (struct __sFILE *, const char *, struct __va_list_tag *)') converts between void pointer and function pointer [-Wpedantic]
vm_options[propNum++].extraInfo = vfprintf_hook;
^ ~~~~~~~~~~~~~
init.c:161:38: warning: assigning to 'void *' from 'void (int)' converts between void pointer and function pointer [-Wpedantic]
vm_options[propNum++].extraInfo = exit_hook;
^ ~~~~~~~~~
2 warnings generated.
/usr/local/opt/llvm/bin/clang -I"/usr/local/Cellar/r/3.5.3/lib/R/include" -DNDEBUG -I. -I/Library/Java/JavaVirtualMachines/openjdk-11.0.2.jdk/Contents/Home/include -I/Library/Java/JavaVirtualMachines/openjdk-11.0.2.jdk/Contents/Home/include/darwin -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c jri_glue.c -o jri_glue.o
/usr/local/opt/llvm/bin/clang -I"/usr/local/Cellar/r/3.5.3/lib/R/include" -DNDEBUG -I. -I/Library/Java/JavaVirtualMachines/openjdk-11.0.2.jdk/Contents/Home/include -I/Library/Java/JavaVirtualMachines/openjdk-11.0.2.jdk/Contents/Home/include/darwin -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c loader.c -o loader.o
/usr/local/opt/llvm/bin/clang -I"/usr/local/Cellar/r/3.5.3/lib/R/include" -DNDEBUG -I. -I/Library/Java/JavaVirtualMachines/openjdk-11.0.2.jdk/Contents/Home/include -I/Library/Java/JavaVirtualMachines/openjdk-11.0.2.jdk/Contents/Home/include/darwin -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c otables.c -o otables.o
/usr/local/opt/llvm/bin/clang -I"/usr/local/Cellar/r/3.5.3/lib/R/include" -DNDEBUG -I. -I/Library/Java/JavaVirtualMachines/openjdk-11.0.2.jdk/Contents/Home/include -I/Library/Java/JavaVirtualMachines/openjdk-11.0.2.jdk/Contents/Home/include/darwin -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c rJava.c -o rJava.o
/usr/local/opt/llvm/bin/clang -I"/usr/local/Cellar/r/3.5.3/lib/R/include" -DNDEBUG -I. -I/Library/Java/JavaVirtualMachines/openjdk-11.0.2.jdk/Contents/Home/include -I/Library/Java/JavaVirtualMachines/openjdk-11.0.2.jdk/Contents/Home/include/darwin -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c tools.c -o tools.o
/usr/local/opt/llvm/bin/clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/Cellar/r/3.5.3/lib/R/lib -L/usr/local/opt/gettext/lib -L/usr/local/opt/llvm/lib -Wl,-rpath,/usr/local/opt/llvm/lib -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/Library/Java/JavaVirtualMachines/openjdk-11.0.2.jdk/Contents/Home/lib/server -ljvm -L/usr/local/Cellar/r/3.5.3/lib/R/lib -lR -lintl -Wl,-framework -Wl,CoreFoundation
ld: warning: text-based stub file /System/Library/Frameworks//CoreFoundation.framework/CoreFoundation.tbd and library file /System/Library/Frameworks//CoreFoundation.framework/CoreFoundation are out of sync. Falling back to library file for linking.
(cd ../jri && make)
make -C src JRI.jar
/Library/Java/JavaVirtualMachines/openjdk-11.0.2.jdk/Contents/Home/bin/javac -h . -target 1.6 -source 1.6 -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 6
warning: [options] source value 6 is obsolete and will be removed in a future release
warning: [options] target value 1.6 is obsolete and will be removed in a future release
warning: [options] To suppress warnings about obsolete options, use -Xlint:-options.
Note: Some input files use or override a deprecated API.
Note: Recompile with -Xlint:deprecation for details.
Note: Some input files use unchecked or unsafe operations.
Note: Recompile with -Xlint:unchecked for details.
4 warnings
if [ -n "" ]; then -d . -classpath . org.rosuda.JRI.Rengine; fi
/usr/local/opt/llvm/bin/clang -c -o Rengine.o Rengine.c -g -Iinclude -DRIF_HAS_CSTACK -DRIF_HAS_RSIGHAND -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -I/Library/Java/JavaVirtualMachines/openjdk-11.0.2.jdk/Contents/Home/include -I/Library/Java/JavaVirtualMachines/openjdk-11.0.2.jdk/Contents/Home/include/darwin -fno-common -I/Library/Java/JavaVirtualMachines/openjdk-11.0.2.jdk/Contents/Home/include -I/Library/Java/JavaVirtualMachines/openjdk-11.0.2.jdk/Contents/Home/include/darwin -I/usr/local/Cellar/r/3.5.3/lib/R/include -I/usr/local/Cellar/r/3.5.3/lib/R/include
/usr/local/opt/llvm/bin/clang -c -o jri.o jri.c -g -Iinclude -DRIF_HAS_CSTACK -DRIF_HAS_RSIGHAND -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -I/Library/Java/JavaVirtualMachines/openjdk-11.0.2.jdk/Contents/Home/include -I/Library/Java/JavaVirtualMachines/openjdk-11.0.2.jdk/Contents/Home/include/darwin -fno-common -I/Library/Java/JavaVirtualMachines/openjdk-11.0.2.jdk/Contents/Home/include -I/Library/Java/JavaVirtualMachines/openjdk-11.0.2.jdk/Contents/Home/include/darwin -I/usr/local/Cellar/r/3.5.3/lib/R/include -I/usr/local/Cellar/r/3.5.3/lib/R/include
/usr/local/opt/llvm/bin/clang -c -o Rcallbacks.o Rcallbacks.c -g -Iinclude -DRIF_HAS_CSTACK -DRIF_HAS_RSIGHAND -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -I/Library/Java/JavaVirtualMachines/openjdk-11.0.2.jdk/Contents/Home/include -I/Library/Java/JavaVirtualMachines/openjdk-11.0.2.jdk/Contents/Home/include/darwin -fno-common -I/Library/Java/JavaVirtualMachines/openjdk-11.0.2.jdk/Contents/Home/include -I/Library/Java/JavaVirtualMachines/openjdk-11.0.2.jdk/Contents/Home/include/darwin -I/usr/local/Cellar/r/3.5.3/lib/R/include -I/usr/local/Cellar/r/3.5.3/lib/R/include
/usr/local/opt/llvm/bin/clang -c -o Rinit.o Rinit.c -g -Iinclude -DRIF_HAS_CSTACK -DRIF_HAS_RSIGHAND -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -I/Library/Java/JavaVirtualMachines/openjdk-11.0.2.jdk/Contents/Home/include -I/Library/Java/JavaVirtualMachines/openjdk-11.0.2.jdk/Contents/Home/include/darwin -fno-common -I/usr/local/Cellar/r/3.5.3/lib/R/include -I/usr/local/Cellar/r/3.5.3/lib/R/include
/usr/local/opt/llvm/bin/clang -c -o globals.o globals.c -g -Iinclude -DRIF_HAS_CSTACK -DRIF_HAS_RSIGHAND -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -I/Library/Java/JavaVirtualMachines/openjdk-11.0.2.jdk/Contents/Home/include -I/Library/Java/JavaVirtualMachines/openjdk-11.0.2.jdk/Contents/Home/include/darwin -fno-common -I/Library/Java/JavaVirtualMachines/openjdk-11.0.2.jdk/Contents/Home/include -I/Library/Java/JavaVirtualMachines/openjdk-11.0.2.jdk/Contents/Home/include/darwin
/usr/local/opt/llvm/bin/clang -c -o rjava.o rjava.c -g -Iinclude -DRIF_HAS_CSTACK -DRIF_HAS_RSIGHAND -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -I/Library/Java/JavaVirtualMachines/openjdk-11.0.2.jdk/Contents/Home/include -I/Library/Java/JavaVirtualMachines/openjdk-11.0.2.jdk/Contents/Home/include/darwin -fno-common -I/Library/Java/JavaVirtualMachines/openjdk-11.0.2.jdk/Contents/Home/include -I/Library/Java/JavaVirtualMachines/openjdk-11.0.2.jdk/Contents/Home/include/darwin
/usr/local/opt/llvm/bin/clang -o libjri.jnilib Rengine.o jri.o Rcallbacks.o Rinit.o globals.o rjava.o -dynamiclib -framework JavaVM -L/usr/local/opt/openblas/lib -L/usr/local/opt/gettext/lib -L/usr/local/opt/readline/lib -L/usr/local/lib -L/usr/local/opt/openblas/lib -L/usr/local/opt/gettext/lib -L/usr/local/opt/readline/lib -L/usr/local/lib -L/usr/local/Cellar/r/3.5.3/lib/R/lib -lR -lpcre -llzma -lbz2 -lz -licucore -lm -liconv
/Library/Java/JavaVirtualMachines/openjdk-11.0.2.jdk/Contents/Home/bin/javac -h . -target 1.6 -source 1.6 -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 6
warning: [options] source value 6 is obsolete and will be removed in a future release
warning: [options] target value 1.6 is obsolete and will be removed in a future release
warning: [options] To suppress warnings about obsolete options, use -Xlint:-options.
Note: Some input files use or override a deprecated API.
Note: Recompile with -Xlint:deprecation for details.
Note: Some input files use unchecked or unsafe operations.
Note: Recompile with -Xlint:unchecked for details.
4 warnings
/Library/Java/JavaVirtualMachines/openjdk-11.0.2.jdk/Contents/Home/bin/jar fc JRI.jar org libjri.jnilib
rm -f libjri.jnilib
cp src/libjri.jnilib libjri.jnilib
/Library/Java/JavaVirtualMachines/openjdk-11.0.2.jdk/Contents/Home/bin/javac -h . -target 1.6 -source 1.6 -classpath src/JRI.jar -d examples examples/rtest.java
warning: [options] bootstrap class path not set in conjunction with -source 6
warning: [options] source value 6 is obsolete and will be removed in a future release
warning: [options] target value 1.6 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
/Library/Java/JavaVirtualMachines/openjdk-11.0.2.jdk/Contents/Home/bin/javac -h . -target 1.6 -source 1.6 -classpath src/JRI.jar -d examples examples/rtest2.java
warning: [options] bootstrap class path not set in conjunction with -source 6
warning: [options] source value 6 is obsolete and will be removed in a future release
warning: [options] target value 1.6 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
installing via 'install.libs.R' to /Users/lpuerto/Library/R/3.x/library/rJava
** R
** inst
** byte-compile and prepare 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
‘/private/var/folders/wf/41gjf2mx7m7fmvfd8dr22_5h0000gn/T/Rtmpxj129u/downloaded_packages’
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