* installing to library ‘/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages’ * installing *source* package ‘rJava’ ... ** package ‘rJava’ successfully unpacked and MD5 sums checked ** using staged installation checking for gcc... clang-19 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 clang-19 accepts -g... yes checking for clang-19 option to accept ISO C89... none needed checking how to run the C preprocessor... clang-19 -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... 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 clang-19 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.: '' cpp flags : '-I/usr/lib/jvm/java-21-openjdk-amd64/include -I/usr/lib/jvm/java-21-openjdk-amd64/include/linux' java libs : '-L/usr/lib/jvm/java-21-openjdk-amd64/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 JVM will be loaded dynamically... no 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... 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 (/home/hornik/tmp/scratch/RtmpBzNCme/R.INSTALL2fe59b70d633d0/rJava/jri) configure: running /bin/bash ./configure --disable-option-checking '--prefix=/usr/local' 'CC=clang-19' 'CFLAGS=-g -O3 -Wall -pedantic' 'LDFLAGS=-Wl,-O1' 'CPPFLAGS=-I/usr/local/include' --cache-file=/dev/null --srcdir=. checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking for gcc... clang-19 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 the compiler supports GNU C... yes checking whether clang-19 accepts -g... yes checking for clang-19 option to enable C11 features... none needed checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for sys/time.h... yes checking for sys/types.h... (cached) yes checking for sys/select.h... yes checking Java version... 21.0.5-ea checking Java compatibility version (integer)... 21 checking whether actually works... no checking whether javah was replaced by javac -h... yes checking for target flags... -h . -target 1.8 -source 1.8 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 using C compiler: ‘Debian clang version 19.1.1 (1)’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpBzNCme/R.INSTALL2fe59b70d633d0/rJava/src' clang-19 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I. -I/usr/lib/jvm/java-21-openjdk-amd64/include -I/usr/lib/jvm/java-21-openjdk-amd64/include/linux -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c Rglue.c -o Rglue.o Rglue.c:262:7: warning: variable 'i' set but not used [-Wunused-but-set-variable] 262 | int i=0; | ^ 1 warning generated. clang-19 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I. -I/usr/lib/jvm/java-21-openjdk-amd64/include -I/usr/lib/jvm/java-21-openjdk-amd64/include/linux -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c arrayc.c -o arrayc.o clang-19 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I. -I/usr/lib/jvm/java-21-openjdk-amd64/include -I/usr/lib/jvm/java-21-openjdk-amd64/include/linux -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c callJNI.c -o callJNI.o clang-19 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I. -I/usr/lib/jvm/java-21-openjdk-amd64/include -I/usr/lib/jvm/java-21-openjdk-amd64/include/linux -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c callback.c -o callback.o clang-19 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I. -I/usr/lib/jvm/java-21-openjdk-amd64/include -I/usr/lib/jvm/java-21-openjdk-amd64/include/linux -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c fields.c -o fields.o clang-19 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I. -I/usr/lib/jvm/java-21-openjdk-amd64/include -I/usr/lib/jvm/java-21-openjdk-amd64/include/linux -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c init.c -o init.o init.c:175:38: warning: assigning to 'void *' from 'int (FILE *, const char *, struct __va_list_tag *)' (aka 'int (struct _IO_FILE *, const char *, struct __va_list_tag *)') converts between void pointer and function pointer [-Wpedantic] 175 | vm_options[propNum++].extraInfo = vfprintf_hook; | ^ ~~~~~~~~~~~~~ init.c:179:38: warning: assigning to 'void *' from 'void (int)' converts between void pointer and function pointer [-Wpedantic] 179 | vm_options[propNum++].extraInfo = exit_hook; | ^ ~~~~~~~~~ 2 warnings generated. clang-19 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I. -I/usr/lib/jvm/java-21-openjdk-amd64/include -I/usr/lib/jvm/java-21-openjdk-amd64/include/linux -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c jri_glue.c -o jri_glue.o clang-19 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I. -I/usr/lib/jvm/java-21-openjdk-amd64/include -I/usr/lib/jvm/java-21-openjdk-amd64/include/linux -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c loader.c -o loader.o clang-19 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I. -I/usr/lib/jvm/java-21-openjdk-amd64/include -I/usr/lib/jvm/java-21-openjdk-amd64/include/linux -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c otables.c -o otables.o clang-19 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I. -I/usr/lib/jvm/java-21-openjdk-amd64/include -I/usr/lib/jvm/java-21-openjdk-amd64/include/linux -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c rJava.c -o rJava.o clang-19 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I. -I/usr/lib/jvm/java-21-openjdk-amd64/include -I/usr/lib/jvm/java-21-openjdk-amd64/include/linux -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c registration.c -o registration.o clang-19 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I. -I/usr/lib/jvm/java-21-openjdk-amd64/include -I/usr/lib/jvm/java-21-openjdk-amd64/include/linux -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c rjstring.c -o rjstring.o clang-19 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I. -I/usr/lib/jvm/java-21-openjdk-amd64/include -I/usr/lib/jvm/java-21-openjdk-amd64/include/linux -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c tools.c -o tools.o clang-19 -shared -L/home/hornik/tmp/R.check/r-devel-clang/Work/build/lib -Wl,-O1 -o rJava.so Rglue.o arrayc.o callJNI.o callback.o fields.o init.o jri_glue.o loader.o otables.o rJava.o registration.o rjstring.o tools.o -L/usr/lib/jvm/java-21-openjdk-amd64/lib/server -ljvm -L/home/hornik/tmp/R.check/r-devel-clang/Work/build/lib -lR (cd ../jri && make) make[2]: Entering directory '/home/hornik/tmp/scratch/RtmpBzNCme/R.INSTALL2fe59b70d633d0/rJava/jri' make -C src JRI.jar make[3]: Entering directory '/home/hornik/tmp/scratch/RtmpBzNCme/R.INSTALL2fe59b70d633d0/rJava/jri/src' /usr/bin/javac -h . -target 1.8 -source 1.8 -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 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. ../REXP.java:170: warning: [removal] finalize() in Object has been deprecated and marked for removal protected void finalize() throws Throwable { ^ ../REXP.java:175: warning: [removal] finalize() in Object has been deprecated and marked for removal super.finalize(); ^ Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 6 warnings if [ -n "" ]; then -d . -classpath . org.rosuda.JRI.Rengine; fi clang-19 -c -o Rengine.o Rengine.c -g -Iinclude -DRIF_HAS_CSTACK -DRIF_HAS_RSIGHAND -DHAVE_CONFIG_H -g -O3 -Wall -pedantic -I/usr/lib/jvm/java-21-openjdk-amd64/include -I/usr/lib/jvm/java-21-openjdk-amd64/include/linux -fpic -I/usr/lib/jvm/java-21-openjdk-amd64/include -I/usr/lib/jvm/java-21-openjdk-amd64/include/linux -I/home/hornik/tmp/R.check/r-devel-clang/Work/build/include -I/home/hornik/tmp/R.check/r-devel-clang/Work/build/include clang-19 -c -o jri.o jri.c -g -Iinclude -DRIF_HAS_CSTACK -DRIF_HAS_RSIGHAND -DHAVE_CONFIG_H -g -O3 -Wall -pedantic -I/usr/lib/jvm/java-21-openjdk-amd64/include -I/usr/lib/jvm/java-21-openjdk-amd64/include/linux -fpic -I/usr/lib/jvm/java-21-openjdk-amd64/include -I/usr/lib/jvm/java-21-openjdk-amd64/include/linux -I/home/hornik/tmp/R.check/r-devel-clang/Work/build/include -I/home/hornik/tmp/R.check/r-devel-clang/Work/build/include clang-19 -c -o Rcallbacks.o Rcallbacks.c -g -Iinclude -DRIF_HAS_CSTACK -DRIF_HAS_RSIGHAND -DHAVE_CONFIG_H -g -O3 -Wall -pedantic -I/usr/lib/jvm/java-21-openjdk-amd64/include -I/usr/lib/jvm/java-21-openjdk-amd64/include/linux -fpic -I/usr/lib/jvm/java-21-openjdk-amd64/include -I/usr/lib/jvm/java-21-openjdk-amd64/include/linux -I/home/hornik/tmp/R.check/r-devel-clang/Work/build/include -I/home/hornik/tmp/R.check/r-devel-clang/Work/build/include clang-19 -c -o Rinit.o Rinit.c -g -Iinclude -DRIF_HAS_CSTACK -DRIF_HAS_RSIGHAND -DHAVE_CONFIG_H -g -O3 -Wall -pedantic -I/usr/lib/jvm/java-21-openjdk-amd64/include -I/usr/lib/jvm/java-21-openjdk-amd64/include/linux -fpic -I/home/hornik/tmp/R.check/r-devel-clang/Work/build/include -I/home/hornik/tmp/R.check/r-devel-clang/Work/build/include clang-19 -c -o globals.o globals.c -g -Iinclude -DRIF_HAS_CSTACK -DRIF_HAS_RSIGHAND -DHAVE_CONFIG_H -g -O3 -Wall -pedantic -I/usr/lib/jvm/java-21-openjdk-amd64/include -I/usr/lib/jvm/java-21-openjdk-amd64/include/linux -fpic -I/usr/lib/jvm/java-21-openjdk-amd64/include -I/usr/lib/jvm/java-21-openjdk-amd64/include/linux clang-19 -c -o rjava.o rjava.c -g -Iinclude -DRIF_HAS_CSTACK -DRIF_HAS_RSIGHAND -DHAVE_CONFIG_H -g -O3 -Wall -pedantic -I/usr/lib/jvm/java-21-openjdk-amd64/include -I/usr/lib/jvm/java-21-openjdk-amd64/include/linux -fpic -I/usr/lib/jvm/java-21-openjdk-amd64/include -I/usr/lib/jvm/java-21-openjdk-amd64/include/linux clang-19 -c -o rjstring.o rjstring.c -g -Iinclude -DRIF_HAS_CSTACK -DRIF_HAS_RSIGHAND -DHAVE_CONFIG_H -g -O3 -Wall -pedantic -I/usr/lib/jvm/java-21-openjdk-amd64/include -I/usr/lib/jvm/java-21-openjdk-amd64/include/linux -fpic -I/usr/lib/jvm/java-21-openjdk-amd64/include -I/usr/lib/jvm/java-21-openjdk-amd64/include/linux -I/home/hornik/tmp/R.check/r-devel-clang/Work/build/include -I/home/hornik/tmp/R.check/r-devel-clang/Work/build/include clang-19 -o libjri.so Rengine.o jri.o Rcallbacks.o Rinit.o globals.o rjava.o rjstring.o -Wl,-O1 -shared -L/usr/lib/jvm/java-21-openjdk-amd64/lib/server -ljvm -Wl,--export-dynamic -Wl,-O1 -L/home/hornik/tmp/R.check/r-devel-clang/Work/build/lib -lR -lpcre2-8 -ldeflate -llzma -lbz2 -lz -ltirpc -lrt -ldl -lm -licuuc -licui18n /usr/bin/javac -h . -target 1.8 -source 1.8 -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 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. ../REXP.java:170: warning: [removal] finalize() in Object has been deprecated and marked for removal protected void finalize() throws Throwable { ^ ../REXP.java:175: warning: [removal] finalize() in Object has been deprecated and marked for removal super.finalize(); ^ Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 6 warnings /usr/bin/jar fc JRI.jar org libjri.so make[3]: Leaving directory '/home/hornik/tmp/scratch/RtmpBzNCme/R.INSTALL2fe59b70d633d0/rJava/jri/src' rm -f libjri.so cp src/libjri.so libjri.so /usr/bin/javac -h . -target 1.8 -source 1.8 -classpath src/JRI.jar -d examples examples/rtest.java warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 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 -h . -target 1.8 -source 1.8 -classpath src/JRI.jar -d examples examples/rtest2.java warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 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[2]: Leaving directory '/home/hornik/tmp/scratch/RtmpBzNCme/R.INSTALL2fe59b70d633d0/rJava/jri' make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpBzNCme/R.INSTALL2fe59b70d633d0/rJava/src' make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpBzNCme/R.INSTALL2fe59b70d633d0/rJava/src' make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpBzNCme/R.INSTALL2fe59b70d633d0/rJava/src' installing via 'install.libs.R' to /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/00LOCK-rJava/00new/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 from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (rJava)