HenrikBengtsson
commented
2 years ago Weird. when installing R to ~/software/cbi/software/ and then rJava, it works in both versions. But, when installing R to /software/c4/cbi/software/ and then rJava, it stalls with that R installation, but when used with R in ~/software/cbi/software/.
rJava installed with ~/software/cbi/software/R-4.2.0-gcc11
$ module load CBI CBI-prototype r/4.2.0-gcc11
$ R
> R.home()
[1] "/c4/home/henrik/software/cbi/software/R-4.2.0-gcc11/lib64/R"
> install.packages("rJava")
Installing package into '/c4/home/henrik/R/x86_64-pc-linux-gnu-library/4.2-CBI-gcc11'
(as 'lib' is unspecified)
trying URL 'https://cloud.r-project.org/src/contrib/rJava_1.0-6.tar.gz'
Content type 'application/x-gzip' length 1047062 bytes (1022 KB)
==================================================
downloaded 1022 KB
* installing *source* package ‘rJava’ ...
** package ‘rJava’ successfully unpacked and MD5 sums checked
** using staged installation
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... /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 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/lib/jvm/java-1.8.0/jre/bin/java'
archiver : '/usr/lib/jvm/java-1.8.0/bin/jar'
compiler : '/usr/lib/jvm/java-1.8.0/bin/javac'
header prep.: '/usr/lib/jvm/java-1.8.0/bin/javah'
cpp flags : '-I/usr/lib/jvm/java-1.8.0/include -I/usr/lib/jvm/java-1.8.0/include/linux'
java libs : '-L/usr/lib/jvm/java-1.8.0/jre/lib/amd64/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 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 (/scratch/henrik/Rtmp35edTR/R.INSTALL455a6e0ac56d/rJava/jri)
configure: running /bin/sh ./configure --disable-option-checking '--prefix=/usr/local' --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... 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 the compiler supports GNU C... yes
checking whether gcc accepts -g... yes
checking for gcc 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 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... 1.8.0_322
checking Java compatibility version (integer)... 8
checking whether /usr/lib/jvm/java-1.8.0/bin/javah actually works... yes
checking for target flags... -target 1.4 -source 1.4
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"/c4/home/henrik/software/cbi/software/R-4.2.0-gcc11/lib64/R/include" -DNDEBUG -I. -I/usr/lib/jvm/java-1.8.0/include -I/usr/lib/jvm/java-1.8.0/include/linux -I/usr/local/include -fpic -I/software/c4/cbi/software/gdal-2.4.4/include -I/software/c4/cbi/software/geos-3.9.1/include -c Rglue.c -o Rglue.o
gcc -I"/c4/home/henrik/software/cbi/software/R-4.2.0-gcc11/lib64/R/include" -DNDEBUG -I. -I/usr/lib/jvm/java-1.8.0/include -I/usr/lib/jvm/java-1.8.0/include/linux -I/usr/local/include -fpic -I/software/c4/cbi/software/gdal-2.4.4/include -I/software/c4/cbi/software/geos-3.9.1/include -c arrayc.c -o arrayc.o
gcc -I"/c4/home/henrik/software/cbi/software/R-4.2.0-gcc11/lib64/R/include" -DNDEBUG -I. -I/usr/lib/jvm/java-1.8.0/include -I/usr/lib/jvm/java-1.8.0/include/linux -I/usr/local/include -fpic -I/software/c4/cbi/software/gdal-2.4.4/include -I/software/c4/cbi/software/geos-3.9.1/include -c callJNI.c -o callJNI.o
gcc -I"/c4/home/henrik/software/cbi/software/R-4.2.0-gcc11/lib64/R/include" -DNDEBUG -I. -I/usr/lib/jvm/java-1.8.0/include -I/usr/lib/jvm/java-1.8.0/include/linux -I/usr/local/include -fpic -I/software/c4/cbi/software/gdal-2.4.4/include -I/software/c4/cbi/software/geos-3.9.1/include -c callback.c -o callback.o
gcc -I"/c4/home/henrik/software/cbi/software/R-4.2.0-gcc11/lib64/R/include" -DNDEBUG -I. -I/usr/lib/jvm/java-1.8.0/include -I/usr/lib/jvm/java-1.8.0/include/linux -I/usr/local/include -fpic -I/software/c4/cbi/software/gdal-2.4.4/include -I/software/c4/cbi/software/geos-3.9.1/include -c fields.c -o fields.o
gcc -I"/c4/home/henrik/software/cbi/software/R-4.2.0-gcc11/lib64/R/include" -DNDEBUG -I. -I/usr/lib/jvm/java-1.8.0/include -I/usr/lib/jvm/java-1.8.0/include/linux -I/usr/local/include -fpic -I/software/c4/cbi/software/gdal-2.4.4/include -I/software/c4/cbi/software/geos-3.9.1/include -c init.c -o init.o
gcc -I"/c4/home/henrik/software/cbi/software/R-4.2.0-gcc11/lib64/R/include" -DNDEBUG -I. -I/usr/lib/jvm/java-1.8.0/include -I/usr/lib/jvm/java-1.8.0/include/linux -I/usr/local/include -fpic -I/software/c4/cbi/software/gdal-2.4.4/include -I/software/c4/cbi/software/geos-3.9.1/include -c jri_glue.c -o jri_glue.o
gcc -I"/c4/home/henrik/software/cbi/software/R-4.2.0-gcc11/lib64/R/include" -DNDEBUG -I. -I/usr/lib/jvm/java-1.8.0/include -I/usr/lib/jvm/java-1.8.0/include/linux -I/usr/local/include -fpic -I/software/c4/cbi/software/gdal-2.4.4/include -I/software/c4/cbi/software/geos-3.9.1/include -c loader.c -o loader.o
gcc -I"/c4/home/henrik/software/cbi/software/R-4.2.0-gcc11/lib64/R/include" -DNDEBUG -I. -I/usr/lib/jvm/java-1.8.0/include -I/usr/lib/jvm/java-1.8.0/include/linux -I/usr/local/include -fpic -I/software/c4/cbi/software/gdal-2.4.4/include -I/software/c4/cbi/software/geos-3.9.1/include -c otables.c -o otables.o
gcc -I"/c4/home/henrik/software/cbi/software/R-4.2.0-gcc11/lib64/R/include" -DNDEBUG -I. -I/usr/lib/jvm/java-1.8.0/include -I/usr/lib/jvm/java-1.8.0/include/linux -I/usr/local/include -fpic -I/software/c4/cbi/software/gdal-2.4.4/include -I/software/c4/cbi/software/geos-3.9.1/include -c rJava.c -o rJava.o
gcc -I"/c4/home/henrik/software/cbi/software/R-4.2.0-gcc11/lib64/R/include" -DNDEBUG -I. -I/usr/lib/jvm/java-1.8.0/include -I/usr/lib/jvm/java-1.8.0/include/linux -I/usr/local/include -fpic -I/software/c4/cbi/software/gdal-2.4.4/include -I/software/c4/cbi/software/geos-3.9.1/include -c registration.c -o registration.o
gcc -I"/c4/home/henrik/software/cbi/software/R-4.2.0-gcc11/lib64/R/include" -DNDEBUG -I. -I/usr/lib/jvm/java-1.8.0/include -I/usr/lib/jvm/java-1.8.0/include/linux -I/usr/local/include -fpic -I/software/c4/cbi/software/gdal-2.4.4/include -I/software/c4/cbi/software/geos-3.9.1/include -c tools.c -o tools.o
gcc -shared -L/c4/home/henrik/software/cbi/software/R-4.2.0-gcc11/lib64/R/lib -L/software/c4/cbi/software/gdal-2.4.4/lib -L/software/c4/cbi/software/geos-3.9.1/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 registration.o tools.o -L/usr/lib/jvm/java-1.8.0/jre/lib/amd64/server -ljvm -L/c4/home/henrik/software/cbi/software/R-4.2.0-gcc11/lib64/R/lib -lR
(cd ../jri && make)
make[1]: Entering directory '/scratch/henrik/Rtmp35edTR/R.INSTALL455a6e0ac56d/rJava/jri'
make -C src JRI.jar
make[2]: Entering directory '/scratch/henrik/Rtmp35edTR/R.INSTALL455a6e0ac56d/rJava/jri/src'
/usr/lib/jvm/java-1.8.0/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
if [ -n "/usr/lib/jvm/java-1.8.0/bin/javah" ]; then /usr/lib/jvm/java-1.8.0/bin/javah -d . -classpath . org.rosuda.JRI.Rengine; fi
gcc -c -o Rengine.o Rengine.c -g -Iinclude -DRIF_HAS_CSTACK -DRIF_HAS_RSIGHAND -DHAVE_CONFIG_H -I/software/c4/cbi/software/gdal-2.4.4/include -I/software/c4/cbi/software/geos-3.9.1/include -I/usr/lib/jvm/java-1.8.0/include -I/usr/lib/jvm/java-1.8.0/include/linux -fpic -I/usr/lib/jvm/java-1.8.0/include -I/usr/lib/jvm/java-1.8.0/include/linux -I/c4/home/henrik/software/cbi/software/R-4.2.0-gcc11/lib64/R/include -I/c4/home/henrik/software/cbi/software/R-4.2.0-gcc11/lib64/R/include
gcc -c -o jri.o jri.c -g -Iinclude -DRIF_HAS_CSTACK -DRIF_HAS_RSIGHAND -DHAVE_CONFIG_H -I/software/c4/cbi/software/gdal-2.4.4/include -I/software/c4/cbi/software/geos-3.9.1/include -I/usr/lib/jvm/java-1.8.0/include -I/usr/lib/jvm/java-1.8.0/include/linux -fpic -I/usr/lib/jvm/java-1.8.0/include -I/usr/lib/jvm/java-1.8.0/include/linux -I/c4/home/henrik/software/cbi/software/R-4.2.0-gcc11/lib64/R/include -I/c4/home/henrik/software/cbi/software/R-4.2.0-gcc11/lib64/R/include
gcc -c -o Rcallbacks.o Rcallbacks.c -g -Iinclude -DRIF_HAS_CSTACK -DRIF_HAS_RSIGHAND -DHAVE_CONFIG_H -I/software/c4/cbi/software/gdal-2.4.4/include -I/software/c4/cbi/software/geos-3.9.1/include -I/usr/lib/jvm/java-1.8.0/include -I/usr/lib/jvm/java-1.8.0/include/linux -fpic -I/usr/lib/jvm/java-1.8.0/include -I/usr/lib/jvm/java-1.8.0/include/linux -I/c4/home/henrik/software/cbi/software/R-4.2.0-gcc11/lib64/R/include -I/c4/home/henrik/software/cbi/software/R-4.2.0-gcc11/lib64/R/include
gcc -c -o Rinit.o Rinit.c -g -Iinclude -DRIF_HAS_CSTACK -DRIF_HAS_RSIGHAND -DHAVE_CONFIG_H -I/software/c4/cbi/software/gdal-2.4.4/include -I/software/c4/cbi/software/geos-3.9.1/include -I/usr/lib/jvm/java-1.8.0/include -I/usr/lib/jvm/java-1.8.0/include/linux -fpic -I/c4/home/henrik/software/cbi/software/R-4.2.0-gcc11/lib64/R/include -I/c4/home/henrik/software/cbi/software/R-4.2.0-gcc11/lib64/R/include
gcc -c -o globals.o globals.c -g -Iinclude -DRIF_HAS_CSTACK -DRIF_HAS_RSIGHAND -DHAVE_CONFIG_H -I/software/c4/cbi/software/gdal-2.4.4/include -I/software/c4/cbi/software/geos-3.9.1/include -I/usr/lib/jvm/java-1.8.0/include -I/usr/lib/jvm/java-1.8.0/include/linux -fpic -I/usr/lib/jvm/java-1.8.0/include -I/usr/lib/jvm/java-1.8.0/include/linux
gcc -c -o rjava.o rjava.c -g -Iinclude -DRIF_HAS_CSTACK -DRIF_HAS_RSIGHAND -DHAVE_CONFIG_H -I/software/c4/cbi/software/gdal-2.4.4/include -I/software/c4/cbi/software/geos-3.9.1/include -I/usr/lib/jvm/java-1.8.0/include -I/usr/lib/jvm/java-1.8.0/include/linux -fpic -I/usr/lib/jvm/java-1.8.0/include -I/usr/lib/jvm/java-1.8.0/include/linux
gcc -o libjri.so Rengine.o jri.o Rcallbacks.o Rinit.o globals.o rjava.o -shared -L/usr/lib/jvm/java-1.8.0/jre/lib/amd64/server -ljvm -Wl,--export-dynamic -fopenmp -L/software/c4/cbi/software/gdal-2.4.4/lib -L/software/c4/cbi/software/geos-3.9.1/lib -L/c4/home/henrik/software/cbi/software/R-4.2.0-gcc11/lib64/R/lib -lR -lpcre2-8 -llzma -lbz2 -lz -lrt -ldl -lm -licuuc -licui18n
/usr/lib/jvm/java-1.8.0/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/lib/jvm/java-1.8.0/bin/jar fc JRI.jar org libjri.so
make[2]: Leaving directory '/scratch/henrik/Rtmp35edTR/R.INSTALL455a6e0ac56d/rJava/jri/src'
rm -f libjri.so
cp src/libjri.so libjri.so
/usr/lib/jvm/java-1.8.0/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
make[1]: Leaving directory '/scratch/henrik/Rtmp35edTR/R.INSTALL455a6e0ac56d/rJava/jri'
installing via 'install.libs.R' to /c4/home/henrik/R/x86_64-pc-linux-gnu-library/4.2-CBI-gcc11/00LOCK-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)
The downloaded source packages are in
'/scratch/henrik/RtmpAk9J0N/downloaded_packages'
> res <- rJava:::.jinit()
TRACKER: Options added: [n=1] 'java.parameters'.
TRACKER: loadedNamespaces() changed: 2 packages loaded ('crayon', 'rJava')
> CBI r/4.2.0-gcc11
$ module unload CBI-prototype
$ module load CBI r/4.2.0-gcc11
$ R
> R.home()
[1] "/software/c4/cbi/software/R-4.2.0-gcc11/lib64/R"
> res <- rJava:::.jinit()
TRACKER: Environment variables changed: [n=2] 'COLUMNS', 'LINES'.
TRACKER: Options added: [n=1] 'java.parameters'.
TRACKER: loadedNamespaces() changed: 2 packages loaded ('crayon', 'rJava')rJava installed with /software/c4/cbi/software/R-4.2.0-gcc11
$ module unload CBI-prototype
$ module load CBI r/4.2.0-gcc11
$ R
> R.home()
[1] "/software/c4/cbi/software/R-4.2.0-gcc11/lib64/R"
> install.packages("rJava")
Installing package into '/c4/home/henrik/R/x86_64-pc-linux-gnu-library/4.2-CBI-gcc11-sandbox'
(as 'lib' is unspecified)
trying URL 'https://cloud.r-project.org/src/contrib/rJava_1.0-6.tar.gz'
Content type 'application/x-gzip' length 1047062 bytes (1022 KB)
==================================================
downloaded 1022 KB
* installing *source* package ‘rJava’ ...
** package ‘rJava’ successfully unpacked and MD5 sums checked
** using staged installation
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... /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 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/lib/jvm/java-1.8.0/jre/bin/java'
archiver : '/usr/lib/jvm/java-1.8.0/bin/jar'
compiler : '/usr/lib/jvm/java-1.8.0/bin/javac'
header prep.: '/usr/lib/jvm/java-1.8.0/bin/javah'
cpp flags : '-I/usr/lib/jvm/java-1.8.0/include -I/usr/lib/jvm/java-1.8.0/include/linux'
java libs : '-L/usr/lib/jvm/java-1.8.0/jre/lib/amd64/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 (/scratch/henrik/RtmpQaBkx7/R.INSTALL5c9d4fb574a5/rJava/jri)
configure: running /bin/sh ./configure --disable-option-checking '--prefix=/usr/local' --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... 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 the compiler supports GNU C... yes
checking whether gcc accepts -g... yes
checking for gcc 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... 1.8.0_322
checking Java compatibility version (integer)... 8
checking whether /usr/lib/jvm/java-1.8.0/bin/javah actually works... yes
checking for target flags... -target 1.4 -source 1.4
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"/software/c4/cbi/software/R-4.2.0-gcc11/lib64/R/include" -DNDEBUG -I. -I/usr/lib/jvm/java-1.8.0/include -I/usr/lib/jvm/java-1.8.0/include/linux -I/usr/local/include -fpic -g -O2 -c Rglue.c -o Rglue.o
gcc -I"/software/c4/cbi/software/R-4.2.0-gcc11/lib64/R/include" -DNDEBUG -I. -I/usr/lib/jvm/java-1.8.0/include -I/usr/lib/jvm/java-1.8.0/include/linux -I/usr/local/include -fpic -g -O2 -c arrayc.c -o arrayc.o
gcc -I"/software/c4/cbi/software/R-4.2.0-gcc11/lib64/R/include" -DNDEBUG -I. -I/usr/lib/jvm/java-1.8.0/include -I/usr/lib/jvm/java-1.8.0/include/linux -I/usr/local/include -fpic -g -O2 -c callJNI.c -o callJNI.o
gcc -I"/software/c4/cbi/software/R-4.2.0-gcc11/lib64/R/include" -DNDEBUG -I. -I/usr/lib/jvm/java-1.8.0/include -I/usr/lib/jvm/java-1.8.0/include/linux -I/usr/local/include -fpic -g -O2 -c callback.c -o callback.o
gcc -I"/software/c4/cbi/software/R-4.2.0-gcc11/lib64/R/include" -DNDEBUG -I. -I/usr/lib/jvm/java-1.8.0/include -I/usr/lib/jvm/java-1.8.0/include/linux -I/usr/local/include -fpic -g -O2 -c fields.c -o fields.o
gcc -I"/software/c4/cbi/software/R-4.2.0-gcc11/lib64/R/include" -DNDEBUG -I. -I/usr/lib/jvm/java-1.8.0/include -I/usr/lib/jvm/java-1.8.0/include/linux -I/usr/local/include -fpic -g -O2 -c init.c -o init.o
gcc -I"/software/c4/cbi/software/R-4.2.0-gcc11/lib64/R/include" -DNDEBUG -I. -I/usr/lib/jvm/java-1.8.0/include -I/usr/lib/jvm/java-1.8.0/include/linux -I/usr/local/include -fpic -g -O2 -c jri_glue.c -o jri_glue.o
gcc -I"/software/c4/cbi/software/R-4.2.0-gcc11/lib64/R/include" -DNDEBUG -I. -I/usr/lib/jvm/java-1.8.0/include -I/usr/lib/jvm/java-1.8.0/include/linux -I/usr/local/include -fpic -g -O2 -c loader.c -o loader.o
gcc -I"/software/c4/cbi/software/R-4.2.0-gcc11/lib64/R/include" -DNDEBUG -I. -I/usr/lib/jvm/java-1.8.0/include -I/usr/lib/jvm/java-1.8.0/include/linux -I/usr/local/include -fpic -g -O2 -c otables.c -o otables.o
gcc -I"/software/c4/cbi/software/R-4.2.0-gcc11/lib64/R/include" -DNDEBUG -I. -I/usr/lib/jvm/java-1.8.0/include -I/usr/lib/jvm/java-1.8.0/include/linux -I/usr/local/include -fpic -g -O2 -c rJava.c -o rJava.o
gcc -I"/software/c4/cbi/software/R-4.2.0-gcc11/lib64/R/include" -DNDEBUG -I. -I/usr/lib/jvm/java-1.8.0/include -I/usr/lib/jvm/java-1.8.0/include/linux -I/usr/local/include -fpic -g -O2 -c registration.c -o registration.o
gcc -I"/software/c4/cbi/software/R-4.2.0-gcc11/lib64/R/include" -DNDEBUG -I. -I/usr/lib/jvm/java-1.8.0/include -I/usr/lib/jvm/java-1.8.0/include/linux -I/usr/local/include -fpic -g -O2 -c tools.c -o tools.o
gcc -shared -L/software/c4/cbi/software/R-4.2.0-gcc11/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 registration.o tools.o -L/usr/lib/jvm/java-1.8.0/jre/lib/amd64/server -ljvm -L/software/c4/cbi/software/R-4.2.0-gcc11/lib64/R/lib -lR
(cd ../jri && make)
make[1]: Entering directory '/scratch/henrik/RtmpQaBkx7/R.INSTALL5c9d4fb574a5/rJava/jri'
make -C src JRI.jar
make[2]: Entering directory '/scratch/henrik/RtmpQaBkx7/R.INSTALL5c9d4fb574a5/rJava/jri/src'
/usr/lib/jvm/java-1.8.0/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
if [ -n "/usr/lib/jvm/java-1.8.0/bin/javah" ]; then /usr/lib/jvm/java-1.8.0/bin/javah -d . -classpath . org.rosuda.JRI.Rengine; fi
gcc -c -o Rengine.o Rengine.c -g -Iinclude -DRIF_HAS_CSTACK -DRIF_HAS_RSIGHAND -DHAVE_CONFIG_H -g -O2 -I/usr/lib/jvm/java-1.8.0/include -I/usr/lib/jvm/java-1.8.0/include/linux -fpic -I/usr/lib/jvm/java-1.8.0/include -I/usr/lib/jvm/java-1.8.0/include/linux -I/software/c4/cbi/software/R-4.2.0-gcc11/lib64/R/include -I/software/c4/cbi/software/R-4.2.0-gcc11/lib64/R/include
gcc -c -o jri.o jri.c -g -Iinclude -DRIF_HAS_CSTACK -DRIF_HAS_RSIGHAND -DHAVE_CONFIG_H -g -O2 -I/usr/lib/jvm/java-1.8.0/include -I/usr/lib/jvm/java-1.8.0/include/linux -fpic -I/usr/lib/jvm/java-1.8.0/include -I/usr/lib/jvm/java-1.8.0/include/linux -I/software/c4/cbi/software/R-4.2.0-gcc11/lib64/R/include -I/software/c4/cbi/software/R-4.2.0-gcc11/lib64/R/include
gcc -c -o Rcallbacks.o Rcallbacks.c -g -Iinclude -DRIF_HAS_CSTACK -DRIF_HAS_RSIGHAND -DHAVE_CONFIG_H -g -O2 -I/usr/lib/jvm/java-1.8.0/include -I/usr/lib/jvm/java-1.8.0/include/linux -fpic -I/usr/lib/jvm/java-1.8.0/include -I/usr/lib/jvm/java-1.8.0/include/linux -I/software/c4/cbi/software/R-4.2.0-gcc11/lib64/R/include -I/software/c4/cbi/software/R-4.2.0-gcc11/lib64/R/include
gcc -c -o Rinit.o Rinit.c -g -Iinclude -DRIF_HAS_CSTACK -DRIF_HAS_RSIGHAND -DHAVE_CONFIG_H -g -O2 -I/usr/lib/jvm/java-1.8.0/include -I/usr/lib/jvm/java-1.8.0/include/linux -fpic -I/software/c4/cbi/software/R-4.2.0-gcc11/lib64/R/include -I/software/c4/cbi/software/R-4.2.0-gcc11/lib64/R/include
gcc -c -o globals.o globals.c -g -Iinclude -DRIF_HAS_CSTACK -DRIF_HAS_RSIGHAND -DHAVE_CONFIG_H -g -O2 -I/usr/lib/jvm/java-1.8.0/include -I/usr/lib/jvm/java-1.8.0/include/linux -fpic -I/usr/lib/jvm/java-1.8.0/include -I/usr/lib/jvm/java-1.8.0/include/linux
gcc -c -o rjava.o rjava.c -g -Iinclude -DRIF_HAS_CSTACK -DRIF_HAS_RSIGHAND -DHAVE_CONFIG_H -g -O2 -I/usr/lib/jvm/java-1.8.0/include -I/usr/lib/jvm/java-1.8.0/include/linux -fpic -I/usr/lib/jvm/java-1.8.0/include -I/usr/lib/jvm/java-1.8.0/include/linux
gcc -o libjri.so Rengine.o jri.o Rcallbacks.o Rinit.o globals.o rjava.o -shared -L/usr/lib/jvm/java-1.8.0/jre/lib/amd64/server -ljvm -Wl,--export-dynamic -fopenmp -L/usr/local/lib64 -L/software/c4/cbi/software/R-4.2.0-gcc11/lib64/R/lib -lR -lpcre2-8 -llzma -lbz2 -lz -lrt -ldl -lm -licuuc -licui18n
/usr/lib/jvm/java-1.8.0/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/lib/jvm/java-1.8.0/bin/jar fc JRI.jar org libjri.so
make[2]: Leaving directory '/scratch/henrik/RtmpQaBkx7/R.INSTALL5c9d4fb574a5/rJava/jri/src'
rm -f libjri.so
cp src/libjri.so libjri.so
/usr/lib/jvm/java-1.8.0/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/lib/jvm/java-1.8.0/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 '/scratch/henrik/RtmpQaBkx7/R.INSTALL5c9d4fb574a5/rJava/jri'
installing via 'install.libs.R' to /c4/home/henrik/R/x86_64-pc-linux-gnu-library/4.2-CBI-gcc11-sandbox/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)
The downloaded source packages are in
'/scratch/henrik/RtmphCfDqN/downloaded_packages'
> res <- rJava:::.jinit()
## ... STALLS! ...$ module load CBI-prototype
$ module load CBI r/4.2.0-gcc11
$ R
> R.home()
[1] "/software/c4/cbi/software/R-4.2.0-gcc11/lib64/R"
> res <- rJava:::.jinit()
>
Issue
The following call stalls on C4:
but it works on Wynton.
Troubleshooting
It happens in the following step:
Session infos
C4
Wynton