* installing *source* package ‘rJava’ ...
** package ‘rJava’ successfully unpacked and MD5 sums checked
** using staged installation
checking for gcc... gcc-13
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-13 accepts -g... yes
checking for gcc-13 option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc-13 -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-13 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-11/bin/java'
archiver : '/usr/lib/jvm/java-11/bin/jar'
compiler : '/usr/lib/jvm/java-11/bin/javac'
header prep.: ''
cpp flags : '-I/usr/lib/jvm/java-11/include -I/usr/lib/jvm/java-11/include/linux'
java libs : '-L/usr/lib/jvm/java-11/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)... no
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... no
configure: creating ./config.status
config.status: creating src/Makevars
config.status: creating R/zzz.R
config.status: creating src/config.h
** libs
using C compiler: ‘gcc-13 (GCC) 13.1.0’
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/rJava/src'
gcc-13 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I. -I/usr/lib/jvm/java-11/include -I/usr/lib/jvm/java-11/include/linux -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c Rglue.c -o Rglue.o
In file included from Rglue.c:2:
rJava.h:123:1: warning: function declaration isn't a prototype [-Wstrict-prototypes]
123 | HIDE JNIEnv* getJNIEnv();
| ^~~~
rJava.h:167:1: warning: function declaration isn't a prototype [-Wstrict-prototypes]
167 | HIDE SEXP R_getUnboundValue() ;
| ^~~~
Rglue.c:39:11: warning: function declaration isn't a prototype [-Wstrict-prototypes]
39 | REPC SEXP RJava_has_jri_cb() {
| ^~~~~~~~~~~~~~~~
Rglue.c:1214:11: warning: function declaration isn't a prototype [-Wstrict-prototypes]
1214 | REPC SEXP RpollException() {
| ^~~~~~~~~~~~~~
Rglue.c:1225:10: warning: function declaration isn't a prototype [-Wstrict-prototypes]
1225 | REP void RclearException() {
| ^~~~~~~~~~~~~~~
Rglue.c:1051:13: warning: 'new_jrectRef' defined but not used [-Wunused-function]
1051 | static SEXP new_jrectRef(JNIEnv *env, jobject a, const char *sig, SEXP dim ) {
| ^~~~~~~~~~~~
gcc-13 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I. -I/usr/lib/jvm/java-11/include -I/usr/lib/jvm/java-11/include/linux -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c arrayc.c -o arrayc.o
In file included from arrayc.c:7:
rJava.h:123:1: warning: function declaration isn't a prototype [-Wstrict-prototypes]
123 | HIDE JNIEnv* getJNIEnv();
| ^~~~
rJava.h:167:1: warning: function declaration isn't a prototype [-Wstrict-prototypes]
167 | HIDE SEXP R_getUnboundValue() ;
| ^~~~
gcc-13 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I. -I/usr/lib/jvm/java-11/include -I/usr/lib/jvm/java-11/include/linux -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c callJNI.c -o callJNI.o
In file included from callJNI.c:3:
rJava.h:123:1: warning: function declaration isn't a prototype [-Wstrict-prototypes]
123 | HIDE JNIEnv* getJNIEnv();
| ^~~~
rJava.h:167:1: warning: function declaration isn't a prototype [-Wstrict-prototypes]
167 | HIDE SEXP R_getUnboundValue() ;
| ^~~~
gcc-13 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I. -I/usr/lib/jvm/java-11/include -I/usr/lib/jvm/java-11/include/linux -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c callback.c -o callback.o
In file included from callback.c:1:
rJava.h:123:1: warning: function declaration isn't a prototype [-Wstrict-prototypes]
123 | HIDE JNIEnv* getJNIEnv();
| ^~~~
rJava.h:167:1: warning: function declaration isn't a prototype [-Wstrict-prototypes]
167 | HIDE SEXP R_getUnboundValue() ;
| ^~~~
gcc-13 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I. -I/usr/lib/jvm/java-11/include -I/usr/lib/jvm/java-11/include/linux -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c fields.c -o fields.o
In file included from fields.c:7:
rJava.h:123:1: warning: function declaration isn't a prototype [-Wstrict-prototypes]
123 | HIDE JNIEnv* getJNIEnv();
| ^~~~
rJava.h:167:1: warning: function declaration isn't a prototype [-Wstrict-prototypes]
167 | HIDE SEXP R_getUnboundValue() ;
| ^~~~
fields.c: In function 'inputToClass':
fields.c:91:13: warning: unused variable 'c' [-Wunused-variable]
91 | char *c = clnam;
| ^
fields.c: In function 'RgetField':
fields.c:149:9: warning: unused variable 'clnam' [-Wunused-variable]
149 | char *clnam = 0, *detsig = 0;
| ^~~~~
gcc-13 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I. -I/usr/lib/jvm/java-11/include -I/usr/lib/jvm/java-11/include/linux -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c init.c -o init.o
In file included from init.c:1:
rJava.h:123:1: warning: function declaration isn't a prototype [-Wstrict-prototypes]
123 | HIDE JNIEnv* getJNIEnv();
| ^~~~
rJava.h:167:1: warning: function declaration isn't a prototype [-Wstrict-prototypes]
167 | HIDE SEXP R_getUnboundValue() ;
| ^~~~
init.c: In function 'initJVM':
init.c:163:38: warning: ISO C forbids assignment between function pointer and 'void *' [-Wpedantic]
163 | vm_options[propNum++].extraInfo = vfprintf_hook;
| ^
init.c:167:38: warning: ISO C forbids assignment between function pointer and 'void *' [-Wpedantic]
167 | vm_options[propNum++].extraInfo = exit_hook;
| ^
init.c: At top level:
init.c:751:10: warning: function declaration isn't a prototype [-Wstrict-prototypes]
751 | REP void doneJVM() {
| ^~~~~~~
init.c:762:11: warning: function declaration isn't a prototype [-Wstrict-prototypes]
762 | REPC SEXP initRJavaTools(){
| ^~~~~~~~~~~~~~
gcc-13 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I. -I/usr/lib/jvm/java-11/include -I/usr/lib/jvm/java-11/include/linux -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c jri_glue.c -o jri_glue.o
In file included from jri_glue.c:3:
rJava.h:123:1: warning: function declaration isn't a prototype [-Wstrict-prototypes]
123 | HIDE JNIEnv* getJNIEnv();
| ^~~~
rJava.h:167:1: warning: function declaration isn't a prototype [-Wstrict-prototypes]
167 | HIDE SEXP R_getUnboundValue() ;
| ^~~~
gcc-13 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I. -I/usr/lib/jvm/java-11/include -I/usr/lib/jvm/java-11/include/linux -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c loader.c -o loader.o
In file included from loader.c:7:
rJava.h:123:1: warning: function declaration isn't a prototype [-Wstrict-prototypes]
123 | HIDE JNIEnv* getJNIEnv();
| ^~~~
rJava.h:167:1: warning: function declaration isn't a prototype [-Wstrict-prototypes]
167 | HIDE SEXP R_getUnboundValue() ;
| ^~~~
loader.c:34:11: warning: function declaration isn't a prototype [-Wstrict-prototypes]
34 | REPC SEXP RJava_primary_class_loader() {
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
gcc-13 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I. -I/usr/lib/jvm/java-11/include -I/usr/lib/jvm/java-11/include/linux -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c otables.c -o otables.o
In file included from otables.c:1:
rJava.h:123:1: warning: function declaration isn't a prototype [-Wstrict-prototypes]
123 | HIDE JNIEnv* getJNIEnv();
| ^~~~
rJava.h:167:1: warning: function declaration isn't a prototype [-Wstrict-prototypes]
167 | HIDE SEXP R_getUnboundValue() ;
| ^~~~
otables.c:11:11: warning: function declaration isn't a prototype [-Wstrict-prototypes]
11 | HIDE SEXP R_getUnboundValue() {
| ^~~~~~~~~~~~~~~~~
gcc-13 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I. -I/usr/lib/jvm/java-11/include -I/usr/lib/jvm/java-11/include/linux -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c rJava.c -o rJava.o
In file included from rJava.c:4:
rJava.h:123:1: warning: function declaration isn't a prototype [-Wstrict-prototypes]
123 | HIDE JNIEnv* getJNIEnv();
| ^~~~
rJava.h:167:1: warning: function declaration isn't a prototype [-Wstrict-prototypes]
167 | HIDE SEXP R_getUnboundValue() ;
| ^~~~
rJava.c:14:13: warning: function declaration isn't a prototype [-Wstrict-prototypes]
14 | static SEXP getCurrentCall() {
| ^~~~~~~~~~~~~~
rJava.c:142:14: warning: function declaration isn't a prototype [-Wstrict-prototypes]
142 | HIDE JNIEnv *getJNIEnv()
| ^~~~~~~~~
gcc-13 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I. -I/usr/lib/jvm/java-11/include -I/usr/lib/jvm/java-11/include/linux -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c registration.c -o registration.o
registration.c:6:5: warning: function declaration isn't a prototype [-Wstrict-prototypes]
6 | int dummy__() {
| ^~~~~~~
gcc-13 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I. -I/usr/lib/jvm/java-11/include -I/usr/lib/jvm/java-11/include/linux -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c tools.c -o tools.o
In file included from tools.c:7:
rJava.h:123:1: warning: function declaration isn't a prototype [-Wstrict-prototypes]
123 | HIDE JNIEnv* getJNIEnv();
| ^~~~
rJava.h:167:1: warning: function declaration isn't a prototype [-Wstrict-prototypes]
167 | HIDE SEXP R_getUnboundValue() ;
| ^~~~
tools.c:109:11: warning: function declaration isn't a prototype [-Wstrict-prototypes]
109 | REPC SEXP RgetNullReference() {
| ^~~~~~~~~~~~~~~~~
tools.c:131:11: warning: function declaration isn't a prototype [-Wstrict-prototypes]
131 | REPC SEXP RJava_checkJVM() {
| ^~~~~~~~~~~~~~
tools.c:141:11: warning: function declaration isn't a prototype [-Wstrict-prototypes]
141 | REPC SEXP RJava_needs_init() {
| ^~~~~~~~~~~~~~~~
gcc-13 -shared -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -L/usr/local/gcc13/lib64 -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-11/lib/server -ljvm
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/rJava/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/rJava/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/rJava/src'
installing via 'install.libs.R' to /data/gannet/ripley/R/packages/tests-devel/rJava.Rcheck/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)