* installing *source* package ‘rJava’ ...
** package ‘rJava’ successfully unpacked and MD5 sums checked
** using staged installation
checking for gcc... /usr/local/clang16/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/clang16/bin/clang accepts -g... yes
checking for /usr/local/clang16/bin/clang option to accept ISO C89... none needed
checking how to run the C preprocessor... /usr/local/clang16/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... 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/clang16/bin/clang supports static inline...
no
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-17/bin/java'
archiver : '/usr/lib/jvm/java-17/bin/jar'
compiler : '/usr/lib/jvm/java-17/bin/javac'
header prep.: ''
cpp flags : '-I/usr/lib/jvm/java-17/include -I/usr/lib/jvm/java-17/include/linux'
java libs : '-L/usr/lib/jvm/java-17/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: ‘clang version 16.0.4’
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/rJava/src'
/usr/local/clang16/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I. -I/usr/lib/jvm/java-17/include -I/usr/lib/jvm/java-17/include/linux -isystem /usr/local/clang16/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c Rglue.c -o Rglue.o
In file included from Rglue.c:2:
./rJava.h:123:23: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
HIDE JNIEnv* getJNIEnv();
^
void
./rJava.h:167:28: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
HIDE SEXP R_getUnboundValue() ;
^
void
Rglue.c:39:27: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
REPC SEXP RJava_has_jri_cb() {
^
void
Rglue.c:406:7: warning: variable 'i' set but not used [-Wunused-but-set-variable]
int i=0;
^
Rglue.c:1214:25: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
REPC SEXP RpollException() {
^
void
Rglue.c:1225:25: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
REP void RclearException() {
^
void
Rglue.c:1051:13: warning: unused function 'new_jrectRef' [-Wunused-function]
static SEXP new_jrectRef(JNIEnv *env, jobject a, const char *sig, SEXP dim ) {
^
7 warnings generated.
/usr/local/clang16/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I. -I/usr/lib/jvm/java-17/include -I/usr/lib/jvm/java-17/include/linux -isystem /usr/local/clang16/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c arrayc.c -o arrayc.o
In file included from arrayc.c:7:
./rJava.h:123:23: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
HIDE JNIEnv* getJNIEnv();
^
void
./rJava.h:167:28: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
HIDE SEXP R_getUnboundValue() ;
^
void
2 warnings generated.
/usr/local/clang16/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I. -I/usr/lib/jvm/java-17/include -I/usr/lib/jvm/java-17/include/linux -isystem /usr/local/clang16/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c callJNI.c -o callJNI.o
In file included from callJNI.c:3:
./rJava.h:123:23: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
HIDE JNIEnv* getJNIEnv();
^
void
./rJava.h:167:28: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
HIDE SEXP R_getUnboundValue() ;
^
void
2 warnings generated.
/usr/local/clang16/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I. -I/usr/lib/jvm/java-17/include -I/usr/lib/jvm/java-17/include/linux -isystem /usr/local/clang16/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c callback.c -o callback.o
In file included from callback.c:1:
./rJava.h:123:23: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
HIDE JNIEnv* getJNIEnv();
^
void
./rJava.h:167:28: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
HIDE SEXP R_getUnboundValue() ;
^
void
2 warnings generated.
/usr/local/clang16/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I. -I/usr/lib/jvm/java-17/include -I/usr/lib/jvm/java-17/include/linux -isystem /usr/local/clang16/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c fields.c -o fields.o
In file included from fields.c:7:
./rJava.h:123:23: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
HIDE JNIEnv* getJNIEnv();
^
void
./rJava.h:167:28: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
HIDE SEXP R_getUnboundValue() ;
^
void
fields.c:91:13: warning: unused variable 'c' [-Wunused-variable]
char *c = clnam;
^
fields.c:149:9: warning: unused variable 'clnam' [-Wunused-variable]
char *clnam = 0, *detsig = 0;
^
4 warnings generated.
/usr/local/clang16/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I. -I/usr/lib/jvm/java-17/include -I/usr/lib/jvm/java-17/include/linux -isystem /usr/local/clang16/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c init.c -o init.o
In file included from init.c:1:
./rJava.h:123:23: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
HIDE JNIEnv* getJNIEnv();
^
void
./rJava.h:167:28: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
HIDE SEXP R_getUnboundValue() ;
^
void
init.c:163:38: 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]
vm_options[propNum++].extraInfo = vfprintf_hook;
^ ~~~~~~~~~~~~~
init.c:167:38: warning: assigning to 'void *' from 'void (int)' converts between void pointer and function pointer [-Wpedantic]
vm_options[propNum++].extraInfo = exit_hook;
^ ~~~~~~~~~
init.c:751:17: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
REP void doneJVM() {
^
void
init.c:762:25: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
REPC SEXP initRJavaTools(){
^
void
6 warnings generated.
/usr/local/clang16/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I. -I/usr/lib/jvm/java-17/include -I/usr/lib/jvm/java-17/include/linux -isystem /usr/local/clang16/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c jri_glue.c -o jri_glue.o
In file included from jri_glue.c:3:
./rJava.h:123:23: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
HIDE JNIEnv* getJNIEnv();
^
void
./rJava.h:167:28: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
HIDE SEXP R_getUnboundValue() ;
^
void
2 warnings generated.
/usr/local/clang16/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I. -I/usr/lib/jvm/java-17/include -I/usr/lib/jvm/java-17/include/linux -isystem /usr/local/clang16/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c loader.c -o loader.o
In file included from loader.c:7:
./rJava.h:123:23: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
HIDE JNIEnv* getJNIEnv();
^
void
./rJava.h:167:28: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
HIDE SEXP R_getUnboundValue() ;
^
void
loader.c:34:37: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
REPC SEXP RJava_primary_class_loader() {
^
void
3 warnings generated.
/usr/local/clang16/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I. -I/usr/lib/jvm/java-17/include -I/usr/lib/jvm/java-17/include/linux -isystem /usr/local/clang16/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c otables.c -o otables.o
In file included from otables.c:1:
./rJava.h:123:23: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
HIDE JNIEnv* getJNIEnv();
^
void
./rJava.h:167:28: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
HIDE SEXP R_getUnboundValue() ;
^
void
otables.c:11:28: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
HIDE SEXP R_getUnboundValue() {
^
void
3 warnings generated.
/usr/local/clang16/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I. -I/usr/lib/jvm/java-17/include -I/usr/lib/jvm/java-17/include/linux -isystem /usr/local/clang16/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c rJava.c -o rJava.o
In file included from rJava.c:4:
./rJava.h:123:23: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
HIDE JNIEnv* getJNIEnv();
^
void
./rJava.h:167:28: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
HIDE SEXP R_getUnboundValue() ;
^
void
rJava.c:14:27: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
static SEXP getCurrentCall() {
^
void
rJava.c:142:23: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
HIDE JNIEnv *getJNIEnv()
^
void
4 warnings generated.
/usr/local/clang16/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I. -I/usr/lib/jvm/java-17/include -I/usr/lib/jvm/java-17/include/linux -isystem /usr/local/clang16/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c registration.c -o registration.o
registration.c:6:12: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
int dummy__() {
^
void
1 warning generated.
/usr/local/clang16/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I. -I/usr/lib/jvm/java-17/include -I/usr/lib/jvm/java-17/include/linux -isystem /usr/local/clang16/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c tools.c -o tools.o
In file included from tools.c:7:
./rJava.h:123:23: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
HIDE JNIEnv* getJNIEnv();
^
void
./rJava.h:167:28: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
HIDE SEXP R_getUnboundValue() ;
^
void
tools.c:109:28: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
REPC SEXP RgetNullReference() {
^
void
tools.c:131:25: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
REPC SEXP RJava_checkJVM() {
^
void
tools.c:141:27: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
REPC SEXP RJava_needs_init() {
^
void
5 warnings generated.
/usr/local/clang16/bin/clang -shared -L/usr/local/clang/lib64 -L/usr/local/clang16/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-17/lib/server -ljvm
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/rJava/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/rJava/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/rJava/src'
installing via 'install.libs.R' to /data/gannet/ripley/R/packages/tests-clang/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)