[R-SIG-Mac] rJava: configure error: One or more JNI types differ from the corresponding native type
Simon Urbanek
simon.urbanek at r-project.org
Tue Nov 3 22:57:53 CET 2015
Please make sure you are using rJava 0.9-8 since your JVM is lacking the path in libjvm and you are on 10.11 which has issues with passing env vars.
Cheers,
Simon
> On Nov 3, 2015, at 4:20 PM, Marius Hofert <marius.hofert at uwaterloo.ca> wrote:
>
> Hi,
>
> I run R (devel and 3.2.2) under Mac OS X 10.11.1. I installed the JDK
> via jdk-8u66-macosx-x64.dmg ("java -version" works in the terminal).
> When I do install.packages("rJava"), I receive:
>
> ...
> checking whether JNI programs can be compiled... yes
> checking JNI data types... configure: error: One or more JNI types
> differ from the corresponding native type. You may need to use
> non-standard compiler flags or a different compiler in order to fix
> this.
> ERROR: configuration failed for package ‘rJava’
>
> I tried:
> - Using R CMD javareconf as recommended on
> http://www.rforge.net/rJava/ (do I need to have R compiled with
> --enable-R-shlib?)
> - Setting R_JAVA_LD_LIBRARY_PATH before starting R (as described on
> https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Java-support)
>
> I also found http://r.789695.n4.nabble.com/Installation-problems-Linux-Java-and-R-not-working-together-td4680718.html.
> Although this concerns Linux, below I included the output of
> rJava/config.log after R CMD INSTALL rJava.
>
> Do I have to configure R in a special way and/or set specific flags?
>
> Cheers,
> Marius
>
>
> $ ./configure
>
> ## --------- ##
> ## Platform. ##
> ## --------- ##
>
> hostname = v1020-wn-126-174.campus-dynamic.uwaterloo.ca
> uname -m = x86_64
> uname -r = 15.0.0
> uname -s = Darwin
> uname -v = Darwin Kernel Version 15.0.0: Sat Sep 19 15:53:46 PDT 2015;
> root:xnu-3247.10.11~1/RELEASE_X86_64
>
> /usr/bin/uname -p = i386
> /bin/uname -X = unknown
>
> /bin/arch = unknown
> /usr/bin/arch -k = unknown
> /usr/convex/getsysinfo = unknown
> /usr/bin/hostinfo = Mach kernel version:
> Darwin Kernel Version 15.0.0: Sat Sep 19 15:53:46 PDT 2015;
> root:xnu-3247.10.11~1/RELEASE_X86_64
> Kernel configured for up to 8 processors.
> 4 processors are physically available.
> 8 processors are logically available.
> Processor type: x86_64h (Intel x86-64h Haswell)
> Processors active: 0 1 2 3 4 5 6 7
> Primary memory available: 16.00 gigabytes
> Default processor set: 305 tasks, 1236 threads, 8 processors
> Load average: 1.24, Mach factor: 6.74
> /bin/machine = unknown
> /usr/bin/oslevel = unknown
> /bin/universe = unknown
>
> PATH: /Applications/Emacs.app/Contents/MacOS
> PATH: /Applications/Emacs.app/Contents/MacOS/bin
> PATH: /usr/local
> PATH: /usr/local/bin
> PATH: /usr/bin
> PATH: /bin
> PATH: /usr/sbin
> PATH: /sbin
> PATH: /opt/X11/bin
> PATH: /Library/TeX/texbin
> PATH: /Applications/Emacs.app/Contents/MacOS/bin-x86_64-10_9
> PATH: /Applications/Emacs.app/Contents/MacOS/libexec-x86_64-10_9
>
>
> ## ----------- ##
> ## Core tests. ##
> ## ----------- ##
>
> configure:2245: checking for gcc
> configure:2272: result: gcc
> configure:2501: checking for C compiler version
> configure:2510: gcc --version >&5
> Apple LLVM version 7.0.0 (clang-700.1.76)
> Target: x86_64-apple-darwin15.0.0
> Thread model: posix
> Configured with:
> --prefix=/Applications/Xcode.app/Contents/Developer/usr
> --with-gxx-include-dir=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.11.sdk/usr/include/c++/4.2.1
> configure:2521: $? = 0
> configure:2510: gcc -v >&5
> Configured with:
> --prefix=/Applications/Xcode.app/Contents/Developer/usr
> --with-gxx-include-dir=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.11.sdk/usr/include/c++/4.2.1
> Apple LLVM version 7.0.0 (clang-700.1.76)
> Target: x86_64-apple-darwin15.0.0
> Thread model: posix
> configure:2521: $? = 0
> configure:2510: gcc -V >&5
> clang: error: argument to '-V' is missing (expected 1 value)
> clang: error: no input files
> configure:2521: $? = 1
> configure:2510: gcc -qversion >&5
> clang: error: unknown argument: '-qversion'
> clang: error: no input files
> configure:2521: $? = 1
> configure:2541: checking whether the C compiler works
> configure:2563: gcc -g -O2 conftest.c >&5
> configure:2567: $? = 0
> configure:2615: result: yes
> configure:2618: checking for C compiler default output file name
> configure:2620: result: a.out
> configure:2626: checking for suffix of executables
> configure:2633: gcc -o conftest -g -O2 conftest.c >&5
> configure:2637: $? = 0
> configure:2659: result:
> configure:2681: checking whether we are cross compiling
> configure:2689: gcc -o conftest -g -O2 conftest.c >&5
> configure:2693: $? = 0
> configure:2700: ./conftest
> configure:2704: $? = 0
> configure:2719: result: no
> configure:2724: checking for suffix of object files
> configure:2746: gcc -c -g -O2 conftest.c >&5
> configure:2750: $? = 0
> configure:2771: result: o
> configure:2775: checking whether we are using the GNU C compiler
> configure:2794: gcc -c -g -O2 conftest.c >&5
> configure:2794: $? = 0
> configure:2803: result: yes
> configure:2812: checking whether gcc accepts -g
> configure:2832: gcc -c -g conftest.c >&5
> configure:2832: $? = 0
> configure:2873: result: yes
> configure:2890: checking for gcc option to accept ISO C89
> configure:2953: gcc -c -g -O2 conftest.c >&5
> configure:2953: $? = 0
> configure:2966: result: none needed
> configure:2996: checking how to run the C preprocessor
> configure:3027: gcc -E conftest.c
> configure:3027: $? = 0
> configure:3041: gcc -E conftest.c
> conftest.c:9:10: fatal error: 'ac_nonexistent.h' file not found
> #include <ac_nonexistent.h>
> ^
> 1 error generated.
> configure:3041: $? = 1
> configure: failed program was:
> | /* confdefs.h */
> | #define PACKAGE_NAME "rJava"
> | #define PACKAGE_TARNAME "rjava"
> | #define PACKAGE_VERSION "0.8"
> | #define PACKAGE_STRING "rJava 0.8"
> | #define PACKAGE_BUGREPORT "Simon.Urbanek at r-project.org"
> | #define PACKAGE_URL ""
> | /* end confdefs.h. */
> | #include <ac_nonexistent.h>
> configure:3066: result: gcc -E
> configure:3086: gcc -E conftest.c
> configure:3086: $? = 0
> configure:3100: gcc -E conftest.c
> conftest.c:9:10: fatal error: 'ac_nonexistent.h' file not found
> #include <ac_nonexistent.h>
> ^
> 1 error generated.
> configure:3100: $? = 1
> configure: failed program was:
> | /* confdefs.h */
> | #define PACKAGE_NAME "rJava"
> | #define PACKAGE_TARNAME "rjava"
> | #define PACKAGE_VERSION "0.8"
> | #define PACKAGE_STRING "rJava 0.8"
> | #define PACKAGE_BUGREPORT "Simon.Urbanek at r-project.org"
> | #define PACKAGE_URL ""
> | /* end confdefs.h. */
> | #include <ac_nonexistent.h>
> configure:3129: checking for grep that handles long lines and -e
> configure:3187: result: /usr/local/bin/grep
> configure:3192: checking for egrep
> configure:3254: result: /usr/local/bin/grep -E
> configure:3259: checking for ANSI C header files
> configure:3279: gcc -c -g -O2 conftest.c >&5
> configure:3279: $? = 0
> configure:3352: gcc -o conftest -g -O2 conftest.c >&5
> configure:3352: $? = 0
> configure:3352: ./conftest
> configure:3352: $? = 0
> configure:3363: result: yes
> configure:3371: checking for sys/wait.h that is POSIX.1 compatible
> configure:3397: gcc -c -g -O2 conftest.c >&5
> configure:3397: $? = 0
> configure:3404: result: yes
> configure:3417: checking for sys/types.h
> configure:3417: gcc -c -g -O2 conftest.c >&5
> configure:3417: $? = 0
> configure:3417: result: yes
> configure:3417: checking for sys/stat.h
> configure:3417: gcc -c -g -O2 conftest.c >&5
> configure:3417: $? = 0
> configure:3417: result: yes
> configure:3417: checking for stdlib.h
> configure:3417: gcc -c -g -O2 conftest.c >&5
> configure:3417: $? = 0
> configure:3417: result: yes
> configure:3417: checking for string.h
> configure:3417: gcc -c -g -O2 conftest.c >&5
> configure:3417: $? = 0
> configure:3417: result: yes
> configure:3417: checking for memory.h
> configure:3417: gcc -c -g -O2 conftest.c >&5
> configure:3417: $? = 0
> configure:3417: result: yes
> configure:3417: checking for strings.h
> configure:3417: gcc -c -g -O2 conftest.c >&5
> configure:3417: $? = 0
> configure:3417: result: yes
> configure:3417: checking for inttypes.h
> configure:3417: gcc -c -g -O2 conftest.c >&5
> configure:3417: $? = 0
> configure:3417: result: yes
> configure:3417: checking for stdint.h
> configure:3417: gcc -c -g -O2 conftest.c >&5
> configure:3417: $? = 0
> configure:3417: result: yes
> configure:3417: checking for unistd.h
> configure:3417: gcc -c -g -O2 conftest.c >&5
> configure:3417: $? = 0
> configure:3417: result: yes
> configure:3432: checking for string.h
> configure:3432: result: yes
> configure:3432: checking sys/time.h usability
> configure:3432: gcc -c -g -O2 conftest.c >&5
> configure:3432: $? = 0
> configure:3432: result: yes
> configure:3432: checking sys/time.h presence
> configure:3432: gcc -E conftest.c
> configure:3432: $? = 0
> configure:3432: result: yes
> configure:3432: checking for sys/time.h
> configure:3432: result: yes
> configure:3432: checking for unistd.h
> configure:3432: result: yes
> configure:3444: checking for an ANSI C-conforming const
> configure:3510: gcc -c -g -O2 conftest.c >&5
> configure:3510: $? = 0
> configure:3517: result: yes
> configure:3525: checking whether time.h and sys/time.h may both be included
> configure:3545: gcc -c -g -O2 conftest.c >&5
> configure:3545: $? = 0
> configure:3552: result: yes
> configure:3561: checking whether gcc supports static inline...
> configure:3574: gcc -c -g -O2 conftest.c >&5
> conftest.c:26:8: warning: type specifier missing, defaults to 'int'
> [-Wimplicit-int]
> static f = 1;
> ~~~~~~ ^
> 1 warning generated.
> configure:3574: $? = 0
> configure:3578: result: yes
> configure:3587: checking whether setjmp.h is POSIX.1 compatible
> configure:3605: gcc -c -g -O2 conftest.c >&5
> configure:3605: $? = 0
> configure:3612: result: yes
> configure:3614: checking whether sigsetjmp is declared
> configure:3614: gcc -c -g -O2 conftest.c >&5
> configure:3614: $? = 0
> configure:3614: result: yes
> configure:3625: checking whether siglongjmp is declared
> configure:3625: gcc -c -g -O2 conftest.c >&5
> configure:3625: $? = 0
> configure:3625: result: yes
> configure:3649: checking Java support in R
> configure:3677: result: present:
> interpreter : '/usr/bin/java'
> archiver : '/usr/bin/jar'
> compiler : '/usr/bin/javac'
> header prep.: '/usr/bin/javah'
> cpp flags : '-I/Library/Java/JavaVirtualMachines/jdk1.8.0_66.jdk/Contents/Home/jre/../include
> -I/Library/Java/JavaVirtualMachines/jdk1.8.0_66.jdk/Contents/Home/jre/../include/darwin'
> java libs : '-L/Library/Java/JavaVirtualMachines/jdk1.8.0_66.jdk/Contents/Home/jre/lib/server
> -ljvm'
> configure:3727: checking whether Java run-time works
> configure:3730: result: yes
> configure:3739: checking whether -Xrs is supported
> configure:3747: result: yes
> configure:3750: checking whether JNI programs can be compiled
> configure:3763: gcc -o conftest -g -O2
> -I/Library/Java/JavaVirtualMachines/jdk1.8.0_66.jdk/Contents/Home/jre/../include
> -I/Library/Java/JavaVirtualMachines/jdk1.8.0_66.jdk/Contents/Home/jre/../include/darwin
> conftest.c -L/Library/Java/JavaVirtualMachines/jdk1.8.0_66.jdk/Contents/Home/jre/lib/server
> -ljvm >&5
> configure:3763: $? = 0
> configure:3764: result: yes
> configure:3776: checking JNI data types
> configure:3791: gcc -o conftest -g -O2
> -I/Library/Java/JavaVirtualMachines/jdk1.8.0_66.jdk/Contents/Home/jre/../include
> -I/Library/Java/JavaVirtualMachines/jdk1.8.0_66.jdk/Contents/Home/jre/../include/darwin
> conftest.c -L/Library/Java/JavaVirtualMachines/jdk1.8.0_66.jdk/Contents/Home/jre/lib/server
> -ljvm >&5
> configure:3791: $? = 0
> configure:3791: ./conftest
> dyld: Library not loaded: @rpath/libjvm.dylib
> Referenced from: /Users/mhofert/Downloads/rJava/./conftest
> Reason: image not found
> ./configure: line 1527: 81965 Trace/BPT trap: 5 ./conftest$ac_exeext
> configure:3791: $? = 133
> configure: program exited with status 133
> configure: failed program was:
> | /* confdefs.h */
> | #define PACKAGE_NAME "rJava"
> | #define PACKAGE_TARNAME "rjava"
> | #define PACKAGE_VERSION "0.8"
> | #define PACKAGE_STRING "rJava 0.8"
> | #define PACKAGE_BUGREPORT "Simon.Urbanek at r-project.org"
> | #define PACKAGE_URL ""
> | #define STDC_HEADERS 1
> | #define HAVE_SYS_WAIT_H 1
> | #define HAVE_SYS_TYPES_H 1
> | #define HAVE_SYS_STAT_H 1
> | #define HAVE_STDLIB_H 1
> | #define HAVE_STRING_H 1
> | #define HAVE_MEMORY_H 1
> | #define HAVE_STRINGS_H 1
> | #define HAVE_INTTYPES_H 1
> | #define HAVE_STDINT_H 1
> | #define HAVE_UNISTD_H 1
> | #define HAVE_STRING_H 1
> | #define HAVE_SYS_TIME_H 1
> | #define HAVE_UNISTD_H 1
> | #define TIME_WITH_SYS_TIME 1
> | #define HAVE_STATIC_INLINE 1
> | #define HAVE_DECL_SIGSETJMP 1
> | #define HAVE_DECL_SIGLONGJMP 1
> | #define HAVE_POSIX_SETJMP 1
> | #define HAVE_XRS 1
> | /* end confdefs.h. */
> |
> | #include <jni.h>
> | int main(void) {
> | return (sizeof(int)==sizeof(jint) && sizeof(long)==sizeof(long) &&
> sizeof(jbyte)==sizeof(char) && sizeof(jshort)==sizeof(short) &&
> sizeof(jfloat)==sizeof(float) && sizeof(jdouble)==sizeof(double))?0:1;
> | }
> |
> configure:3795: error: One or more JNI types differ from the
> corresponding native type. You may need to use non-standard compiler
> flags or a different compiler in order to fix this.
>
> ## ---------------- ##
> ## Cache variables. ##
> ## ---------------- ##
>
> ac_cv_c_compiler_gnu=yes
> ac_cv_c_const=yes
> ac_cv_env_CC_set=
> ac_cv_env_CC_value=
> ac_cv_env_CFLAGS_set=
> ac_cv_env_CFLAGS_value=
> ac_cv_env_CPPFLAGS_set=
> ac_cv_env_CPPFLAGS_value=
> ac_cv_env_CPP_set=
> ac_cv_env_CPP_value=
> ac_cv_env_LDFLAGS_set=
> ac_cv_env_LDFLAGS_value=
> ac_cv_env_LIBS_set=
> ac_cv_env_LIBS_value=
> ac_cv_env_build_alias_set=
> ac_cv_env_build_alias_value=
> ac_cv_env_host_alias_set=
> ac_cv_env_host_alias_value=
> ac_cv_env_target_alias_set=
> ac_cv_env_target_alias_value=
> ac_cv_have_decl_siglongjmp=yes
> ac_cv_have_decl_sigsetjmp=yes
> ac_cv_header_inttypes_h=yes
> ac_cv_header_memory_h=yes
> ac_cv_header_stdc=yes
> ac_cv_header_stdint_h=yes
> ac_cv_header_stdlib_h=yes
> ac_cv_header_string_h=yes
> ac_cv_header_strings_h=yes
> ac_cv_header_sys_stat_h=yes
> ac_cv_header_sys_time_h=yes
> ac_cv_header_sys_types_h=yes
> ac_cv_header_sys_wait_h=yes
> ac_cv_header_time=yes
> ac_cv_header_unistd_h=yes
> ac_cv_objext=o
> ac_cv_path_EGREP='/usr/local/bin/grep -E'
> ac_cv_path_GREP=/usr/local/bin/grep
> ac_cv_prog_CPP='gcc -E'
> ac_cv_prog_ac_ct_CC=gcc
> ac_cv_prog_cc_c89=
> ac_cv_prog_cc_g=yes
> r_cv_header_setjmp_posix=yes
>
> ## ----------------- ##
> ## Output variables. ##
> ## ----------------- ##
>
> CC='gcc'
> CFLAGS='-g -O2 -I/Library/Java/JavaVirtualMachines/jdk1.8.0_66.jdk/Contents/Home/jre/../include
> -I/Library/Java/JavaVirtualMachines/jdk1.8.0_66.jdk/Contents/Home/jre/../include/darwin'
> CPP='gcc -E'
> CPPFLAGS=''
> DEFS=''
> ECHO_C='\c'
> ECHO_N=''
> ECHO_T=''
> EGREP='/usr/local/bin/grep -E'
> EXEEXT=''
> GREP='/usr/local/bin/grep'
> JAVA='/usr/bin/java'
> JAVAC='/usr/bin/javac'
> JAVAH='/usr/bin/javah'
> JAVA_CPPFLAGS='-I/Library/Java/JavaVirtualMachines/jdk1.8.0_66.jdk/Contents/Home/jre/../include
> -I/Library/Java/JavaVirtualMachines/jdk1.8.0_66.jdk/Contents/Home/jre/../include/darwin'
> JAVA_HOME='/Library/Java/JavaVirtualMachines/jdk1.8.0_66.jdk/Contents/Home/jre'
> JAVA_LIBS='-L/Library/Java/JavaVirtualMachines/jdk1.8.0_66.jdk/Contents/Home/jre/lib/server
> -ljvm'
> LDFLAGS=''
> LIBOBJS=''
> LIBS=' -L/Library/Java/JavaVirtualMachines/jdk1.8.0_66.jdk/Contents/Home/jre/lib/server
> -ljvm'
> LTLIBOBJS=''
> OBJEXT='o'
> PACKAGE_BUGREPORT='Simon.Urbanek at r-project.org'
> PACKAGE_NAME='rJava'
> PACKAGE_STRING='rJava 0.8'
> PACKAGE_TARNAME='rjava'
> PACKAGE_URL=''
> PACKAGE_VERSION='0.8'
> PATH_SEPARATOR=':'
> R_HOME='/usr/local/R/R-devel_build'
> SHELL='/bin/sh'
> WANT_JRI_FALSE=''
> WANT_JRI_TRUE=''
> ac_ct_CC='gcc'
> bindir='${exec_prefix}/bin'
> build_alias=''
> datadir='${datarootdir}'
> datarootdir='${prefix}/share'
> docdir='${datarootdir}/doc/${PACKAGE_TARNAME}'
> dvidir='${docdir}'
> exec_prefix='NONE'
> host_alias=''
> htmldir='${docdir}'
> includedir='${prefix}/include'
> infodir='${datarootdir}/info'
> libdir='${exec_prefix}/lib'
> libexecdir='${exec_prefix}/libexec'
> localedir='${datarootdir}/locale'
> localstatedir='${prefix}/var'
> mandir='${datarootdir}/man'
> oldincludedir='/usr/include'
> pdfdir='${docdir}'
> prefix='NONE'
> program_transform_name='s,x,x,'
> psdir='${docdir}'
> sbindir='${exec_prefix}/sbin'
> sharedstatedir='${prefix}/com'
> subdirs=''
> sysconfdir='${prefix}/etc'
> target_alias=''
>
> ## ----------- ##
> ## confdefs.h. ##
> ## ----------- ##
>
> /* confdefs.h */
> #define PACKAGE_NAME "rJava"
> #define PACKAGE_TARNAME "rjava"
> #define PACKAGE_VERSION "0.8"
> #define PACKAGE_STRING "rJava 0.8"
> #define PACKAGE_BUGREPORT "Simon.Urbanek at r-project.org"
> #define PACKAGE_URL ""
> #define STDC_HEADERS 1
> #define HAVE_SYS_WAIT_H 1
> #define HAVE_SYS_TYPES_H 1
> #define HAVE_SYS_STAT_H 1
> #define HAVE_STDLIB_H 1
> #define HAVE_STRING_H 1
> #define HAVE_MEMORY_H 1
> #define HAVE_STRINGS_H 1
> #define HAVE_INTTYPES_H 1
> #define HAVE_STDINT_H 1
> #define HAVE_UNISTD_H 1
> #define HAVE_STRING_H 1
> #define HAVE_SYS_TIME_H 1
> #define HAVE_UNISTD_H 1
> #define TIME_WITH_SYS_TIME 1
> #define HAVE_STATIC_INLINE 1
> #define HAVE_DECL_SIGSETJMP 1
> #define HAVE_DECL_SIGLONGJMP 1
> #define HAVE_POSIX_SETJMP 1
> #define HAVE_XRS 1
>
> configure: exit 133
>
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