This file contains any messages produced by compilers while running configure, to aid debugging if configure makes a mistake. It was created by JRI configure 0.3, which was generated by GNU Autoconf 2.61. Invocation command line was $ ./configure ## --------- ## ## Platform. ## ## --------- ## hostname = cc01 uname -m = x86_64 uname -r = 2.6.18-238.19.1.el5 uname -s = Linux uname -v = #1 SMP Fri Jul 15 07:31:24 EDT 2011 /usr/bin/uname -p = unknown /bin/uname -X = unknown /bin/arch = x86_64 /usr/bin/arch -k = unknown /usr/convex/getsysinfo = unknown /usr/bin/hostinfo = unknown /bin/machine = unknown /usr/bin/oslevel = unknown /bin/universe = unknown PATH: /local/workspace01/zhangju/bin PATH: /home/psgendb/local/pkg/consed_phrapPhred/bin PATH: /home/psgendb/local/pkg/MUMmer3.22 PATH: /home/psgendb/zhangju/MeV_4_6_1/R-2.9.1/bin PATH: /home/psgendb/local/pkg/454/bin PATH: /home/u4/zhangju/bin PATH: /home/psgendb/local/pkg/blast-2.2.25/bin PATH: /home/psgendb/local/pkg/amos_build/bin PATH: /home/psgendb/local/script PATH: /home/psgendb/local/bin-linux-x86_64 PATH: /gridware/sge/bin/lx24-amd64 PATH: /usr/kerberos/bin PATH: /usr/local/bin PATH: /bin PATH: /usr/bin PATH: /home/psgendb/script PATH: /home/psgendb/bin-linux-x86_64 PATH: /home/psgendb/local/pkg/EMBOSS/linux-x86_64/bin ## ----------- ## ## Core tests. ## ## ----------- ## configure:1722: checking build system type configure:1740: result: x86_64-unknown-linux-gnu configure:1762: checking host system type configure:1777: result: x86_64-unknown-linux-gnu configure:1910: checking for gcc configure:1937: result: gcc -std=gnu99 configure:2175: checking for C compiler version configure:2182: gcc -std=gnu99 --version >&5 gcc (GCC) 4.1.2 20080704 (Red Hat 4.1.2-51) Copyright (C) 2006 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. configure:2185: $? = 0 configure:2192: gcc -std=gnu99 -v >&5 Using built-in specs. Target: x86_64-redhat-linux Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --enable-shared --enable-threads=posix --enable-checking=release --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-libgcj-multifile --enable-languages=c,c++,objc,obj-c++,java,fortran,ada --enable-java-awt=gtk --disable-dssi --disable-plugin --with-java-home=/usr/lib/jvm/java-1.4.2-gcj-1.4.2.0/jre --with-cpu=generic --host=x86_64-redhat-linux Thread model: posix gcc version 4.1.2 20080704 (Red Hat 4.1.2-51) configure:2195: $? = 0 configure:2202: gcc -std=gnu99 -V >&5 gcc: '-V' must come at the start of the command line configure:2205: $? = 1 configure:2228: checking for C compiler default output file name configure:2255: gcc -std=gnu99 -g -O2 conftest.c >&5 configure:2258: $? = 0 configure:2296: result: a.out configure:2313: checking whether the C compiler works configure:2323: ./a.out configure:2326: $? = 0 configure:2343: result: yes configure:2350: checking whether we are cross compiling configure:2352: result: no configure:2355: checking for suffix of executables configure:2362: gcc -std=gnu99 -o conftest -g -O2 conftest.c >&5 configure:2365: $? = 0 configure:2389: result: configure:2395: checking for suffix of object files configure:2421: gcc -std=gnu99 -c -g -O2 conftest.c >&5 configure:2424: $? = 0 configure:2447: result: o configure:2451: checking whether we are using the GNU C compiler configure:2480: gcc -std=gnu99 -c -g -O2 conftest.c >&5 configure:2486: $? = 0 configure:2503: result: yes configure:2508: checking whether gcc -std=gnu99 accepts -g configure:2538: gcc -std=gnu99 -c -g conftest.c >&5 configure:2544: $? = 0 configure:2643: result: yes configure:2660: checking for gcc -std=gnu99 option to accept ISO C89 configure:2734: gcc -std=gnu99 -c -g -O2 conftest.c >&5 configure:2740: $? = 0 configure:2763: result: none needed configure:2787: checking how to run the C preprocessor configure:2903: result: gcc -std=gnu99 -E configure:2932: gcc -std=gnu99 -E conftest.c configure:2938: $? = 0 configure:2969: gcc -std=gnu99 -E conftest.c conftest.c:8:28: error: ac_nonexistent.h: No such file or directory configure:2975: $? = 1 configure: failed program was: | /* confdefs.h. */ | #define PACKAGE_NAME "JRI" | #define PACKAGE_TARNAME "jri" | #define PACKAGE_VERSION "0.3" | #define PACKAGE_STRING "JRI 0.3" | #define PACKAGE_BUGREPORT "simon.urbanek@r-project.org" | /* end confdefs.h. */ | #include configure:3013: checking for grep that handles long lines and -e configure:3087: result: /bin/grep configure:3092: checking for egrep configure:3170: result: /bin/grep -E configure:3175: checking for ANSI C header files configure:3205: gcc -std=gnu99 -c -g -O2 conftest.c >&5 configure:3211: $? = 0 configure:3310: gcc -std=gnu99 -o conftest -g -O2 conftest.c >&5 configure:3313: $? = 0 configure:3319: ./conftest configure:3322: $? = 0 configure:3339: result: yes configure:3377: checking for java configure:3395: found /usr/bin/java configure:3407: result: /usr/bin/java configure:3423: checking for javac configure:3441: found /usr/bin/javac configure:3453: result: /usr/bin/javac configure:3468: checking for javah configure:3486: found /usr/bin/javah configure:3498: result: /usr/bin/javah configure:3513: checking for jar configure:3531: found /usr/bin/jar configure:3543: result: /usr/bin/jar configure:3574: checking whether Java interpreter works configure:3583: running /usr/bin/java -classpath tools getsp -test configure:3585: output: 'Test1234OK' configure:3598: result: yes configure:3601: checking for Java environment configure:3610: running /usr/bin/java -classpath tools getsp java.home configure:3612: output: '/usr/lib/jvm/java-1.6.0-openjdk-1.6.0.0.x86_64/jre' configure:3625: result: in /usr/lib/jvm/java-1.6.0-openjdk-1.6.0.0.x86_64/jre configure:3639: running /usr/bin/java -classpath tools getsp -libs configure:3641: output: '-L/usr/lib/jvm/java-1.6.0-openjdk-1.6.0.0.x86_64/jre/lib/amd64/server -L/usr/lib/jvm/java-1.6.0-openjdk-1.6.0.0.x86_64/jre/lib/amd64 -L/usr/lib/jvm/java-1.6.0-openjdk-1.6.0.0.x86_64/jre/../lib/amd64 -L/usr/java/packages/lib/amd64 -L/usr/lib64 -L/lib64 -L/lib -L/usr/lib' configure:3651: running /usr/bin/java -classpath tools getsp java.library.path configure:3653: output: '/usr/lib/jvm/java-1.6.0-openjdk-1.6.0.0.x86_64/jre/lib/amd64/server:/usr/lib/jvm/java-1.6.0-openjdk-1.6.0.0.x86_64/jre/lib/amd64:/usr/lib/jvm/java-1.6.0-openjdk-1.6.0.0.x86_64/jre/../lib/amd64:/usr/java/packages/lib/amd64:/usr/lib64:/lib64:/lib:/usr/lib' configure:3673: checking for /usr/lib/jvm/java-1.6.0-openjdk-1.6.0.0.x86_64/jre/include/jni.h configure:3689: result: no configure:3695: checking for /usr/lib/jvm/java-1.6.0-openjdk-1.6.0.0.x86_64/jre/jni.h configure:3711: result: no configure:3717: checking for /usr/lib/jvm/java-1.6.0-openjdk-1.6.0.0.x86_64/jre/../include/jni.h configure:3733: result: yes configure:3761: checking for /usr/lib/jvm/java-1.6.0-openjdk-1.6.0.0.x86_64/jre/../include/./jni_md.h configure:3777: result: no configure:3761: checking for /usr/lib/jvm/java-1.6.0-openjdk-1.6.0.0.x86_64/jre/../include/linux/jni_md.h configure:3777: result: yes configure:3804: checking whether JNI programs can be compiled configure:3821: gcc -std=gnu99 -o conftest -g -O2 -D_REENTRANT -I/usr/lib/jvm/java-1.6.0-openjdk-1.6.0.0.x86_64/jre/../include -I/usr/lib/jvm/java-1.6.0-openjdk-1.6.0.0.x86_64/jre/../include/linux conftest.c -L/usr/lib/jvm/java-1.6.0-openjdk-1.6.0.0.x86_64/jre/lib/amd64/server -L/usr/lib/jvm/java-1.6.0-openjdk-1.6.0.0.x86_64/jre/lib/amd64 -L/usr/lib/jvm/java-1.6.0-openjdk-1.6.0.0.x86_64/jre/../lib/amd64 -L/usr/java/packages/lib/amd64 -L/usr/lib64 -L/lib64 -L/lib -L/usr/lib -ljvm >&5 configure:3827: $? = 0 configure:3833: result: yes configure:3850: checking whether JNI programs can be run configure:3874: gcc -std=gnu99 -o conftest -g -O2 -D_REENTRANT -I/usr/lib/jvm/java-1.6.0-openjdk-1.6.0.0.x86_64/jre/../include -I/usr/lib/jvm/java-1.6.0-openjdk-1.6.0.0.x86_64/jre/../include/linux conftest.c -L/usr/lib/jvm/java-1.6.0-openjdk-1.6.0.0.x86_64/jre/lib/amd64/server -L/usr/lib/jvm/java-1.6.0-openjdk-1.6.0.0.x86_64/jre/lib/amd64 -L/usr/lib/jvm/java-1.6.0-openjdk-1.6.0.0.x86_64/jre/../lib/amd64 -L/usr/java/packages/lib/amd64 -L/usr/lib64 -L/lib64 -L/lib -L/usr/lib -ljvm >&5 configure:3877: $? = 0 configure:3883: ./conftest configure:3886: $? = 0 configure:3888: result: yes configure:3905: checking JNI data types configure:3933: gcc -std=gnu99 -o conftest -g -O2 -D_REENTRANT -I/usr/lib/jvm/java-1.6.0-openjdk-1.6.0.0.x86_64/jre/../include -I/usr/lib/jvm/java-1.6.0-openjdk-1.6.0.0.x86_64/jre/../include/linux conftest.c -L/usr/lib/jvm/java-1.6.0-openjdk-1.6.0.0.x86_64/jre/lib/amd64/server -L/usr/lib/jvm/java-1.6.0-openjdk-1.6.0.0.x86_64/jre/lib/amd64 -L/usr/lib/jvm/java-1.6.0-openjdk-1.6.0.0.x86_64/jre/../lib/amd64 -L/usr/java/packages/lib/amd64 -L/usr/lib64 -L/lib64 -L/lib -L/usr/lib -ljvm >&5 configure:3936: $? = 0 configure:3942: ./conftest configure:3945: $? = 0 configure:3947: result: ok configure:4008: checking whether Rinterface.h exports R_CStackXXX variables configure:4026: gcc -std=gnu99 -c -g -O2 -D_REENTRANT -I/usr/lib/jvm/java-1.6.0-openjdk-1.6.0.0.x86_64/jre/../include -I/usr/lib/jvm/java-1.6.0-openjdk-1.6.0.0.x86_64/jre/../include/linux -g -O2 -I/home/psgendb/local/pkg/R_language/lib64/R/include conftest.c >&5 configure:4032: $? = 0 configure:4037: result: yes configure:4050: checking whether Rinterface.h exports R_SignalHandlers configure:4067: gcc -std=gnu99 -c -g -O2 -D_REENTRANT -I/usr/lib/jvm/java-1.6.0-openjdk-1.6.0.0.x86_64/jre/../include -I/usr/lib/jvm/java-1.6.0-openjdk-1.6.0.0.x86_64/jre/../include/linux -g -O2 -I/home/psgendb/local/pkg/R_language/lib64/R/include conftest.c >&5 configure:4073: $? = 0 configure:4078: result: yes configure:4220: creating ./config.status ## ---------------------- ## ## Running config.status. ## ## ---------------------- ## This file was extended by JRI config.status 0.3, which was generated by GNU Autoconf 2.61. Invocation command line was CONFIG_FILES = CONFIG_HEADERS = CONFIG_LINKS = CONFIG_COMMANDS = $ ./config.status on cc01 config.status:621: creating src/Makefile config.status:621: creating Makefile config.status:621: creating run config.status:621: creating src/config.h ## ---------------- ## ## Cache variables. ## ## ---------------- ## ac_cv_build=x86_64-unknown-linux-gnu ac_cv_c_compiler_gnu=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_file__usr_lib_jvm_java_1_6_0_openjdk_1_6_0_0_x86_64_jre____include___jni_md_h=no ac_cv_file__usr_lib_jvm_java_1_6_0_openjdk_1_6_0_0_x86_64_jre____include_jni_h=yes ac_cv_file__usr_lib_jvm_java_1_6_0_openjdk_1_6_0_0_x86_64_jre____include_linux_jni_md_h=yes ac_cv_file__usr_lib_jvm_java_1_6_0_openjdk_1_6_0_0_x86_64_jre_include_jni_h=no ac_cv_file__usr_lib_jvm_java_1_6_0_openjdk_1_6_0_0_x86_64_jre_jni_h=no ac_cv_header_stdc=yes ac_cv_host=x86_64-unknown-linux-gnu ac_cv_objext=o ac_cv_path_EGREP='/bin/grep -E' ac_cv_path_GREP=/bin/grep ac_cv_path_JAR=/usr/bin/jar ac_cv_path_JAVAC=/usr/bin/javac ac_cv_path_JAVAH=/usr/bin/javah ac_cv_path_JAVA_PROG=/usr/bin/java ac_cv_prog_CPP='gcc -std=gnu99 -E' ac_cv_prog_ac_ct_CC='gcc -std=gnu99' ac_cv_prog_cc_c89= ac_cv_prog_cc_g=yes ## ----------------- ## ## Output variables. ## ## ----------------- ## CC='gcc -std=gnu99' CFLAGS='-g -O2 -D_REENTRANT -I/usr/lib/jvm/java-1.6.0-openjdk-1.6.0.0.x86_64/jre/../include -I/usr/lib/jvm/java-1.6.0-openjdk-1.6.0.0.x86_64/jre/../include/linux' CPICF='-fpic' CPP='gcc -std=gnu99 -E' CPPFLAGS='' DEFFLAGS=' -DRIF_HAS_CSTACK -DRIF_HAS_RSIGHAND' DEFS='-DHAVE_CONFIG_H' ECHO_C='' ECHO_N='-n' ECHO_T='' EGREP='/bin/grep -E' EXEEXT='' GREP='/bin/grep' JAR='/usr/bin/jar' JAVAC='/usr/bin/javac' JAVAH='/usr/bin/javah' JAVA_CFLAGS='-D_REENTRANT' JAVA_HOME='/usr/lib/jvm/java-1.6.0-openjdk-1.6.0.0.x86_64/jre' JAVA_INC='-I/usr/lib/jvm/java-1.6.0-openjdk-1.6.0.0.x86_64/jre/../include -I/usr/lib/jvm/java-1.6.0-openjdk-1.6.0.0.x86_64/jre/../include/linux' JAVA_LD_PATH='/usr/lib/jvm/java-1.6.0-openjdk-1.6.0.0.x86_64/jre/lib/amd64/server:/usr/lib/jvm/java-1.6.0-openjdk-1.6.0.0.x86_64/jre/lib/amd64:/usr/lib/jvm/java-1.6.0-openjdk-1.6.0.0.x86_64/jre/../lib/amd64:/usr/java/packages/lib/amd64:/usr/lib64:/lib64:/lib:/usr/lib' JAVA_LIBS='-L/usr/lib/jvm/java-1.6.0-openjdk-1.6.0.0.x86_64/jre/lib/amd64/server -L/usr/lib/jvm/java-1.6.0-openjdk-1.6.0.0.x86_64/jre/lib/amd64 -L/usr/lib/jvm/java-1.6.0-openjdk-1.6.0.0.x86_64/jre/../lib/amd64 -L/usr/java/packages/lib/amd64 -L/usr/lib64 -L/lib64 -L/lib -L/usr/lib -ljvm' JAVA_PROG='/usr/bin/java' JNILD='-shared -L/usr/lib/jvm/java-1.6.0-openjdk-1.6.0.0.x86_64/jre/lib/amd64/server -L/usr/lib/jvm/java-1.6.0-openjdk-1.6.0.0.x86_64/jre/lib/amd64 -L/usr/lib/jvm/java-1.6.0-openjdk-1.6.0.0.x86_64/jre/../lib/amd64 -L/usr/java/packages/lib/amd64 -L/usr/lib64 -L/lib64 -L/lib -L/usr/lib -ljvm' JNIPREFIX='lib' JNISO='.so' LDFLAGS='' LIBOBJS='' LIBS=' -L/usr/lib/jvm/java-1.6.0-openjdk-1.6.0.0.x86_64/jre/lib/amd64/server -L/usr/lib/jvm/java-1.6.0-openjdk-1.6.0.0.x86_64/jre/lib/amd64 -L/usr/lib/jvm/java-1.6.0-openjdk-1.6.0.0.x86_64/jre/../lib/amd64 -L/usr/java/packages/lib/amd64 -L/usr/lib64 -L/lib64 -L/lib -L/usr/lib -ljvm' LTLIBOBJS='' OBJEXT='o' PACKAGE_BUGREPORT='simon.urbanek@r-project.org' PACKAGE_NAME='JRI' PACKAGE_STRING='JRI 0.3' PACKAGE_TARNAME='jri' PACKAGE_VERSION='0.3' PATH_SEPARATOR=':' RINC='-I/home/psgendb/local/pkg/R_language/lib64/R/include' RLD='-L/home/psgendb/local/pkg/R_language/lib64/R/lib -lR' R_DOC_DIR='/home/psgendb/local/pkg/R_language/lib64/R/doc' R_HOME='/home/psgendb/local/pkg/R_language/lib64/R' R_INCLUDE_DIR='/home/psgendb/local/pkg/R_language/lib64/R/include' R_SHARE_DIR='/home/psgendb/local/pkg/R_language/lib64/R/share' SHELL='/bin/sh' ac_ct_CC='gcc -std=gnu99' bindir='${exec_prefix}/bin' build='x86_64-unknown-linux-gnu' build_alias='' build_cpu='x86_64' build_os='linux-gnu' build_vendor='unknown' datadir='${datarootdir}' datarootdir='${prefix}/share' docdir='${datarootdir}/doc/${PACKAGE_TARNAME}' dvidir='${docdir}' exec_prefix='${prefix}' host='x86_64-unknown-linux-gnu' host_alias='' host_cpu='x86_64' host_os='linux-gnu' host_vendor='unknown' htmldir='${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='/usr/local' program_transform_name='s,x,x,' psdir='${docdir}' sbindir='${exec_prefix}/sbin' sharedstatedir='${prefix}/com' sysconfdir='${prefix}/etc' target_alias='' ## ----------- ## ## confdefs.h. ## ## ----------- ## #define PACKAGE_NAME "JRI" #define PACKAGE_TARNAME "jri" #define PACKAGE_VERSION "0.3" #define PACKAGE_STRING "JRI 0.3" #define PACKAGE_BUGREPORT "simon.urbanek@r-project.org" #define STDC_HEADERS 1 configure: exit 0