This file contains any messages produced by compilers while running configure, to aid debugging if configure makes a mistake. It was created by configure, which was generated by GNU Autoconf 2.63. Invocation command line was $ ./configure --disable-option-checking --prefix=/projects/remc_bigdata/miR/vRNA-2.0.0 --cache-file=/dev/null --srcdir=. ## --------- ## ## Platform. ## ## --------- ## hostname = xhost09.bcgsc.ca uname -m = x86_64 uname -r = 2.6.18-194.3.1.el5 uname -s = Linux uname -v = #1 SMP Thu May 13 13:08:30 EDT 2010 /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: /home/grobertson/linux_x86_64/EPD/epd-6.2-2-rh5-x86_64/lib/python2.6/site-packages PATH: /home/grobertson/linux_x86_64/EPD/epd-6.2-2-rh5-x86_64/lib PATH: /home/grobertson/linux_x86_64/EPD/epd-6.2-2-rh5-x86_64/bin PATH: /home/grobertson/linux_x86_64/libxml2/libxml2-2.7.3/bin PATH: /home/grobertson/linux_x86_64/libxml2/libxml2-2.7.3/lib PATH: /home/grobertson/linux_x86_64/samtools/samtools-0.1.12a PATH: /home/grobertson/linux_x86_64/ruby/ruby-1.8.7-p302/bin PATH: /home/grobertson/linux_x86_64/ruby/rubygems-1.3.5/bin PATH: /home/grobertson/linux_x86_64/Git/git-1.6.5.1/bin PATH: /home/grobertson/bin/x86_64 PATH: /home/grobertson/linux_x86_64/pysam/pysam-0.2/pysam PATH: /home/grobertson/linux_x86_64/Pyrex/bin PATH: /home/grobertson/linux_x86_64/Hg/bin PATH: /home/grobertson/linux_x86_64/zlib/zlib-1.2.3 PATH: /home/grobertson/Pairagon/gmap-2007-09-28/bin PATH: /home/grobertson/linux_x86_64/glib/glib-2.20.3/bin PATH: /home/grobertson/linux_x86_64/Hg/mercurial-1.3.1 PATH: /home/grobertson/linux_x86_64/boost/boost_1_42_0/boost PATH: /home/grobertson/linux_x86_64/BLAT/blatSrc/bin/x86_64-redhat-linux-gnu PATH: /home/grobertson/linux_x86_64/perl_5.10/bin PATH: /usr/lib/pkgconfig PATH: /home/grobertson/linux_x86_64/R/R-2.12.1/bin PATH: /home/grobertson/linux_x86_64/R/R-2.12.1/etc PATH: /home/grobertson/apache-ant-1.7.1/bin PATH: /home/grobertson/linux_x86_64/Cufflinks/tophat-1.0.13/bin PATH: /home/grobertson/linux_x86_64/Cufflinks/bowtie-0.12.5 PATH: /home/grobertson/linux_x86_64/Cufflinks/cufflinks-0.8.2.Linux_x86_64 PATH: /home/grobertson/linux_x86_64/gsl/gsl-1.14/bin PATH: /home/grobertson/linux_x86_64/gsl/gsl-1.14/lib PATH: /home/grobertson/linux_x86_64/gsl/gsl-1.14/include/gsl PATH: #{JAVA_HOME}/usr/bin PATH: /usr/kerberos/bin PATH: /usr/local/bin PATH: /bin PATH: /usr/bin PATH: /home/grobertson/bin ## ----------- ## ## Core tests. ## ## ----------- ## configure:1861: checking build system type configure:1879: result: x86_64-unknown-linux-gnu configure:1901: checking host system type configure:1916: result: x86_64-unknown-linux-gnu configure:2030: checking for gcc configure:2046: found /usr/bin/gcc configure:2057: result: gcc configure:2289: checking for C compiler version configure:2297: gcc --version >&5 gcc (GCC) 4.1.2 20080704 (Red Hat 4.1.2-48) 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:2301: $? = 0 configure:2308: gcc -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 --enable-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 4.1.2-48) configure:2312: $? = 0 configure:2319: gcc -V >&5 gcc: '-V' option must have argument configure:2323: $? = 1 configure:2346: checking for C compiler default output file name configure:2368: gcc conftest.c >&5 configure:2372: $? = 0 configure:2410: result: a.out configure:2429: checking whether the C compiler works configure:2439: ./a.out configure:2443: $? = 0 configure:2462: result: yes configure:2469: checking whether we are cross compiling configure:2471: result: no configure:2474: checking for suffix of executables configure:2481: gcc -o conftest conftest.c >&5 configure:2485: $? = 0 configure:2511: result: configure:2517: checking for suffix of object files configure:2543: gcc -c conftest.c >&5 configure:2547: $? = 0 configure:2572: result: o configure:2576: checking whether we are using the GNU C compiler configure:2605: gcc -c conftest.c >&5 configure:2612: $? = 0 configure:2629: result: yes configure:2638: checking whether gcc accepts -g configure:2668: gcc -c -g conftest.c >&5 configure:2675: $? = 0 configure:2776: result: yes configure:2793: checking for gcc option to accept ISO C89 configure:2867: gcc -c -g -O2 conftest.c >&5 configure:2874: $? = 0 configure:2897: result: none needed configure:2920: checking how to run the C preprocessor configure:2960: gcc -E conftest.c configure:2967: $? = 0 configure:2998: gcc -E conftest.c conftest.c:9:28: error: ac_nonexistent.h: No such file or directory configure:3005: $? = 1 configure: failed program was: | /* confdefs.h. */ | #define PACKAGE_NAME "" | #define PACKAGE_TARNAME "" | #define PACKAGE_VERSION "" | #define PACKAGE_STRING "" | #define PACKAGE_BUGREPORT "" | #define LINUX 1 | /* end confdefs.h. */ | #include configure:3038: result: gcc -E configure:3067: gcc -E conftest.c configure:3074: $? = 0 configure:3105: gcc -E conftest.c conftest.c:9:28: error: ac_nonexistent.h: No such file or directory configure:3112: $? = 1 configure: failed program was: | /* confdefs.h. */ | #define PACKAGE_NAME "" | #define PACKAGE_TARNAME "" | #define PACKAGE_VERSION "" | #define PACKAGE_STRING "" | #define PACKAGE_BUGREPORT "" | #define LINUX 1 | /* end confdefs.h. */ | #include configure:3209: checking for g++ configure:3225: found /usr/bin/g++ configure:3236: result: g++ configure:3263: checking for C++ compiler version configure:3271: g++ --version >&5 g++ (GCC) 4.1.2 20080704 (Red Hat 4.1.2-48) 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:3275: $? = 0 configure:3282: g++ -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 --enable-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 4.1.2-48) configure:3286: $? = 0 configure:3293: g++ -V >&5 g++: '-V' option must have argument configure:3297: $? = 1 configure:3300: checking whether we are using the GNU C++ compiler configure:3329: g++ -c conftest.cpp >&5 configure:3336: $? = 0 configure:3353: result: yes configure:3362: checking whether g++ accepts -g configure:3392: g++ -c -g conftest.cpp >&5 configure:3399: $? = 0 configure:3500: result: yes configure:3566: checking for ranlib configure:3582: found /usr/bin/ranlib configure:3593: result: ranlib configure:3629: checking for a BSD-compatible install configure:3697: result: /usr/bin/install -c configure:3710: checking for find configure:3726: found /usr/bin/find configure:3738: result: find configure:3748: checking for makedepend configure:3764: found /usr/bin/makedepend configure:3776: result: makedepend configure:3785: checking for dlopen in -ldl configure:3820: gcc -o conftest -g -O2 conftest.c -ldl >&5 configure:3827: $? = 0 configure:3848: result: yes configure:3863: checking for X configure:4034: gcc -o conftest -g -O2 conftest.c -lX11 >&5 configure:4041: $? = 0 configure:4103: result: libraries , headers configure:4272: gcc -o conftest -g -O2 conftest.c -lX11 >&5 configure:4279: $? = 0 configure:4447: checking for gethostbyname configure:4503: gcc -o conftest -g -O2 conftest.c >&5 configure:4510: $? = 0 configure:4530: result: yes configure:4683: checking for connect configure:4739: gcc -o conftest -g -O2 conftest.c >&5 configure:4746: $? = 0 configure:4766: result: yes configure:4842: checking for remove configure:4898: gcc -o conftest -g -O2 conftest.c >&5 configure:4905: $? = 0 configure:4925: result: yes configure:5001: checking for shmat configure:5057: gcc -o conftest -g -O2 conftest.c >&5 configure:5064: $? = 0 configure:5084: result: yes configure:5169: checking for IceConnectionNumber in -lICE configure:5204: gcc -o conftest -g -O2 conftest.c -lICE >&5 configure:5211: $? = 0 configure:5232: result: yes configure:5256: checking for main in -lm configure:5285: gcc -o conftest -g -O2 -I/usr/local/include -L/usr/local/lib conftest.c -lm >&5 configure:5292: $? = 0 configure:5313: result: yes configure:5327: checking for main in -lX11 configure:5356: gcc -o conftest -g -O2 -I/usr/local/include -L/usr/local/lib -lm conftest.c -lX11 >&5 configure:5363: $? = 0 configure:5384: result: yes configure:5393: checking for main in -lgd configure:5422: gcc -o conftest -g -O2 -I/usr/local/include -L/usr/local/lib -lm -lX11 conftest.c -lgd >&5 configure:5429: $? = 0 configure:5450: result: yes configure:5461: checking for gdImagePng configure:5517: gcc -o conftest -g -O2 -I/usr/local/include -L/usr/local/lib -lm -lX11 -lgd conftest.c >&5 configure:5524: $? = 0 configure:5544: result: yes configure:5558: checking host system type configure:5573: result: x86_64-unknown-linux-gnu configure:5841: checking for grep that handles long lines and -e configure:5901: result: /bin/grep configure:5906: checking for egrep configure:5970: result: /bin/grep -E configure:5975: checking for ANSI C header files configure:6005: gcc -c -g -O2 -I/usr/local/include conftest.c >&5 configure:6012: $? = 0 configure:6111: gcc -o conftest -g -O2 -I/usr/local/include -L/usr/local/lib -lm -lX11 -lgd conftest.c >&5 configure:6115: $? = 0 configure:6121: ./conftest configure:6125: $? = 0 configure:6143: result: yes configure:6167: checking for sys/types.h configure:6188: gcc -c -g -O2 -I/usr/local/include conftest.c >&5 configure:6195: $? = 0 configure:6212: result: yes configure:6167: checking for sys/stat.h configure:6188: gcc -c -g -O2 -I/usr/local/include conftest.c >&5 configure:6195: $? = 0 configure:6212: result: yes configure:6167: checking for stdlib.h configure:6188: gcc -c -g -O2 -I/usr/local/include conftest.c >&5 configure:6195: $? = 0 configure:6212: result: yes configure:6167: checking for string.h configure:6188: gcc -c -g -O2 -I/usr/local/include conftest.c >&5 configure:6195: $? = 0 configure:6212: result: yes configure:6167: checking for memory.h configure:6188: gcc -c -g -O2 -I/usr/local/include conftest.c >&5 configure:6195: $? = 0 configure:6212: result: yes configure:6167: checking for strings.h configure:6188: gcc -c -g -O2 -I/usr/local/include conftest.c >&5 configure:6195: $? = 0 configure:6212: result: yes configure:6167: checking for inttypes.h configure:6188: gcc -c -g -O2 -I/usr/local/include conftest.c >&5 configure:6195: $? = 0 configure:6212: result: yes configure:6167: checking for stdint.h configure:6188: gcc -c -g -O2 -I/usr/local/include conftest.c >&5 configure:6195: $? = 0 configure:6212: result: yes configure:6167: checking for unistd.h configure:6188: gcc -c -g -O2 -I/usr/local/include conftest.c >&5 configure:6195: $? = 0 configure:6212: result: yes configure:6242: checking limits.h usability configure:6259: gcc -c -g -O2 -I/usr/local/include conftest.c >&5 configure:6266: $? = 0 configure:6280: result: yes configure:6284: checking limits.h presence configure:6299: gcc -E conftest.c configure:6306: $? = 0 configure:6320: result: yes configure:6348: checking for limits.h configure:6357: result: yes configure:6519: creating ./config.status ## ---------------------- ## ## Running config.status. ## ## ---------------------- ## This file was extended by config.status, which was generated by GNU Autoconf 2.63. Invocation command line was CONFIG_FILES = CONFIG_HEADERS = CONFIG_LINKS = CONFIG_COMMANDS = $ ./config.status on xhost09.bcgsc.ca config.status:679: creating Makefile config.status:679: creating demo/Makefile config.status:679: creating g2_perl/Makefile.PL ## ---------------- ## ## Cache variables. ## ## ---------------- ## ac_cv_build=x86_64-unknown-linux-gnu ac_cv_c_compiler_gnu=yes ac_cv_cxx_compiler_gnu=yes ac_cv_env_CCC_set= ac_cv_env_CCC_value= 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_CXXFLAGS_set= ac_cv_env_CXXFLAGS_value= ac_cv_env_CXX_set= ac_cv_env_CXX_value= ac_cv_env_LDFLAGS_set= ac_cv_env_LDFLAGS_value= ac_cv_env_LIBS_set= ac_cv_env_LIBS_value= ac_cv_env_XMKMF_set= ac_cv_env_XMKMF_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_func_connect=yes ac_cv_func_gdImagePng=yes ac_cv_func_gethostbyname=yes ac_cv_func_remove=yes ac_cv_func_shmat=yes ac_cv_have_x='have_x=yes ac_x_includes='\'''\'' ac_x_libraries='\'''\''' ac_cv_header_inttypes_h=yes ac_cv_header_limits_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_types_h=yes ac_cv_header_unistd_h=yes ac_cv_host=x86_64-unknown-linux-gnu ac_cv_lib_ICE_IceConnectionNumber=yes ac_cv_lib_X11_main=yes ac_cv_lib_dl_dlopen=yes ac_cv_lib_gd_main=yes ac_cv_lib_m_main=yes ac_cv_objext=o ac_cv_path_EGREP='/bin/grep -E' ac_cv_path_GREP=/bin/grep ac_cv_path_install='/usr/bin/install -c' ac_cv_prog_CPP='gcc -E' ac_cv_prog_FIND=find ac_cv_prog_MAKEDEPEND=makedepend ac_cv_prog_ac_ct_CC=gcc ac_cv_prog_ac_ct_CXX=g++ ac_cv_prog_ac_ct_RANLIB=ranlib ac_cv_prog_cc_c89= ac_cv_prog_cc_g=yes ac_cv_prog_cxx_g=yes ## ----------------- ## ## Output variables. ## ## ----------------- ## CC='gcc' CFLAGS='-g -O2 -I/usr/local/include' CPP='gcc -E' CPPFLAGS='' CXX='g++' CXXFLAGS='-g -O2' DEFS='-DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DLINUX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DDO_GD=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1' DO_FIG='' DO_GD='' DO_PS='' DO_WIN32='#' DO_X11='' ECHO_C='' ECHO_N='-n' ECHO_T='' EGREP='/bin/grep -E' EXEEXT='' FIND='find' GREP='/bin/grep' INSTALL_DATA='${INSTALL} -m 644' INSTALL_PROGRAM='${INSTALL}' INSTALL_SCRIPT='${INSTALL}' LDFLAGS=' -L/usr/local/lib -lm -lX11 -lgd' LD_SHARED='ld' LD_SHARED_EXT='so.0.$(G2_VERSION)' LD_SHARED_FLAGS='-shared -soname libg2.so.0' LD_SHARED_OPT='' LIBOBJS='' LIBS='' LTLIBOBJS='' MAKEDEPEND='makedepend' OBJEXT='o' PACKAGE_BUGREPORT='' PACKAGE_NAME='' PACKAGE_STRING='' PACKAGE_TARNAME='' PACKAGE_VERSION='' PATH_SEPARATOR=':' RANLIB='ranlib' SHELL='/bin/sh' XMKMF='' X_CFLAGS='' X_EXTRA_LIBS='' X_LIBS='' X_PRE_LIBS=' -lSM -lICE' ac_ct_CC='gcc' ac_ct_CXX='g++' 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/${PACKAGE}' dvidir='${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='/projects/remc_bigdata/miR/vRNA-2.0.0' 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 "" #define PACKAGE_TARNAME "" #define PACKAGE_VERSION "" #define PACKAGE_STRING "" #define PACKAGE_BUGREPORT "" #define LINUX 1 #define DO_PS 1 #define DO_FIG 1 #define DO_X11 1 #define DO_GD 1 #define STDC_HEADERS 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_LIMITS_H 1 configure: exit 0