This file contains any messages produced by compilers while running configure, to aid debugging if configure makes a mistake. It was created by ViennaRNA configure 2.0.0, which was generated by GNU Autoconf 2.63. Invocation command line was $ ./configure --prefix=/projects/remc_bigdata/TCGA/RNA/ViennaRNA-2.0.0 ## --------- ## ## 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:1950: checking for a BSD-compatible install configure:2018: result: /usr/bin/install -c configure:2029: checking whether build environment is sane configure:2089: result: yes configure:2230: checking for a thread-safe mkdir -p configure:2269: result: /bin/mkdir -p configure:2282: checking for gawk configure:2298: found /bin/gawk configure:2309: result: gawk configure:2320: checking whether make sets $(MAKE) configure:2342: result: yes configure:2431: checking if malloc debugging is wanted configure:2451: result: no configure:2508: checking build system type configure:2526: result: x86_64-unknown-linux-gnu configure:2548: checking host system type configure:2563: result: x86_64-unknown-linux-gnu configure:2644: checking for g++ configure:2660: found /usr/bin/g++ configure:2671: result: g++ configure:2698: checking for C++ compiler version configure:2706: 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:2710: $? = 0 configure:2717: 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:2721: $? = 0 configure:2728: g++ -V >&5 g++: '-V' option must have argument configure:2732: $? = 1 configure:2755: checking for C++ compiler default output file name configure:2777: g++ conftest.cpp >&5 configure:2781: $? = 0 configure:2819: result: a.out configure:2838: checking whether the C++ compiler works configure:2848: ./a.out configure:2852: $? = 0 configure:2871: result: yes configure:2878: checking whether we are cross compiling configure:2880: result: no configure:2883: checking for suffix of executables configure:2890: g++ -o conftest conftest.cpp >&5 configure:2894: $? = 0 configure:2920: result: configure:2926: checking for suffix of object files configure:2952: g++ -c conftest.cpp >&5 configure:2956: $? = 0 configure:2981: result: o configure:2985: checking whether we are using the GNU C++ compiler configure:3014: g++ -c conftest.cpp >&5 configure:3021: $? = 0 configure:3038: result: yes configure:3047: checking whether g++ accepts -g configure:3077: g++ -c -g conftest.cpp >&5 configure:3084: $? = 0 configure:3185: result: yes configure:3219: checking for style of include used by make configure:3247: result: GNU configure:3272: checking dependency style of g++ configure:3382: result: gcc3 configure:3402: checking how to run the C++ preprocessor configure:3438: g++ -E conftest.cpp configure:3445: $? = 0 configure:3476: g++ -E conftest.cpp conftest.cpp:10:28: error: ac_nonexistent.h: No such file or directory configure:3483: $? = 1 configure: failed program was: | /* confdefs.h. */ | #define PACKAGE_NAME "ViennaRNA" | #define PACKAGE_TARNAME "ViennaRNA" | #define PACKAGE_VERSION "2.0.0" | #define PACKAGE_STRING "ViennaRNA 2.0.0" | #define PACKAGE_BUGREPORT "rna@tbi.univie.ac.at" | #define PACKAGE "ViennaRNA" | #define VERSION "2.0.0" | /* end confdefs.h. */ | #include configure:3516: result: g++ -E configure:3545: g++ -E conftest.cpp configure:3552: $? = 0 configure:3583: g++ -E conftest.cpp conftest.cpp:10:28: error: ac_nonexistent.h: No such file or directory configure:3590: $? = 1 configure: failed program was: | /* confdefs.h. */ | #define PACKAGE_NAME "ViennaRNA" | #define PACKAGE_TARNAME "ViennaRNA" | #define PACKAGE_VERSION "2.0.0" | #define PACKAGE_STRING "ViennaRNA 2.0.0" | #define PACKAGE_BUGREPORT "rna@tbi.univie.ac.at" | #define PACKAGE "ViennaRNA" | #define VERSION "2.0.0" | /* end confdefs.h. */ | #include configure:3677: checking for gcc configure:3693: found /usr/bin/gcc configure:3704: result: gcc configure:3936: checking for C compiler version configure:3944: 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:3948: $? = 0 configure:3955: 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:3959: $? = 0 configure:3966: gcc -V >&5 gcc: '-V' option must have argument configure:3970: $? = 1 configure:3973: checking whether we are using the GNU C compiler configure:4002: gcc -c conftest.c >&5 configure:4009: $? = 0 configure:4026: result: yes configure:4035: checking whether gcc accepts -g configure:4065: gcc -c -g conftest.c >&5 configure:4072: $? = 0 configure:4173: result: yes configure:4190: checking for gcc option to accept ISO C89 configure:4264: gcc -c -g -O2 conftest.c >&5 configure:4271: $? = 0 configure:4294: result: none needed configure:4314: checking dependency style of gcc configure:4424: result: gcc3 configure:4444: checking how to run the C preprocessor configure:4484: gcc -E conftest.c configure:4491: $? = 0 configure:4522: gcc -E conftest.c conftest.c:10:28: error: ac_nonexistent.h: No such file or directory configure:4529: $? = 1 configure: failed program was: | /* confdefs.h. */ | #define PACKAGE_NAME "ViennaRNA" | #define PACKAGE_TARNAME "ViennaRNA" | #define PACKAGE_VERSION "2.0.0" | #define PACKAGE_STRING "ViennaRNA 2.0.0" | #define PACKAGE_BUGREPORT "rna@tbi.univie.ac.at" | #define PACKAGE "ViennaRNA" | #define VERSION "2.0.0" | /* end confdefs.h. */ | #include configure:4562: result: gcc -E configure:4591: gcc -E conftest.c configure:4598: $? = 0 configure:4629: gcc -E conftest.c conftest.c:10:28: error: ac_nonexistent.h: No such file or directory configure:4636: $? = 1 configure: failed program was: | /* confdefs.h. */ | #define PACKAGE_NAME "ViennaRNA" | #define PACKAGE_TARNAME "ViennaRNA" | #define PACKAGE_VERSION "2.0.0" | #define PACKAGE_STRING "ViennaRNA 2.0.0" | #define PACKAGE_BUGREPORT "rna@tbi.univie.ac.at" | #define PACKAGE "ViennaRNA" | #define VERSION "2.0.0" | /* end confdefs.h. */ | #include configure:4678: checking whether gcc accepts -fpic configure:4704: gcc -c -fpic conftest.c >&5 configure:4711: $? = 0 configure:4726: result: yes configure:4762: checking for a BSD-compatible install configure:4830: result: /usr/bin/install -c configure:4884: checking for ranlib configure:4900: found /usr/bin/ranlib configure:4911: result: ranlib configure:4934: checking whether gcc and cc understand -c and -o together configure:4969: gcc -c conftest.c -o conftest2.o >&5 configure:4973: $? = 0 configure:4979: gcc -c conftest.c -o conftest2.o >&5 configure:4983: $? = 0 configure:4994: cc -c conftest.c >&5 configure:4998: $? = 0 configure:5006: cc -c conftest.c -o conftest2.o >&5 configure:5010: $? = 0 configure:5016: cc -c conftest.c -o conftest2.o >&5 configure:5020: $? = 0 configure:5038: result: yes configure:5069: checking for perl configure:5087: found /home/grobertson/linux_x86_64/perl_5.10/bin/perl configure:5099: result: /home/grobertson/linux_x86_64/perl_5.10/bin/perl configure:5174: performing libSVM specific checks configure:5179: checking for grep that handles long lines and -e configure:5239: result: /bin/grep configure:5244: checking for egrep configure:5308: result: /bin/grep -E configure:5313: checking for ANSI C header files configure:5343: gcc -c -g -O2 conftest.c >&5 configure:5350: $? = 0 configure:5449: gcc -o conftest -g -O2 conftest.c >&5 configure:5453: $? = 0 configure:5459: ./conftest configure:5463: $? = 0 configure:5481: result: yes configure:5505: checking for sys/types.h configure:5526: gcc -c -g -O2 conftest.c >&5 configure:5533: $? = 0 configure:5550: result: yes configure:5505: checking for sys/stat.h configure:5526: gcc -c -g -O2 conftest.c >&5 configure:5533: $? = 0 configure:5550: result: yes configure:5505: checking for stdlib.h configure:5526: gcc -c -g -O2 conftest.c >&5 configure:5533: $? = 0 configure:5550: result: yes configure:5505: checking for string.h configure:5526: gcc -c -g -O2 conftest.c >&5 configure:5533: $? = 0 configure:5550: result: yes configure:5505: checking for memory.h configure:5526: gcc -c -g -O2 conftest.c >&5 configure:5533: $? = 0 configure:5550: result: yes configure:5505: checking for strings.h configure:5526: gcc -c -g -O2 conftest.c >&5 configure:5533: $? = 0 configure:5550: result: yes configure:5505: checking for inttypes.h configure:5526: gcc -c -g -O2 conftest.c >&5 configure:5533: $? = 0 configure:5550: result: yes configure:5505: checking for stdint.h configure:5526: gcc -c -g -O2 conftest.c >&5 configure:5533: $? = 0 configure:5550: result: yes configure:5505: checking for unistd.h configure:5526: gcc -c -g -O2 conftest.c >&5 configure:5533: $? = 0 configure:5550: result: yes configure:5585: checking float.h usability configure:5602: gcc -c -g -O2 conftest.c >&5 configure:5609: $? = 0 configure:5623: result: yes configure:5627: checking float.h presence configure:5642: gcc -E conftest.c configure:5649: $? = 0 configure:5663: result: yes configure:5696: checking for float.h configure:5705: result: yes configure:5585: checking limits.h usability configure:5602: gcc -c -g -O2 conftest.c >&5 configure:5609: $? = 0 configure:5623: result: yes configure:5627: checking limits.h presence configure:5642: gcc -E conftest.c configure:5649: $? = 0 configure:5663: result: yes configure:5696: checking for limits.h configure:5705: result: yes configure:5574: checking for stdlib.h configure:5581: result: yes configure:5574: checking for string.h configure:5581: result: yes configure:5574: checking for strings.h configure:5581: result: yes configure:5574: checking for unistd.h configure:5581: result: yes configure:5721: checking for stdbool.h that conforms to C99 configure:5816: gcc -c -g -O2 conftest.c >&5 configure:5823: $? = 0 configure:5838: result: yes configure:5840: checking for _Bool configure:5868: gcc -c -g -O2 conftest.c >&5 configure:5875: $? = 0 configure:5902: gcc -c -g -O2 conftest.c >&5 conftest.c: In function 'main': conftest.c:63: error: expected expression before ')' token configure:5909: $? = 1 configure: failed program was: | /* confdefs.h. */ | #define PACKAGE_NAME "ViennaRNA" | #define PACKAGE_TARNAME "ViennaRNA" | #define PACKAGE_VERSION "2.0.0" | #define PACKAGE_STRING "ViennaRNA 2.0.0" | #define PACKAGE_BUGREPORT "rna@tbi.univie.ac.at" | #define PACKAGE "ViennaRNA" | #define VERSION "2.0.0" | #define UNUSED __attribute__ ((unused)) | #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_FLOAT_H 1 | #define HAVE_LIMITS_H 1 | #define HAVE_STDLIB_H 1 | #define HAVE_STRING_H 1 | #define HAVE_STRINGS_H 1 | #define HAVE_UNISTD_H 1 | /* end confdefs.h. */ | #include | #ifdef HAVE_SYS_TYPES_H | # include | #endif | #ifdef HAVE_SYS_STAT_H | # include | #endif | #ifdef STDC_HEADERS | # include | # include | #else | # ifdef HAVE_STDLIB_H | # include | # endif | #endif | #ifdef HAVE_STRING_H | # if !defined STDC_HEADERS && defined HAVE_MEMORY_H | # include | # endif | # include | #endif | #ifdef HAVE_STRINGS_H | # include | #endif | #ifdef HAVE_INTTYPES_H | # include | #endif | #ifdef HAVE_STDINT_H | # include | #endif | #ifdef HAVE_UNISTD_H | # include | #endif | int | main () | { | if (sizeof ((_Bool))) | return 0; | ; | return 0; | } configure:5932: result: yes configure:5951: checking for inline configure:5977: gcc -c -g -O2 conftest.c >&5 configure:5984: $? = 0 configure:6002: result: inline configure:6021: checking for size_t configure:6049: gcc -c -g -O2 conftest.c >&5 configure:6056: $? = 0 configure:6083: gcc -c -g -O2 conftest.c >&5 conftest.c: In function 'main': conftest.c:65: error: expected expression before ')' token configure:6090: $? = 1 configure: failed program was: | /* confdefs.h. */ | #define PACKAGE_NAME "ViennaRNA" | #define PACKAGE_TARNAME "ViennaRNA" | #define PACKAGE_VERSION "2.0.0" | #define PACKAGE_STRING "ViennaRNA 2.0.0" | #define PACKAGE_BUGREPORT "rna@tbi.univie.ac.at" | #define PACKAGE "ViennaRNA" | #define VERSION "2.0.0" | #define UNUSED __attribute__ ((unused)) | #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_FLOAT_H 1 | #define HAVE_LIMITS_H 1 | #define HAVE_STDLIB_H 1 | #define HAVE_STRING_H 1 | #define HAVE_STRINGS_H 1 | #define HAVE_UNISTD_H 1 | #define HAVE__BOOL 1 | #define HAVE_STDBOOL_H 1 | /* end confdefs.h. */ | #include | #ifdef HAVE_SYS_TYPES_H | # include | #endif | #ifdef HAVE_SYS_STAT_H | # include | #endif | #ifdef STDC_HEADERS | # include | # include | #else | # ifdef HAVE_STDLIB_H | # include | # endif | #endif | #ifdef HAVE_STRING_H | # if !defined STDC_HEADERS && defined HAVE_MEMORY_H | # include | # endif | # include | #endif | #ifdef HAVE_STRINGS_H | # include | #endif | #ifdef HAVE_INTTYPES_H | # include | #endif | #ifdef HAVE_STDINT_H | # include | #endif | #ifdef HAVE_UNISTD_H | # include | #endif | int | main () | { | if (sizeof ((size_t))) | return 0; | ; | return 0; | } configure:6113: result: yes configure:6131: checking for stdlib.h configure:6138: result: yes configure:6277: checking for GNU libc compatible malloc configure:6311: gcc -o conftest -g -O2 conftest.c >&5 configure:6315: $? = 0 configure:6321: ./conftest configure:6325: $? = 0 configure:6342: result: yes configure:6375: checking for stdlib.h configure:6382: result: yes configure:6521: checking for GNU libc compatible realloc configure:6555: gcc -o conftest -g -O2 conftest.c >&5 configure:6559: $? = 0 configure:6565: ./conftest configure:6569: $? = 0 configure:6586: result: yes configure:6614: checking for working strtod configure:6665: gcc -o conftest -g -O2 conftest.c >&5 configure:6669: $? = 0 configure:6675: ./conftest configure:6679: $? = 0 configure:6696: result: yes configure:6883: checking for floor configure:6939: gcc -o conftest -g -O2 conftest.c >&5 conftest.c:56: warning: conflicting types for built-in function 'floor' /tmp/cckDqieo.o: In function `main': /projects/remc_bigdata/TCGA/RNA/ViennaRNA-2.0.0/conftest.c:67: undefined reference to `floor' collect2: ld returned 1 exit status configure:6946: $? = 1 configure: failed program was: | /* confdefs.h. */ | #define PACKAGE_NAME "ViennaRNA" | #define PACKAGE_TARNAME "ViennaRNA" | #define PACKAGE_VERSION "2.0.0" | #define PACKAGE_STRING "ViennaRNA 2.0.0" | #define PACKAGE_BUGREPORT "rna@tbi.univie.ac.at" | #define PACKAGE "ViennaRNA" | #define VERSION "2.0.0" | #define UNUSED __attribute__ ((unused)) | #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_FLOAT_H 1 | #define HAVE_LIMITS_H 1 | #define HAVE_STDLIB_H 1 | #define HAVE_STRING_H 1 | #define HAVE_STRINGS_H 1 | #define HAVE_UNISTD_H 1 | #define HAVE__BOOL 1 | #define HAVE_STDBOOL_H 1 | #define HAVE_STDLIB_H 1 | #define HAVE_MALLOC 1 | #define HAVE_STDLIB_H 1 | #define HAVE_REALLOC 1 | /* end confdefs.h. */ | /* Define floor to an innocuous variant, in case declares floor. | For example, HP-UX 11i declares gettimeofday. */ | #define floor innocuous_floor | | /* System header to define __stub macros and hopefully few prototypes, | which can conflict with char floor (); below. | Prefer to if __STDC__ is defined, since | exists even on freestanding compilers. */ | | #ifdef __STDC__ | # include | #else | # include | #endif | | #undef floor | | /* Override any GCC internal prototype to avoid an error. | Use char because int might match the return type of a GCC | builtin and then its argument prototype would still apply. */ | #ifdef __cplusplus | extern "C" | #endif | char floor (); | /* The GNU C library defines this for functions which it implements | to always fail with ENOSYS. Some functions are actually named | something starting with __ and the normal name is an alias. */ | #if defined __stub_floor || defined __stub___floor | choke me | #endif | | int | main () | { | return floor (); | ; | return 0; | } configure:6968: result: no configure:6883: checking for memmove configure:6939: gcc -o conftest -g -O2 conftest.c >&5 conftest.c:56: warning: conflicting types for built-in function 'memmove' configure:6946: $? = 0 configure:6968: result: yes configure:6883: checking for memset configure:6939: gcc -o conftest -g -O2 conftest.c >&5 conftest.c:57: warning: conflicting types for built-in function 'memset' configure:6946: $? = 0 configure:6968: result: yes configure:6883: checking for pow configure:6939: gcc -o conftest -g -O2 conftest.c >&5 conftest.c:58: warning: conflicting types for built-in function 'pow' /tmp/cckeD7CD.o: In function `main': /projects/remc_bigdata/TCGA/RNA/ViennaRNA-2.0.0/conftest.c:69: undefined reference to `pow' collect2: ld returned 1 exit status configure:6946: $? = 1 configure: failed program was: | /* confdefs.h. */ | #define PACKAGE_NAME "ViennaRNA" | #define PACKAGE_TARNAME "ViennaRNA" | #define PACKAGE_VERSION "2.0.0" | #define PACKAGE_STRING "ViennaRNA 2.0.0" | #define PACKAGE_BUGREPORT "rna@tbi.univie.ac.at" | #define PACKAGE "ViennaRNA" | #define VERSION "2.0.0" | #define UNUSED __attribute__ ((unused)) | #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_FLOAT_H 1 | #define HAVE_LIMITS_H 1 | #define HAVE_STDLIB_H 1 | #define HAVE_STRING_H 1 | #define HAVE_STRINGS_H 1 | #define HAVE_UNISTD_H 1 | #define HAVE__BOOL 1 | #define HAVE_STDBOOL_H 1 | #define HAVE_STDLIB_H 1 | #define HAVE_MALLOC 1 | #define HAVE_STDLIB_H 1 | #define HAVE_REALLOC 1 | #define HAVE_MEMMOVE 1 | #define HAVE_MEMSET 1 | /* end confdefs.h. */ | /* Define pow to an innocuous variant, in case declares pow. | For example, HP-UX 11i declares gettimeofday. */ | #define pow innocuous_pow | | /* System header to define __stub macros and hopefully few prototypes, | which can conflict with char pow (); below. | Prefer to if __STDC__ is defined, since | exists even on freestanding compilers. */ | | #ifdef __STDC__ | # include | #else | # include | #endif | | #undef pow | | /* Override any GCC internal prototype to avoid an error. | Use char because int might match the return type of a GCC | builtin and then its argument prototype would still apply. */ | #ifdef __cplusplus | extern "C" | #endif | char pow (); | /* The GNU C library defines this for functions which it implements | to always fail with ENOSYS. Some functions are actually named | something starting with __ and the normal name is an alias. */ | #if defined __stub_pow || defined __stub___pow | choke me | #endif | | int | main () | { | return pow (); | ; | return 0; | } configure:6968: result: no configure:6883: checking for sqrt configure:6939: gcc -o conftest -g -O2 conftest.c >&5 conftest.c:58: warning: conflicting types for built-in function 'sqrt' /tmp/cc4jiTJO.o: In function `main': /projects/remc_bigdata/TCGA/RNA/ViennaRNA-2.0.0/conftest.c:69: undefined reference to `sqrt' collect2: ld returned 1 exit status configure:6946: $? = 1 configure: failed program was: | /* confdefs.h. */ | #define PACKAGE_NAME "ViennaRNA" | #define PACKAGE_TARNAME "ViennaRNA" | #define PACKAGE_VERSION "2.0.0" | #define PACKAGE_STRING "ViennaRNA 2.0.0" | #define PACKAGE_BUGREPORT "rna@tbi.univie.ac.at" | #define PACKAGE "ViennaRNA" | #define VERSION "2.0.0" | #define UNUSED __attribute__ ((unused)) | #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_FLOAT_H 1 | #define HAVE_LIMITS_H 1 | #define HAVE_STDLIB_H 1 | #define HAVE_STRING_H 1 | #define HAVE_STRINGS_H 1 | #define HAVE_UNISTD_H 1 | #define HAVE__BOOL 1 | #define HAVE_STDBOOL_H 1 | #define HAVE_STDLIB_H 1 | #define HAVE_MALLOC 1 | #define HAVE_STDLIB_H 1 | #define HAVE_REALLOC 1 | #define HAVE_MEMMOVE 1 | #define HAVE_MEMSET 1 | /* end confdefs.h. */ | /* Define sqrt to an innocuous variant, in case declares sqrt. | For example, HP-UX 11i declares gettimeofday. */ | #define sqrt innocuous_sqrt | | /* System header to define __stub macros and hopefully few prototypes, | which can conflict with char sqrt (); below. | Prefer to if __STDC__ is defined, since | exists even on freestanding compilers. */ | | #ifdef __STDC__ | # include | #else | # include | #endif | | #undef sqrt | | /* Override any GCC internal prototype to avoid an error. | Use char because int might match the return type of a GCC | builtin and then its argument prototype would still apply. */ | #ifdef __cplusplus | extern "C" | #endif | char sqrt (); | /* The GNU C library defines this for functions which it implements | to always fail with ENOSYS. Some functions are actually named | something starting with __ and the normal name is an alias. */ | #if defined __stub_sqrt || defined __stub___sqrt | choke me | #endif | | int | main () | { | return sqrt (); | ; | return 0; | } configure:6968: result: no configure:6883: checking for strchr configure:6939: gcc -o conftest -g -O2 conftest.c >&5 conftest.c:58: warning: conflicting types for built-in function 'strchr' configure:6946: $? = 0 configure:6968: result: yes configure:6883: checking for strdup configure:6939: gcc -o conftest -g -O2 conftest.c >&5 conftest.c:59: warning: conflicting types for built-in function 'strdup' configure:6946: $? = 0 configure:6968: result: yes configure:6883: checking for strndup configure:6939: gcc -o conftest -g -O2 conftest.c >&5 conftest.c:60: warning: conflicting types for built-in function 'strndup' configure:6946: $? = 0 configure:6968: result: yes configure:6883: checking for strrchr configure:6939: gcc -o conftest -g -O2 conftest.c >&5 conftest.c:61: warning: conflicting types for built-in function 'strrchr' configure:6946: $? = 0 configure:6968: result: yes configure:6883: checking for strstr configure:6939: gcc -o conftest -g -O2 conftest.c >&5 conftest.c:62: warning: conflicting types for built-in function 'strstr' configure:6946: $? = 0 configure:6968: result: yes configure:6883: checking for strtol configure:6939: gcc -o conftest -g -O2 conftest.c >&5 configure:6946: $? = 0 configure:6968: result: yes configure:6883: checking for strtoul configure:6939: gcc -o conftest -g -O2 conftest.c >&5 configure:6946: $? = 0 configure:6968: result: yes configure:6980: checking whether provided libSVM source is present... configure:7069: result: yes configure:7084: checking for gcc option to support OpenMP configure:7104: gcc -o conftest -g -O2 conftest.c >&5 conftest.c:3: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'me' In file included from conftest.c:5: /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/omp.h:68: error: expected ')' before '*' token /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/omp.h:69: error: expected ')' before '*' token /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/omp.h:70: error: expected ')' before '*' token /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/omp.h:71: error: expected ')' before '*' token /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/omp.h:72: error: expected ')' before '*' token configure:7111: $? = 1 configure: failed program was: | | #ifndef _OPENMP | choke me | #endif | #include | int main () { return omp_get_num_threads (); } | configure:7143: gcc -o conftest -g -O2 -fopenmp conftest.c >&5 configure:7150: $? = 0 configure:7180: result: -fopenmp configure:7241: checking for ANSI C header files configure:7409: result: yes configure:7438: checking malloc.h usability configure:7455: gcc -c -g -O2 conftest.c >&5 configure:7462: $? = 0 configure:7476: result: yes configure:7480: checking malloc.h presence configure:7495: gcc -E conftest.c configure:7502: $? = 0 configure:7516: result: yes configure:7549: checking for malloc.h configure:7558: result: yes configure:7427: checking for strings.h configure:7434: result: yes configure:7427: checking for unistd.h configure:7434: result: yes configure:7438: checking math.h usability configure:7455: gcc -c -g -O2 conftest.c >&5 configure:7462: $? = 0 configure:7476: result: yes configure:7480: checking math.h presence configure:7495: gcc -E conftest.c configure:7502: $? = 0 configure:7516: result: yes configure:7549: checking for math.h configure:7558: result: yes configure:7578: checking for memset configure:7663: result: yes configure:7578: checking for memmove configure:7663: result: yes configure:7676: checking for an ANSI C-conforming const configure:7751: gcc -c -g -O2 conftest.c >&5 configure:7758: $? = 0 configure:7773: result: yes configure:7783: checking for size_t configure:7875: result: yes configure:7887: checking for inline configure:7938: result: inline configure:7965: checking for strdup configure:8050: result: yes configure:7965: checking for strstr configure:8050: result: yes configure:7965: checking for strchr configure:8050: result: yes configure:7965: checking for erand48 configure:8021: gcc -o conftest -g -O2 conftest.c >&5 configure:8028: $? = 0 configure:8050: result: yes configure:8233: creating ./config.status ## ---------------------- ## ## Running config.status. ## ## ---------------------- ## This file was extended by ViennaRNA config.status 2.0.0, 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:852: creating Makefile config.status:852: creating ViennaRNA.spec config.status:852: creating Utils/Makefile config.status:852: creating Progs/Makefile config.status:852: creating lib/Makefile config.status:852: creating man/Makefile config.status:852: creating Cluster/Makefile config.status:852: creating H/Makefile config.status:852: creating Perl/Makefile config.status:852: creating Perl/Makefile.PL config.status:852: creating man/cmdlopt.sh config.status:852: creating config.h config.status:1126: executing depfiles commands configure:9646: === configuring in Perl (/projects/remc_bigdata/TCGA/RNA/ViennaRNA-2.0.0/Perl) configure:9735: WARNING: no configuration information is in Perl configure:9646: === configuring in Kinfold (/projects/remc_bigdata/TCGA/RNA/ViennaRNA-2.0.0/Kinfold) configure:9749: running /bin/sh ./configure --disable-option-checking '--prefix=/projects/remc_bigdata/TCGA/RNA/ViennaRNA-2.0.0' --cache-file=/dev/null --srcdir=. configure:9646: === configuring in RNAforester (/projects/remc_bigdata/TCGA/RNA/ViennaRNA-2.0.0/RNAforester) configure:9749: running /bin/sh ./configure --disable-option-checking '--prefix=/projects/remc_bigdata/TCGA/RNA/ViennaRNA-2.0.0' --cache-file=/dev/null --srcdir=. configure:9646: === configuring in Cluster (/projects/remc_bigdata/TCGA/RNA/ViennaRNA-2.0.0/Cluster) configure:9735: WARNING: no configuration information is in Cluster configure:9790: Configure successful with the following options: Perl Extension: yes Analyse{Dists,Seqs}: no Kinfold: yes RNAforester: yes SVM: yes Files will be installed in the following directories: Executables: /projects/remc_bigdata/TCGA/RNA/ViennaRNA-2.0.0/bin Libraries: /projects/remc_bigdata/TCGA/RNA/ViennaRNA-2.0.0/lib Header files: /projects/remc_bigdata/TCGA/RNA/ViennaRNA-2.0.0/include Extra Data: ${prefix}/share Man pages: ${prefix}/share/man ## ---------------- ## ## Cache variables. ## ## ---------------- ## ac_cv_build=x86_64-unknown-linux-gnu ac_cv_c_compiler_gnu=yes ac_cv_c_const=yes ac_cv_c_inline=inline 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_CXXCPP_set= ac_cv_env_CXXCPP_value= ac_cv_env_CXXFLAGS_set= ac_cv_env_CXXFLAGS_value= ac_cv_env_CXX_set= ac_cv_env_CXX_value= ac_cv_env_FPIC_set= ac_cv_env_FPIC_value= ac_cv_env_LDFLAGS_set= ac_cv_env_LDFLAGS_value= ac_cv_env_LIBS_set= ac_cv_env_LIBS_value= ac_cv_env_PERLPREFIX_set= ac_cv_env_PERLPREFIX_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_erand48=yes ac_cv_func_floor=no ac_cv_func_malloc_0_nonnull=yes ac_cv_func_memmove=yes ac_cv_func_memset=yes ac_cv_func_pow=no ac_cv_func_realloc_0_nonnull=yes ac_cv_func_sqrt=no ac_cv_func_strchr=yes ac_cv_func_strdup=yes ac_cv_func_strndup=yes ac_cv_func_strrchr=yes ac_cv_func_strstr=yes ac_cv_func_strtod=yes ac_cv_func_strtol=yes ac_cv_func_strtoul=yes ac_cv_header_float_h=yes ac_cv_header_inttypes_h=yes ac_cv_header_limits_h=yes ac_cv_header_malloc_h=yes ac_cv_header_math_h=yes ac_cv_header_memory_h=yes ac_cv_header_stdbool_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_objext=o ac_cv_path_EGREP='/bin/grep -E' ac_cv_path_GREP=/bin/grep ac_cv_path_PerlCmd=/home/grobertson/linux_x86_64/perl_5.10/bin/perl ac_cv_path_install='/usr/bin/install -c' ac_cv_path_mkdir=/bin/mkdir ac_cv_prog_AWK=gawk ac_cv_prog_CPP='gcc -E' ac_cv_prog_CXXCPP='g++ -E' ac_cv_prog_ac_ct_CC=gcc ac_cv_prog_ac_ct_CXX=g++ ac_cv_prog_ac_ct_RANLIB=ranlib ac_cv_prog_c_openmp=-fopenmp ac_cv_prog_cc_c89= ac_cv_prog_cc_fpic=yes ac_cv_prog_cc_g=yes ac_cv_prog_cc_gcc_c_o=yes ac_cv_prog_cxx_g=yes ac_cv_prog_make_make_set=yes ac_cv_type__Bool=yes ac_cv_type_size_t=yes am_cv_CC_dependencies_compiler_type=gcc3 am_cv_CXX_dependencies_compiler_type=gcc3 ## ----------------- ## ## Output variables. ## ## ----------------- ## ACLOCAL='${SHELL} /projects/remc_bigdata/TCGA/RNA/ViennaRNA-2.0.0/missing --run aclocal-1.11' AMDEPBACKSLASH='\' AMDEP_FALSE='#' AMDEP_TRUE='' AMTAR='${SHELL} /projects/remc_bigdata/TCGA/RNA/ViennaRNA-2.0.0/missing --run tar' AUTOCONF='${SHELL} /projects/remc_bigdata/TCGA/RNA/ViennaRNA-2.0.0/missing --run autoconf' AUTOHEADER='${SHELL} /projects/remc_bigdata/TCGA/RNA/ViennaRNA-2.0.0/missing --run autoheader' AUTOMAKE='${SHELL} /projects/remc_bigdata/TCGA/RNA/ViennaRNA-2.0.0/missing --run automake-1.11' AWK='gawk' CC='gcc' CCDEPMODE='depmode=gcc3' CFLAGS='-g -O2' CPP='gcc -E' CPPFLAGS='' CXX='g++' CXXCPP='g++ -E' CXXDEPMODE='depmode=gcc3' CXXFLAGS='-g -O2' CXXLD='g++' CYGPATH_W='echo' DEFS='-DHAVE_CONFIG_H' DEPDIR='.deps' ECHO_C='' ECHO_N='-n' ECHO_T='' EGREP='/bin/grep -E' EXEEXT='' FPIC='-fpic' GREP='/bin/grep' INSTALL_DATA='${INSTALL} -m 644' INSTALL_PROGRAM='${INSTALL}' INSTALL_SCRIPT='${INSTALL}' INSTALL_STRIP_PROGRAM='$(install_sh) -c -s' ISODATE='2011-05-09' LDFLAGS='' LIBOBJS='' LIBS='' LIBSVM_DIR='./libsvm-2.91' LTLIBOBJS='' MAKEINFO='${SHELL} /projects/remc_bigdata/TCGA/RNA/ViennaRNA-2.0.0/missing --run makeinfo' MAKE_CLUSTER_FALSE='' MAKE_CLUSTER_TRUE='#' MAKE_FORESTER_FALSE='#' MAKE_FORESTER_TRUE='' MAKE_KINFOLD_FALSE='#' MAKE_KINFOLD_TRUE='' MAKE_PERL_EXT_FALSE='#' MAKE_PERL_EXT_TRUE='' MKDIR_P='/bin/mkdir -p' OBJEXT='o' OPENMP_CFLAGS='-fopenmp' PACKAGE='ViennaRNA' PACKAGE_BUGREPORT='rna@tbi.univie.ac.at' PACKAGE_NAME='ViennaRNA' PACKAGE_STRING='ViennaRNA 2.0.0' PACKAGE_TARNAME='ViennaRNA' PACKAGE_VERSION='2.0.0' PATH_SEPARATOR=':' PERLPREFIX='' POW_LIB='' PerlCmd='/home/grobertson/linux_x86_64/perl_5.10/bin/perl' RANLIB='ranlib' SET_MAKE='' SHELL='/bin/sh' STRIP='' SVM_SOURCE_ARCHIVE='libsvm-2.91.tar.gz' TAR='' VERSION='2.0.0' WITH_LIBSVM_FALSE='#' WITH_LIBSVM_TRUE='' ac_ct_CC='gcc' ac_ct_CXX='g++' am__EXEEXT_FALSE='' am__EXEEXT_TRUE='#' am__fastdepCC_FALSE='#' am__fastdepCC_TRUE='' am__fastdepCXX_FALSE='#' am__fastdepCXX_TRUE='' am__include='include' am__isrc='' am__leading_dot='.' am__quote='' am__tar='${AMTAR} chof - "$$tardir"' am__untar='${AMTAR} xf -' bindir='${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='${datarootdir}/info' install_sh='${SHELL} /projects/remc_bigdata/TCGA/RNA/ViennaRNA-2.0.0/install-sh' libdir='${exec_prefix}/lib' libexecdir='${exec_prefix}/libexec' localedir='${datarootdir}/locale' localstatedir='${prefix}/var' mandir='${datarootdir}/man' mkdir_p='/bin/mkdir -p' oldincludedir='/usr/include' pdfdir='${docdir}' prefix='/projects/remc_bigdata/TCGA/RNA/ViennaRNA-2.0.0' program_transform_name='s,x,x,' psdir='${docdir}' sbindir='${exec_prefix}/sbin' sharedstatedir='${prefix}/com' subdirs=' Perl Kinfold RNAforester Cluster' sysconfdir='${prefix}/etc' target_alias='' ## ----------- ## ## confdefs.h. ## ## ----------- ## #define PACKAGE_NAME "ViennaRNA" #define PACKAGE_TARNAME "ViennaRNA" #define PACKAGE_VERSION "2.0.0" #define PACKAGE_STRING "ViennaRNA 2.0.0" #define PACKAGE_BUGREPORT "rna@tbi.univie.ac.at" #define PACKAGE "ViennaRNA" #define VERSION "2.0.0" #define UNUSED __attribute__ ((unused)) #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_FLOAT_H 1 #define HAVE_LIMITS_H 1 #define HAVE_STDLIB_H 1 #define HAVE_STRING_H 1 #define HAVE_STRINGS_H 1 #define HAVE_UNISTD_H 1 #define HAVE__BOOL 1 #define HAVE_STDBOOL_H 1 #define HAVE_STDLIB_H 1 #define HAVE_MALLOC 1 #define HAVE_STDLIB_H 1 #define HAVE_REALLOC 1 #define HAVE_MEMMOVE 1 #define HAVE_MEMSET 1 #define HAVE_STRCHR 1 #define HAVE_STRDUP 1 #define HAVE_STRNDUP 1 #define HAVE_STRRCHR 1 #define HAVE_STRSTR 1 #define HAVE_STRTOL 1 #define HAVE_STRTOUL 1 #define USE_SVM 1 #define STDC_HEADERS 1 #define HAVE_MALLOC_H 1 #define HAVE_STRINGS_H 1 #define HAVE_UNISTD_H 1 #define HAVE_MATH_H 1 #define HAVE_MEMSET 1 #define HAVE_MEMMOVE 1 #define HAVE_STRDUP 1 #define HAVE_STRSTR 1 #define HAVE_STRCHR 1 #define HAVE_ERAND48 1 configure: exit 0