This file contains any messages produced by compilers while running configure, to aid debugging if configure makes a mistake. It was created by dafs configure 0.0.3, which was generated by GNU Autoconf 2.69. Invocation command line was $ ./configure --with-vienna-rna=/home/slab/aoki/tools/ViennaRNA-2.4.1 --prefix=/home/slab/aoki/tools/dafs --with-glpk ## --------- ## ## Platform. ## ## --------- ## hostname = ssh uname -m = x86_64 uname -r = 3.2.0-4-amd64 uname -s = Linux uname -v = #1 SMP Debian 3.2.73-2+deb7u3 /usr/bin/uname -p = unknown /bin/uname -X = unknown /bin/arch = unknown /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/slab/aoki/.pyenv/shims PATH: /home/slab/aoki/tools/protobuf-3.0.0/bin PATH: /home/slab/aoki/tools/ViennaRNA-2.4.1/bin/ PATH: /home/slab/aoki/tools/EnsembleClust-1.0.1/src/wpgma PATH: /home/slab/saito/test/EnsembleClust-1.0.1/src/similarity/bpla_kernel PATH: /home/slab/aoki/tools/perl-5.24.2/bin/ PATH: /home/slab/aoki/tools/swig-3.0.12/bin/ PATH: /home/slab/aoki/tools/RNAclust-1.3/bin/ PATH: /home/slab/aoki/tools/locarna-1.9.2/bin/ PATH: /home/slab/aoki/tools/dafs-CNN/bin/ PATH: /home/slab/aoki/tools/PicXAA-v1.03/bin/ PATH: /home/slab/aoki/tools/glpk-4.62/bin/ PATH: /home/slab/aoki/tools/centroid-rna-package/bin/ PATH: /home/slab/aoki/tools/bedops/bin/ PATH: /home/slab/aoki/tools/bamtools/bin/ PATH: /home/slab/aoki/tools/miRanda-3.3a/bin/ PATH: /home/slab/aoki/tools/infernal-1.1.1/bin/ PATH: /home/slab/aoki/.local/bin/ PATH: /home/proj/solexa/ PATH: /home/slab/aoki/tools/fastx_toolkit-0.0.14/bin/ PATH: /home/slab/aoki/archive/cutadapt-1.8.1/bin/ PATH: /home/slab/aoki/tools/sharaku_v2/ PATH: /home/slab/aoki/tools/dafs-sharaku/bin/ PATH: /home/slab/aoki/tools/Graph-theoretic_method/MACE/ PATH: /home/slab/aoki/.pyenv/bin/ PATH: /home/slab/aoki/tools/R-3.2.0/bin/ PATH: /home/slab/aoki/tools/cufflinks-2.2.1.Linux_x86_64/ PATH: /home/slab/aoki/tools/tophat-2.0.14.Linux_x86_64/ PATH: /home/slab/aoki/tools/bowtie2-2.2.5/ PATH: /home/slab/aoki/tools/samtools-1.2/ PATH: /home/slab/aoki/tools/bedtools-2.17.0/bin/ PATH: /home/slab/aoki/tools/bwa-0.7.10/ PATH: /usr/local/bin PATH: /usr/bin PATH: /bin PATH: /usr/local/games PATH: /usr/games PATH: /usr/local/cuda/bin PATH: /home/slab/tsuchiya/tools/mirdeep2_0_0_6 PATH: /home/slab/tsuchiya/tools/mirdeep2_0_0_6/essentials/ViennaRNA-1.8.4/install_dir/bin PATH: /home/slab/tsuchiya/tools/mirdeep2_0_0_6/essentials/randfold-2.0 ## ----------- ## ## Core tests. ## ## ----------- ## configure:2313: checking for a BSD-compatible install configure:2381: result: /usr/bin/install -c configure:2392: checking whether build environment is sane configure:2447: result: yes configure:2598: checking for a thread-safe mkdir -p configure:2637: result: /bin/mkdir -p configure:2644: checking for gawk configure:2660: found /usr/bin/gawk configure:2671: result: gawk configure:2682: checking whether make sets $(MAKE) configure:2704: result: yes configure:2733: checking whether make supports nested variables configure:2750: result: yes configure:2939: checking for g++ configure:2955: found /home/slab/aoki/.pyenv/shims/g++ configure:2966: result: g++ configure:2993: checking for C++ compiler version configure:3002: g++ --version >&5 g++ (GCC) 4.8.5 Copyright (C) 2015 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:3013: $? = 0 configure:3002: g++ -v >&5 Reading specs from /home/slab/aoki/.pyenv/versions/anaconda3-4.1.0/bin/../lib/gcc/x86_64-unknown-linux-gnu/4.8.5/specs COLLECT_GCC=g++ COLLECT_LTO_WRAPPER=/home/slab/aoki/.pyenv/versions/anaconda3-4.1.0/bin/../libexec/gcc/x86_64-unknown-linux-gnu/4.8.5/lto-wrapper Target: x86_64-unknown-linux-gnu Configured with: ./configure --prefix=/home/ray/mc-x64-2.7/conda-bld/gcc_1479223211463/_b_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold --with-gxx-include-dir=/home/ray/mc-x64-2.7/conda-bld/gcc_1479223211463/_b_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/gcc/include/c++ --bindir=/home/ray/mc-x64-2.7/conda-bld/gcc_1479223211463/_b_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/bin --datarootdir=/home/ray/mc-x64-2.7/conda-bld/gcc_1479223211463/_b_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/share --libdir=/home/ray/mc-x64-2.7/conda-bld/gcc_1479223211463/_b_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/lib --with-gmp=/home/ray/mc-x64-2.7/conda-bld/gcc_1479223211463/_b_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold --with-mpfr=/home/ray/mc-x64-2.7/conda-bld/gcc_1479223211463/_b_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold --with-mpc=/home/ray/mc-x64-2.7/conda-bld/gcc_1479223211463/_b_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold --with-isl=/home/ray/mc-x64-2.7/conda-bld/gcc_1479223211463/_b_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold --with-cloog=/home/ray/mc-x64-2.7/conda-bld/gcc_1479223211463/_b_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold --enable-checking=release --with-tune=generic --disable-multilib Thread model: posix gcc version 4.8.5 (GCC) configure:3013: $? = 0 configure:3002: g++ -V >&5 g++: error: unrecognized command line option '-V' g++: fatal error: no input files compilation terminated. configure:3013: $? = 1 configure:3002: g++ -qversion >&5 g++: error: unrecognized command line option '-qversion' g++: fatal error: no input files compilation terminated. configure:3013: $? = 1 configure:3033: checking whether the C++ compiler works configure:3055: g++ conftest.cpp >&5 configure:3059: $? = 0 configure:3107: result: yes configure:3110: checking for C++ compiler default output file name configure:3112: result: a.out configure:3118: checking for suffix of executables configure:3125: g++ -o conftest conftest.cpp >&5 configure:3129: $? = 0 configure:3151: result: configure:3173: checking whether we are cross compiling configure:3181: g++ -o conftest conftest.cpp >&5 configure:3185: $? = 0 configure:3192: ./conftest configure:3196: $? = 0 configure:3211: result: no configure:3216: checking for suffix of object files configure:3238: g++ -c conftest.cpp >&5 configure:3242: $? = 0 configure:3263: result: o configure:3267: checking whether we are using the GNU C++ compiler configure:3286: g++ -c conftest.cpp >&5 configure:3286: $? = 0 configure:3295: result: yes configure:3304: checking whether g++ accepts -g configure:3324: g++ -c -g conftest.cpp >&5 configure:3324: $? = 0 configure:3365: result: yes configure:3399: checking for style of include used by make configure:3427: result: GNU configure:3453: checking dependency style of g++ configure:3564: result: gcc3 configure:3627: checking for gcc configure:3643: found /home/slab/aoki/.pyenv/shims/gcc configure:3654: result: gcc configure:3883: checking for C compiler version configure:3892: gcc --version >&5 gcc (GCC) 4.8.5 Copyright (C) 2015 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:3903: $? = 0 configure:3892: gcc -v >&5 Reading specs from /home/slab/aoki/.pyenv/versions/anaconda3-4.1.0/bin/../lib/gcc/x86_64-unknown-linux-gnu/4.8.5/specs COLLECT_GCC=gcc COLLECT_LTO_WRAPPER=/home/slab/aoki/.pyenv/versions/anaconda3-4.1.0/bin/../libexec/gcc/x86_64-unknown-linux-gnu/4.8.5/lto-wrapper Target: x86_64-unknown-linux-gnu Configured with: ./configure --prefix=/home/ray/mc-x64-2.7/conda-bld/gcc_1479223211463/_b_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold --with-gxx-include-dir=/home/ray/mc-x64-2.7/conda-bld/gcc_1479223211463/_b_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/gcc/include/c++ --bindir=/home/ray/mc-x64-2.7/conda-bld/gcc_1479223211463/_b_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/bin --datarootdir=/home/ray/mc-x64-2.7/conda-bld/gcc_1479223211463/_b_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/share --libdir=/home/ray/mc-x64-2.7/conda-bld/gcc_1479223211463/_b_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/lib --with-gmp=/home/ray/mc-x64-2.7/conda-bld/gcc_1479223211463/_b_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold --with-mpfr=/home/ray/mc-x64-2.7/conda-bld/gcc_1479223211463/_b_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold --with-mpc=/home/ray/mc-x64-2.7/conda-bld/gcc_1479223211463/_b_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold --with-isl=/home/ray/mc-x64-2.7/conda-bld/gcc_1479223211463/_b_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold --with-cloog=/home/ray/mc-x64-2.7/conda-bld/gcc_1479223211463/_b_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold --enable-checking=release --with-tune=generic --disable-multilib Thread model: posix gcc version 4.8.5 (GCC) configure:3903: $? = 0 configure:3892: gcc -V >&5 gcc: error: unrecognized command line option '-V' gcc: fatal error: no input files compilation terminated. configure:3903: $? = 1 configure:3892: gcc -qversion >&5 gcc: error: unrecognized command line option '-qversion' gcc: fatal error: no input files compilation terminated. configure:3903: $? = 1 configure:3907: checking whether we are using the GNU C compiler configure:3926: gcc -c conftest.c >&5 configure:3926: $? = 0 configure:3935: result: yes configure:3944: checking whether gcc accepts -g configure:3964: gcc -c -g conftest.c >&5 configure:3964: $? = 0 configure:4005: result: yes configure:4022: checking for gcc option to accept ISO C89 configure:4085: gcc -c -g -O2 conftest.c >&5 configure:4085: $? = 0 configure:4098: result: none needed configure:4123: checking whether gcc understands -c and -o together configure:4145: gcc -c conftest.c -o conftest2.o configure:4148: $? = 0 configure:4145: gcc -c conftest.c -o conftest2.o configure:4148: $? = 0 configure:4160: result: yes configure:4179: checking dependency style of gcc configure:4290: result: gcc3 configure:4312: checking whether the compiler implements namespaces configure:4335: g++ -c -g -O2 conftest.cpp >&5 configure:4335: $? = 0 configure:4349: result: yes configure:4357: checking whether the compiler supports Standard Template Library configure:4386: g++ -c -g -O2 conftest.cpp >&5 configure:4386: $? = 0 configure:4400: result: yes configure:4451: checking for ranlib configure:4467: found /usr/bin/ranlib configure:4478: result: ranlib configure:4550: checking for ar configure:4566: found /usr/bin/ar configure:4577: result: ar configure:4603: checking the archiver (ar) interface configure:4619: gcc -c -g -O2 conftest.c >&5 configure:4619: $? = 0 configure:4621: ar cru libconftest.a conftest.o >&5 configure:4624: $? = 0 configure:4652: result: ar configure:4688: checking for pthread_create in -lpthread configure:4713: g++ -o conftest -DNDEBUG -g -O2 conftest.cpp -lpthread >&5 configure:4713: $? = 0 configure:4722: result: yes configure:4740: checking how to run the C++ preprocessor configure:4767: g++ -E conftest.cpp configure:4767: $? = 0 configure:4781: g++ -E conftest.cpp conftest.cpp:14:28: fatal error: ac_nonexistent.h: No such file or directory #include ^ compilation terminated. configure:4781: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "dafs" | #define PACKAGE_TARNAME "dafs" | #define PACKAGE_VERSION "0.0.3" | #define PACKAGE_STRING "dafs 0.0.3" | #define PACKAGE_BUGREPORT "no-define" | #define PACKAGE_URL "" | #define PACKAGE "dafs" | #define VERSION "0.0.3" | #define HAVE_NAMESPACES /**/ | #define HAVE_STL /**/ | #define HAVE_LIBPTHREAD 1 | /* end confdefs.h. */ | #include configure:4806: result: g++ -E configure:4826: g++ -E conftest.cpp configure:4826: $? = 0 configure:4840: g++ -E conftest.cpp conftest.cpp:14:28: fatal error: ac_nonexistent.h: No such file or directory #include ^ compilation terminated. configure:4840: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "dafs" | #define PACKAGE_TARNAME "dafs" | #define PACKAGE_VERSION "0.0.3" | #define PACKAGE_STRING "dafs 0.0.3" | #define PACKAGE_BUGREPORT "no-define" | #define PACKAGE_URL "" | #define PACKAGE "dafs" | #define VERSION "0.0.3" | #define HAVE_NAMESPACES /**/ | #define HAVE_STL /**/ | #define HAVE_LIBPTHREAD 1 | /* end confdefs.h. */ | #include configure:4869: checking for grep that handles long lines and -e configure:4927: result: /bin/grep configure:4932: checking for egrep configure:4994: result: /bin/grep -E configure:4999: checking for ANSI C header files configure:5019: g++ -c -DNDEBUG -g -O2 conftest.cpp >&5 configure:5019: $? = 0 configure:5092: g++ -o conftest -DNDEBUG -g -O2 conftest.cpp -lpthread >&5 configure:5092: $? = 0 configure:5092: ./conftest configure:5092: $? = 0 configure:5103: result: yes configure:5116: checking for sys/types.h configure:5116: g++ -c -DNDEBUG -g -O2 conftest.cpp >&5 configure:5116: $? = 0 configure:5116: result: yes configure:5116: checking for sys/stat.h configure:5116: g++ -c -DNDEBUG -g -O2 conftest.cpp >&5 configure:5116: $? = 0 configure:5116: result: yes configure:5116: checking for stdlib.h configure:5116: g++ -c -DNDEBUG -g -O2 conftest.cpp >&5 configure:5116: $? = 0 configure:5116: result: yes configure:5116: checking for string.h configure:5116: g++ -c -DNDEBUG -g -O2 conftest.cpp >&5 configure:5116: $? = 0 configure:5116: result: yes configure:5116: checking for memory.h configure:5116: g++ -c -DNDEBUG -g -O2 conftest.cpp >&5 configure:5116: $? = 0 configure:5116: result: yes configure:5116: checking for strings.h configure:5116: g++ -c -DNDEBUG -g -O2 conftest.cpp >&5 configure:5116: $? = 0 configure:5116: result: yes configure:5116: checking for inttypes.h configure:5116: g++ -c -DNDEBUG -g -O2 conftest.cpp >&5 configure:5116: $? = 0 configure:5116: result: yes configure:5116: checking for stdint.h configure:5116: g++ -c -DNDEBUG -g -O2 conftest.cpp >&5 configure:5116: $? = 0 configure:5116: result: yes configure:5116: checking for unistd.h configure:5116: g++ -c -DNDEBUG -g -O2 conftest.cpp >&5 configure:5116: $? = 0 configure:5116: result: yes configure:5140: checking glpk.h usability configure:5140: g++ -c -DNDEBUG -g -O2 -DWITH_GLPK conftest.cpp >&5 configure:5140: $? = 0 configure:5140: result: yes configure:5140: checking glpk.h presence configure:5140: g++ -E -DWITH_GLPK conftest.cpp configure:5140: $? = 0 configure:5140: result: yes configure:5140: checking for glpk.h configure:5140: result: yes configure:5150: checking for main in -lz configure:5169: g++ -o conftest -DNDEBUG -g -O2 -DWITH_GLPK conftest.cpp -lz -lpthread >&5 configure:5169: $? = 0 configure:5178: result: yes configure:5189: checking for main in -lgmp configure:5208: g++ -o conftest -DNDEBUG -g -O2 -DWITH_GLPK conftest.cpp -lgmp -lz -lpthread >&5 configure:5208: $? = 0 configure:5217: result: yes configure:5228: checking for main in -ldl configure:5247: g++ -o conftest -DNDEBUG -g -O2 -DWITH_GLPK conftest.cpp -ldl -lgmp -lz -lpthread >&5 configure:5247: $? = 0 configure:5256: result: yes configure:5267: checking for main in -lltdl configure:5286: g++ -o conftest -DNDEBUG -g -O2 -DWITH_GLPK conftest.cpp -lltdl -ldl -lgmp -lz -lpthread >&5 configure:5286: $? = 0 configure:5295: result: yes configure:5306: checking for glp_create_prob in -lglpk configure:5331: g++ -o conftest -DNDEBUG -g -O2 -DWITH_GLPK conftest.cpp -lglpk -lltdl -ldl -lgmp -lz -lpthread >&5 configure:5331: $? = 0 configure:5340: result: yes configure:5521: checking for pf_fold in -lRNA configure:5546: g++ -o conftest -DNDEBUG -g -O2 -I/home/slab/aoki/tools/ViennaRNA-2.4.1/include -DWITH_GLPK -L/home/slab/aoki/tools/ViennaRNA-2.4.1/lib conftest.cpp -lRNA -lglpk -lltdl -ldl -lgmp -lz -lpthread >&5 /home/slab/aoki/tools/ViennaRNA-2.4.1/lib/libRNA.a(part_func.o): In function `vrna_pf': part_func.c:(.text+0xc4): undefined reference to `omp_set_dynamic' collect2: error: ld returned 1 exit status configure:5546: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "dafs" | #define PACKAGE_TARNAME "dafs" | #define PACKAGE_VERSION "0.0.3" | #define PACKAGE_STRING "dafs 0.0.3" | #define PACKAGE_BUGREPORT "no-define" | #define PACKAGE_URL "" | #define PACKAGE "dafs" | #define VERSION "0.0.3" | #define HAVE_NAMESPACES /**/ | #define HAVE_STL /**/ | #define HAVE_LIBPTHREAD 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_GLPK_H 1 | #define HAVE_LIBZ 1 | #define HAVE_LIBGMP 1 | #define HAVE_LIBDL 1 | #define HAVE_LIBLTDL 1 | #define HAVE_LIBGLPK 1 | /* end confdefs.h. */ | | /* 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 pf_fold (); | int | main () | { | return pf_fold (); | ; | return 0; | } configure:5555: result: no configure:5566: try '-fopenmp' configure:5571: checking for pf_fold in -lRNA configure:5596: g++ -o conftest -fopenmp -DNDEBUG -g -O2 -I/home/slab/aoki/tools/ViennaRNA-2.4.1/include -DWITH_GLPK -L/home/slab/aoki/tools/ViennaRNA-2.4.1/lib conftest.cpp -lRNA -lglpk -lltdl -ldl -lgmp -lz -lpthread >&5 configure:5596: $? = 0 configure:5605: result: yes configure:5621: checking ViennaRNA/ribo.h usability configure:5621: g++ -c -fopenmp -DNDEBUG -g -O2 -I/home/slab/aoki/tools/ViennaRNA-2.4.1/include -DWITH_GLPK conftest.cpp >&5 configure:5621: $? = 0 configure:5621: result: yes configure:5621: checking ViennaRNA/ribo.h presence configure:5621: g++ -E -I/home/slab/aoki/tools/ViennaRNA-2.4.1/include -DWITH_GLPK conftest.cpp configure:5621: $? = 0 configure:5621: result: yes configure:5621: checking for ViennaRNA/ribo.h configure:5621: result: yes configure:5629: checking for energy_of_structure configure:5629: g++ -o conftest -fopenmp -DNDEBUG -g -O2 -I/home/slab/aoki/tools/ViennaRNA-2.4.1/include -DWITH_GLPK -L/home/slab/aoki/tools/ViennaRNA-2.4.1/lib conftest.cpp -lRNA -lglpk -lltdl -ldl -lgmp -lz -lpthread >&5 configure:5629: $? = 0 configure:5629: result: yes configure:5643: checking getopt.h usability configure:5643: g++ -c -fopenmp -DNDEBUG -g -O2 -I/home/slab/aoki/tools/ViennaRNA-2.4.1/include -DWITH_GLPK conftest.cpp >&5 configure:5643: $? = 0 configure:5643: result: yes configure:5643: checking getopt.h presence configure:5643: g++ -E -I/home/slab/aoki/tools/ViennaRNA-2.4.1/include -DWITH_GLPK conftest.cpp configure:5643: $? = 0 configure:5643: result: yes configure:5643: checking for getopt.h configure:5643: result: yes configure:5655: checking for getopt_long configure:5655: g++ -o conftest -fopenmp -DNDEBUG -g -O2 -I/home/slab/aoki/tools/ViennaRNA-2.4.1/include -DWITH_GLPK -L/home/slab/aoki/tools/ViennaRNA-2.4.1/lib conftest.cpp -lRNA -lglpk -lltdl -ldl -lgmp -lz -lpthread >&5 configure:5655: $? = 0 configure:5655: result: yes configure:5725: checking for stdbool.h that conforms to C99 configure:5792: g++ -c -fopenmp -DNDEBUG -g -O2 -I/home/slab/aoki/tools/ViennaRNA-2.4.1/include -DWITH_GLPK conftest.cpp >&5 configure:5792: $? = 0 configure:5799: result: yes configure:5801: checking for _Bool configure:5801: g++ -c -fopenmp -DNDEBUG -g -O2 -I/home/slab/aoki/tools/ViennaRNA-2.4.1/include -DWITH_GLPK conftest.cpp >&5 conftest.cpp: In function 'int main()': conftest.cpp:71:13: error: '_Bool' was not declared in this scope if (sizeof (_Bool)) ^ configure:5801: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "dafs" | #define PACKAGE_TARNAME "dafs" | #define PACKAGE_VERSION "0.0.3" | #define PACKAGE_STRING "dafs 0.0.3" | #define PACKAGE_BUGREPORT "no-define" | #define PACKAGE_URL "" | #define PACKAGE "dafs" | #define VERSION "0.0.3" | #define HAVE_NAMESPACES /**/ | #define HAVE_STL /**/ | #define HAVE_LIBPTHREAD 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_GLPK_H 1 | #define HAVE_LIBZ 1 | #define HAVE_LIBGMP 1 | #define HAVE_LIBDL 1 | #define HAVE_LIBLTDL 1 | #define HAVE_LIBGLPK 1 | #define HAVE_LIBRNA 1 | #define HAVE_VIENNA18 /**/ | #define HAVE_VIENNA20 /**/ | #define HAVE_GETOPT_H 1 | #define HAVE_GETOPT_LONG 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:5801: result: no configure:5818: checking for an ANSI C-conforming const configure:5884: g++ -c -fopenmp -DNDEBUG -g -O2 -I/home/slab/aoki/tools/ViennaRNA-2.4.1/include -DWITH_GLPK conftest.cpp >&5 configure:5884: $? = 0 configure:5891: result: yes configure:5899: checking for inline configure:5915: g++ -c -fopenmp -DNDEBUG -g -O2 -I/home/slab/aoki/tools/ViennaRNA-2.4.1/include -DWITH_GLPK conftest.cpp >&5 configure:5915: $? = 0 configure:5923: result: inline configure:5941: checking for ANSI C header files configure:6045: result: yes configure:6164: checking that generated files are newer than configure configure:6170: result: done configure:6197: creating ./config.status ## ---------------------- ## ## Running config.status. ## ## ---------------------- ## This file was extended by dafs config.status 0.0.3, which was generated by GNU Autoconf 2.69. Invocation command line was CONFIG_FILES = CONFIG_HEADERS = CONFIG_LINKS = CONFIG_COMMANDS = $ ./config.status on ssh config.status:887: creating Makefile config.status:887: creating src/Makefile config.status:887: creating src/contrafold/Makefile config.status:887: creating src/probconsRNA/Makefile config.status:887: creating src/contralign/Makefile config.status:887: creating config.h config.status:1068: config.h is unchanged config.status:1147: executing depfiles commands ## ---------------- ## ## Cache variables. ## ## ---------------- ## ac_cv_c_compiler_gnu=yes ac_cv_c_const=yes ac_cv_c_inline=inline ac_cv_cxx_compiler_gnu=yes ac_cv_cxx_have_stl=yes ac_cv_cxx_namespaces=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_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_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_func_energy_of_structure=yes ac_cv_func_getopt_long=yes ac_cv_header_ViennaRNA_ribo_h=yes ac_cv_header_getopt_h=yes ac_cv_header_glpk_h=yes ac_cv_header_inttypes_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_lib_RNA_pf_fold=yes ac_cv_lib_dl_main=yes ac_cv_lib_glpk_glp_create_prob=yes ac_cv_lib_gmp_main=yes ac_cv_lib_ltdl_main=yes ac_cv_lib_pthread_pthread_create=yes ac_cv_lib_z_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_path_mkdir=/bin/mkdir ac_cv_prog_AWK=gawk ac_cv_prog_CXXCPP='g++ -E' ac_cv_prog_ac_ct_AR=ar 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 ac_cv_prog_make_make_set=yes ac_cv_type__Bool=no am_cv_CC_dependencies_compiler_type=gcc3 am_cv_CXX_dependencies_compiler_type=gcc3 am_cv_ar_interface=ar am_cv_make_support_nested_variables=yes am_cv_prog_cc_c_o=yes ## ----------------- ## ## Output variables. ## ## ----------------- ## ACLOCAL='${SHELL} /home/slab/aoki/tools/dafs/missing aclocal-1.15' AMDEPBACKSLASH='\' AMDEP_FALSE='#' AMDEP_TRUE='' AMTAR='$${TAR-tar}' AM_BACKSLASH='\' AM_DEFAULT_V='$(AM_DEFAULT_VERBOSITY)' AM_DEFAULT_VERBOSITY='1' AM_V='$(V)' AR='ar' AUTOCONF='${SHELL} /home/slab/aoki/tools/dafs/missing autoconf' AUTOHEADER='${SHELL} /home/slab/aoki/tools/dafs/missing autoheader' AUTOMAKE='${SHELL} /home/slab/aoki/tools/dafs/missing automake-1.15' AWK='gawk' CC='gcc' CCDEPMODE='depmode=gcc3' CFLAGS='-DNDEBUG -g -O2' CPPFLAGS='-I/home/slab/aoki/tools/ViennaRNA-2.4.1/include -DWITH_GLPK ' CXX='g++' CXXCPP='g++ -E' CXXDEPMODE='depmode=gcc3' CXXFLAGS='-fopenmp -DNDEBUG -g -O2' CYGPATH_W='echo' DEFS='-DHAVE_CONFIG_H' DEPDIR='.deps' ECHO_C='' ECHO_N='-n' ECHO_T='' EGREP='/bin/grep -E' EXEEXT='' GREP='/bin/grep' INSTALL_DATA='${INSTALL} -m 644' INSTALL_PROGRAM='${INSTALL}' INSTALL_SCRIPT='${INSTALL}' INSTALL_STRIP_PROGRAM='$(install_sh) -c -s' LDFLAGS='-L/home/slab/aoki/tools/ViennaRNA-2.4.1/lib ' LIBOBJS='' LIBS='-lRNA -lglpk -lltdl -ldl -lgmp -lz -lpthread ' LTLIBOBJS='' MAKEINFO='${SHELL} /home/slab/aoki/tools/dafs/missing makeinfo' MKDIR_P='/bin/mkdir -p' OBJEXT='o' PACKAGE='dafs' PACKAGE_BUGREPORT='no-define' PACKAGE_NAME='dafs' PACKAGE_STRING='dafs 0.0.3' PACKAGE_TARNAME='dafs' PACKAGE_URL='' PACKAGE_VERSION='0.0.3' PATH_SEPARATOR=':' RANLIB='ranlib' SET_MAKE='' SHELL='/bin/bash' STRIP='' VERSION='0.0.3' ac_ct_AR='ar' ac_ct_CC='gcc' ac_ct_CXX='g++' am__EXEEXT_FALSE='' am__EXEEXT_TRUE='#' am__fastdepCC_FALSE='#' am__fastdepCC_TRUE='' am__fastdepCXX_FALSE='#' am__fastdepCXX_TRUE='' am__include='include' am__isrc='' am__leading_dot='.' am__nodep='_no' am__quote='' am__tar='$${TAR-tar} chof - "$$tardir"' am__untar='$${TAR-tar} xf -' bindir='${exec_prefix}/bin' build_alias='' datadir='${datarootdir}' datarootdir='${prefix}/share' docdir='${datarootdir}/doc/${PACKAGE_TARNAME}' dvidir='${docdir}' exec_prefix='${prefix}' host_alias='' htmldir='${docdir}' includedir='${prefix}/include' infodir='${datarootdir}/info' install_sh='${SHELL} /home/slab/aoki/tools/dafs/install-sh' libdir='${exec_prefix}/lib' libexecdir='${exec_prefix}/libexec' localedir='${datarootdir}/locale' localstatedir='${prefix}/var' mandir='${datarootdir}/man' mkdir_p='$(MKDIR_P)' oldincludedir='/usr/include' pdfdir='${docdir}' prefix='/home/slab/aoki/tools/dafs' program_transform_name='s,x,x,' psdir='${docdir}' sbindir='${exec_prefix}/sbin' sharedstatedir='${prefix}/com' sysconfdir='${prefix}/etc' target_alias='' ## ----------- ## ## confdefs.h. ## ## ----------- ## /* confdefs.h */ #define PACKAGE_NAME "dafs" #define PACKAGE_TARNAME "dafs" #define PACKAGE_VERSION "0.0.3" #define PACKAGE_STRING "dafs 0.0.3" #define PACKAGE_BUGREPORT "no-define" #define PACKAGE_URL "" #define PACKAGE "dafs" #define VERSION "0.0.3" #define HAVE_NAMESPACES /**/ #define HAVE_STL /**/ #define HAVE_LIBPTHREAD 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_GLPK_H 1 #define HAVE_LIBZ 1 #define HAVE_LIBGMP 1 #define HAVE_LIBDL 1 #define HAVE_LIBLTDL 1 #define HAVE_LIBGLPK 1 #define HAVE_LIBRNA 1 #define HAVE_VIENNA18 /**/ #define HAVE_VIENNA20 /**/ #define HAVE_GETOPT_H 1 #define HAVE_GETOPT_LONG 1 #define HAVE_STDBOOL_H 1 #define STDC_HEADERS 1 configure: exit 0