This file contains any messages produced by compilers while running configure, to aid debugging if configure makes a mistake. It was created by EMBOSS configure 6.6.0, which was generated by GNU Autoconf 2.69. Invocation command line was $ ./configure --prefix=/bmlfast/bml_casp15/tools/casp14/casp14_qa/tools/EMBOSS-6.6.0/ ## --------- ## ## Platform. ## ## --------- ## hostname = orchid.rnet.missouri.edu uname -m = x86_64 uname -r = 4.18.0-513.18.1.el8_9.x86_64 uname -s = Linux uname -v = #1 SMP Thu Feb 22 03:02:37 EST 2024 /usr/bin/uname -p = x86_64 /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: /bmlfast/bml_casp15/tools/casp14/casp14_qa//tools/EMBOSS-6.6.0/bin/ PATH: /bmlfast/bml_casp15/tools/casp14/DeepRank_db_tools/tools/python_virtualenv/bin PATH: /home/jl4mc/mambaforge/condabin PATH: /home/jl4mc/.local/bin PATH: /home/jl4mc/bin PATH: /usr/share/Modules/bin PATH: /usr/lib64/ccache PATH: /usr/local/bin PATH: /usr/bin PATH: /usr/local/sbin PATH: /usr/sbin PATH: /opt/puppetlabs/bin ## ----------- ## ## Core tests. ## ## ----------- ## configure:2556: checking for gawk configure:2572: found /usr/bin/gawk configure:2583: result: gawk configure:2648: checking for icc configure:2678: result: no configure:2648: checking for gcc configure:2664: found /usr/lib64/ccache/gcc configure:2675: result: gcc configure:2706: checking for C compiler version configure:2715: gcc --version >&5 gcc (GCC) 8.5.0 20210514 (Red Hat 8.5.0-20) Copyright (C) 2018 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:2726: $? = 0 configure:2715: gcc -v >&5 Using built-in specs. COLLECT_GCC=/usr/bin/gcc COLLECT_LTO_WRAPPER=/usr/libexec/gcc/x86_64-redhat-linux/8/lto-wrapper OFFLOAD_TARGET_NAMES=nvptx-none OFFLOAD_TARGET_DEFAULT=1 Target: x86_64-redhat-linux Configured with: ../configure --enable-bootstrap --enable-languages=c,c++,fortran,lto --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --with-bugurl=http://bugs.almalinux.org/ --enable-shared --enable-threads=posix --enable-checking=release --enable-multilib --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-gnu-unique-object --enable-linker-build-id --with-gcc-major-version-only --with-linker-hash-style=gnu --enable-plugin --enable-initfini-array --with-isl --disable-libmpx --enable-offload-targets=nvptx-none --without-cuda-driver --enable-gnu-indirect-function --enable-cet --with-tune=generic --with-arch_32=x86-64 --build=x86_64-redhat-linux Thread model: posix gcc version 8.5.0 20210514 (Red Hat 8.5.0-20) (GCC) configure:2726: $? = 0 configure:2715: gcc -V >&5 gcc: error: unrecognized command line option '-V' gcc: fatal error: no input files compilation terminated. configure:2726: $? = 1 configure:2715: gcc -qversion >&5 gcc: error: unrecognized command line option '-qversion'; did you mean '--version'? gcc: fatal error: no input files compilation terminated. configure:2726: $? = 1 configure:2746: checking whether the C compiler works configure:2768: gcc conftest.c >&5 configure:2772: $? = 0 configure:2820: result: yes configure:2823: checking for C compiler default output file name configure:2825: result: a.out configure:2831: checking for suffix of executables configure:2838: gcc -o conftest conftest.c >&5 configure:2842: $? = 0 configure:2864: result: configure:2886: checking whether we are cross compiling configure:2894: gcc -o conftest conftest.c >&5 configure:2898: $? = 0 configure:2905: ./conftest configure:2909: $? = 0 configure:2924: result: no configure:2929: checking for suffix of object files configure:2951: gcc -c conftest.c >&5 configure:2955: $? = 0 configure:2976: result: o configure:2980: checking whether we are using the GNU C compiler configure:2999: gcc -c conftest.c >&5 configure:2999: $? = 0 configure:3008: result: yes configure:3017: checking whether gcc accepts -g configure:3037: gcc -c -g conftest.c >&5 configure:3037: $? = 0 configure:3078: result: yes configure:3095: checking for gcc option to accept ISO C89 configure:3158: gcc -c conftest.c >&5 configure:3158: $? = 0 configure:3171: result: none needed configure:3249: checking for icpc configure:3279: result: no configure:3249: checking for g++ configure:3265: found /usr/lib64/ccache/g++ configure:3276: result: g++ configure:3303: checking for C++ compiler version configure:3312: g++ --version >&5 g++ (GCC) 8.5.0 20210514 (Red Hat 8.5.0-20) Copyright (C) 2018 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:3323: $? = 0 configure:3312: g++ -v >&5 Using built-in specs. COLLECT_GCC=/usr/bin/g++ COLLECT_LTO_WRAPPER=/usr/libexec/gcc/x86_64-redhat-linux/8/lto-wrapper OFFLOAD_TARGET_NAMES=nvptx-none OFFLOAD_TARGET_DEFAULT=1 Target: x86_64-redhat-linux Configured with: ../configure --enable-bootstrap --enable-languages=c,c++,fortran,lto --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --with-bugurl=http://bugs.almalinux.org/ --enable-shared --enable-threads=posix --enable-checking=release --enable-multilib --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-gnu-unique-object --enable-linker-build-id --with-gcc-major-version-only --with-linker-hash-style=gnu --enable-plugin --enable-initfini-array --with-isl --disable-libmpx --enable-offload-targets=nvptx-none --without-cuda-driver --enable-gnu-indirect-function --enable-cet --with-tune=generic --with-arch_32=x86-64 --build=x86_64-redhat-linux Thread model: posix gcc version 8.5.0 20210514 (Red Hat 8.5.0-20) (GCC) configure:3323: $? = 0 configure:3312: g++ -V >&5 g++: error: unrecognized command line option '-V' g++: fatal error: no input files compilation terminated. configure:3323: $? = 1 configure:3312: g++ -qversion >&5 g++: error: unrecognized command line option '-qversion'; did you mean '--version'? g++: fatal error: no input files compilation terminated. configure:3323: $? = 1 configure:3327: checking whether we are using the GNU C++ compiler configure:3346: g++ -c conftest.cpp >&5 configure:3346: $? = 0 configure:3355: result: yes configure:3364: checking whether g++ accepts -g configure:3384: g++ -c -g conftest.cpp >&5 configure:3384: $? = 0 configure:3425: result: yes configure:3453: checking how to run the C preprocessor configure:3484: gcc -E conftest.c configure:3484: $? = 0 configure:3498: gcc -E conftest.c conftest.c:9:10: fatal error: ac_nonexistent.h: No such file or directory #include ^~~~~~~~~~~~~~~~~~ compilation terminated. configure:3498: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "EMBOSS" | #define PACKAGE_TARNAME "EMBOSS" | #define PACKAGE_VERSION "6.6.0" | #define PACKAGE_STRING "EMBOSS 6.6.0" | #define PACKAGE_BUGREPORT "emboss-bug@emboss.open-bio.org" | #define PACKAGE_URL "http://emboss.open-bio.org/" | /* end confdefs.h. */ | #include configure:3523: result: gcc -E configure:3543: gcc -E conftest.c configure:3543: $? = 0 configure:3557: gcc -E conftest.c conftest.c:9:10: fatal error: ac_nonexistent.h: No such file or directory #include ^~~~~~~~~~~~~~~~~~ compilation terminated. configure:3557: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "EMBOSS" | #define PACKAGE_TARNAME "EMBOSS" | #define PACKAGE_VERSION "6.6.0" | #define PACKAGE_STRING "EMBOSS 6.6.0" | #define PACKAGE_BUGREPORT "emboss-bug@emboss.open-bio.org" | #define PACKAGE_URL "http://emboss.open-bio.org/" | /* end confdefs.h. */ | #include configure:3628: checking for a BSD-compatible install configure:3696: result: /usr/bin/install -c configure:3707: checking whether ln -s works configure:3711: result: yes configure:3718: checking whether make sets $(MAKE) configure:3740: result: yes configure:3749: checking for a thread-safe mkdir -p configure:3788: result: /usr/bin/mkdir -p configure:3794: checking whether build environment is sane configure:3849: result: yes configure:4021: checking for style of include used by make configure:4049: result: GNU configure:4141: checking dependency style of gcc configure:4252: result: gcc3 configure:4269: checking dependency style of g++ configure:4380: result: gcc3 configure:4427: checking build system type configure:4441: result: x86_64-unknown-linux-gnu configure:4461: checking host system type configure:4474: result: x86_64-unknown-linux-gnu configure:4515: checking how to print strings configure:4542: result: printf configure:4563: checking for a sed that does not truncate output configure:4627: result: /usr/bin/sed configure:4645: checking for grep that handles long lines and -e configure:4703: result: /usr/bin/grep configure:4708: checking for egrep configure:4770: result: /usr/bin/grep -E configure:4775: checking for fgrep configure:4837: result: /usr/bin/grep -F configure:4872: checking for ld used by gcc configure:4939: result: /usr/bin/ld configure:4946: checking if the linker (/usr/bin/ld) is GNU ld configure:4961: result: yes configure:4973: checking for BSD- or MS-compatible name lister (nm) configure:5022: result: /usr/bin/nm -B configure:5152: checking the name lister (/usr/bin/nm -B) interface configure:5159: gcc -c conftest.c >&5 configure:5162: /usr/bin/nm -B "conftest.o" configure:5165: output 0000000000000000 B some_variable configure:5172: result: BSD nm configure:5176: checking the maximum length of command line arguments configure:5306: result: 1572864 configure:5323: checking whether the shell understands some XSI constructs configure:5333: result: yes configure:5337: checking whether the shell understands "+=" configure:5343: result: yes configure:5378: checking how to convert x86_64-unknown-linux-gnu file names to x86_64-unknown-linux-gnu format configure:5418: result: func_convert_file_noop configure:5425: checking how to convert x86_64-unknown-linux-gnu file names to toolchain format configure:5445: result: func_convert_file_noop configure:5452: checking for /usr/bin/ld option to reload object files configure:5459: result: -r configure:5533: checking for objdump configure:5549: found /usr/bin/objdump configure:5560: result: objdump configure:5592: checking how to recognize dependent libraries configure:5794: result: pass_all configure:5879: checking for dlltool configure:5909: result: no configure:5939: checking how to associate runtime and link libraries configure:5966: result: printf %s\n configure:6027: checking for ar configure:6043: found /usr/bin/ar configure:6054: result: ar configure:6091: checking for archiver @FILE support configure:6108: gcc -c conftest.c >&5 configure:6108: $? = 0 configure:6111: ar cru libconftest.a @conftest.lst >&5 configure:6114: $? = 0 configure:6119: ar cru libconftest.a @conftest.lst >&5 ar: conftest.o: No such file or directory configure:6122: $? = 1 configure:6134: result: @ configure:6192: checking for strip configure:6208: found /usr/bin/strip configure:6219: result: strip configure:6291: checking for ranlib configure:6307: found /usr/bin/ranlib configure:6318: result: ranlib configure:6420: checking command to parse /usr/bin/nm -B output from gcc object configure:6540: gcc -c conftest.c >&5 configure:6543: $? = 0 configure:6547: /usr/bin/nm -B conftest.o \| sed -n -e 's/^.*[ ]\([ABCDGIRSTW][ABCDGIRSTW]*\)[ ][ ]*\([_A-Za-z][_A-Za-z0-9]*\)$/\1 \2 \2/p' | sed '/ __gnu_lto/d' \> conftest.nm configure:6550: $? = 0 configure:6616: gcc -o conftest conftest.c conftstm.o >&5 configure:6619: $? = 0 configure:6657: result: ok configure:6694: checking for sysroot configure:6724: result: no configure:6801: gcc -c conftest.c >&5 configure:6804: $? = 0 configure:6980: checking for mt configure:7010: result: no configure:7030: checking if : is a manifest tool configure:7036: : '-?' configure:7044: result: no configure:7682: checking for ANSI C header files configure:7702: gcc -c conftest.c >&5 configure:7702: $? = 0 configure:7775: gcc -o conftest conftest.c >&5 configure:7775: $? = 0 configure:7775: ./conftest configure:7775: $? = 0 configure:7786: result: yes configure:7799: checking for sys/types.h configure:7799: gcc -c conftest.c >&5 configure:7799: $? = 0 configure:7799: result: yes configure:7799: checking for sys/stat.h configure:7799: gcc -c conftest.c >&5 configure:7799: $? = 0 configure:7799: result: yes configure:7799: checking for stdlib.h configure:7799: gcc -c conftest.c >&5 configure:7799: $? = 0 configure:7799: result: yes configure:7799: checking for string.h configure:7799: gcc -c conftest.c >&5 configure:7799: $? = 0 configure:7799: result: yes configure:7799: checking for memory.h configure:7799: gcc -c conftest.c >&5 configure:7799: $? = 0 configure:7799: result: yes configure:7799: checking for strings.h configure:7799: gcc -c conftest.c >&5 configure:7799: $? = 0 configure:7799: result: yes configure:7799: checking for inttypes.h configure:7799: gcc -c conftest.c >&5 configure:7799: $? = 0 configure:7799: result: yes configure:7799: checking for stdint.h configure:7799: gcc -c conftest.c >&5 configure:7799: $? = 0 configure:7799: result: yes configure:7799: checking for unistd.h configure:7799: gcc -c conftest.c >&5 configure:7799: $? = 0 configure:7799: result: yes configure:7813: checking for dlfcn.h configure:7813: gcc -c conftest.c >&5 configure:7813: $? = 0 configure:7813: result: yes configure:8030: checking for objdir configure:8045: result: .libs configure:8316: checking if gcc supports -fno-rtti -fno-exceptions configure:8334: gcc -c -fno-rtti -fno-exceptions conftest.c >&5 cc1: warning: command line option '-fno-rtti' is valid for C++/ObjC++ but not for C configure:8338: $? = 0 configure:8351: result: no configure:8678: checking for gcc option to produce PIC configure:8685: result: -fPIC -DPIC configure:8693: checking if gcc PIC flag -fPIC -DPIC works configure:8711: gcc -c -fPIC -DPIC -DPIC conftest.c >&5 configure:8715: $? = 0 configure:8728: result: yes configure:8757: checking if gcc static flag -static works configure:8785: result: no configure:8800: checking if gcc supports -c -o file.o configure:8821: gcc -c -o out/conftest2.o conftest.c >&5 configure:8825: $? = 0 configure:8847: result: yes configure:8855: checking if gcc supports -c -o file.o configure:8902: result: yes configure:8935: checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries configure:10088: result: yes configure:10125: checking whether -lc should be explicitly linked in configure:10133: gcc -c conftest.c >&5 configure:10136: $? = 0 configure:10151: gcc -shared -fPIC -DPIC conftest.o -v -Wl,-soname -Wl,conftest -o conftest 2\>\&1 \| /usr/bin/grep -lc \>/dev/null 2\>\&1 configure:10154: $? = 0 configure:10168: result: no configure:10328: checking dynamic linker characteristics configure:10839: gcc -o conftest -Wl,-rpath -Wl,/foo conftest.c >&5 configure:10839: $? = 0 configure:11065: result: GNU/Linux ld.so configure:11172: checking how to hardcode library paths into programs configure:11197: result: immediate configure:11737: checking whether stripping libraries is possible configure:11742: result: yes configure:11777: checking if libtool supports shared libraries configure:11779: result: yes configure:11782: checking whether to build shared libraries configure:11803: result: yes configure:11806: checking whether to build static libraries configure:11810: result: yes configure:11833: checking how to run the C++ preprocessor configure:11860: g++ -E conftest.cpp configure:11860: $? = 0 configure:11874: g++ -E conftest.cpp conftest.cpp:23:10: fatal error: ac_nonexistent.h: No such file or directory #include ^~~~~~~~~~~~~~~~~~ compilation terminated. configure:11874: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "EMBOSS" | #define PACKAGE_TARNAME "EMBOSS" | #define PACKAGE_VERSION "6.6.0" | #define PACKAGE_STRING "EMBOSS 6.6.0" | #define PACKAGE_BUGREPORT "emboss-bug@emboss.open-bio.org" | #define PACKAGE_URL "http://emboss.open-bio.org/" | #define PACKAGE "EMBOSS" | #define VERSION "6.6.0" | #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_DLFCN_H 1 | #define LT_OBJDIR ".libs/" | /* end confdefs.h. */ | #include configure:11899: result: g++ -E configure:11919: g++ -E conftest.cpp configure:11919: $? = 0 configure:11933: g++ -E conftest.cpp conftest.cpp:23:10: fatal error: ac_nonexistent.h: No such file or directory #include ^~~~~~~~~~~~~~~~~~ compilation terminated. configure:11933: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "EMBOSS" | #define PACKAGE_TARNAME "EMBOSS" | #define PACKAGE_VERSION "6.6.0" | #define PACKAGE_STRING "EMBOSS 6.6.0" | #define PACKAGE_BUGREPORT "emboss-bug@emboss.open-bio.org" | #define PACKAGE_URL "http://emboss.open-bio.org/" | #define PACKAGE "EMBOSS" | #define VERSION "6.6.0" | #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_DLFCN_H 1 | #define LT_OBJDIR ".libs/" | /* end confdefs.h. */ | #include configure:12102: checking for ld used by g++ configure:12169: result: /usr/bin/ld -m elf_x86_64 configure:12176: checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld configure:12191: result: yes configure:12246: checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries configure:13251: result: yes configure:13287: g++ -c -g -O2 conftest.cpp >&5 configure:13290: $? = 0 configure:13810: checking for g++ option to produce PIC configure:13817: result: -fPIC -DPIC configure:13825: checking if g++ PIC flag -fPIC -DPIC works configure:13843: g++ -c -g -O2 -fPIC -DPIC -DPIC conftest.cpp >&5 configure:13847: $? = 0 configure:13860: result: yes configure:13883: checking if g++ static flag -static works configure:13911: result: no configure:13923: checking if g++ supports -c -o file.o configure:13944: g++ -c -g -O2 -o out/conftest2.o conftest.cpp >&5 configure:13948: $? = 0 configure:13970: result: yes configure:13975: checking if g++ supports -c -o file.o configure:14022: result: yes configure:14052: checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries configure:14088: result: yes configure:14229: checking dynamic linker characteristics configure:14900: result: GNU/Linux ld.so configure:14953: checking how to hardcode library paths into programs configure:14978: result: immediate configure:15795: checking for X configure:15903: gcc -E conftest.c configure:15903: $? = 0 configure:15934: gcc -o conftest -O2 conftest.c -lX11 >&5 configure:15934: $? = 0 configure:15984: result: libraries , headers configure:16083: gcc -o conftest -O2 conftest.c -lX11 >&5 configure:16083: $? = 0 configure:16181: checking for gethostbyname configure:16181: gcc -o conftest -O2 conftest.c >&5 configure:16181: $? = 0 configure:16181: result: yes configure:16278: checking for connect configure:16278: gcc -o conftest -O2 conftest.c >&5 configure:16278: $? = 0 configure:16278: result: yes configure:16327: checking for remove configure:16327: gcc -o conftest -O2 conftest.c >&5 configure:16327: $? = 0 configure:16327: result: yes configure:16376: checking for shmat configure:16376: gcc -o conftest -O2 conftest.c >&5 configure:16376: $? = 0 configure:16376: result: yes configure:16434: checking for IceConnectionNumber in -lICE configure:16459: gcc -o conftest -O2 conftest.c -lICE >&5 configure:16459: $? = 0 configure:16468: result: yes configure:16481: checking for dirent.h that defines DIR configure:16500: gcc -c -O2 conftest.c >&5 configure:16500: $? = 0 configure:16508: result: yes configure:16521: checking for library containing opendir configure:16552: gcc -o conftest -O2 conftest.c >&5 configure:16552: $? = 0 configure:16569: result: none required configure:16636: checking for ANSI C header files configure:16740: result: yes configure:16752: checking for unistd.h configure:16752: result: yes configure:16752: checking TargetConfig.h usability configure:16752: gcc -c -O2 conftest.c >&5 conftest.c:59:10: fatal error: TargetConfig.h: No such file or directory #include ^~~~~~~~~~~~~~~~ compilation terminated. configure:16752: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "EMBOSS" | #define PACKAGE_TARNAME "EMBOSS" | #define PACKAGE_VERSION "6.6.0" | #define PACKAGE_STRING "EMBOSS 6.6.0" | #define PACKAGE_BUGREPORT "emboss-bug@emboss.open-bio.org" | #define PACKAGE_URL "http://emboss.open-bio.org/" | #define PACKAGE "EMBOSS" | #define VERSION "6.6.0" | #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_DLFCN_H 1 | #define LT_OBJDIR ".libs/" | #define HAVE_DIRENT_H 1 | #define STDC_HEADERS 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 | #include configure:16752: result: no configure:16752: checking TargetConfig.h presence configure:16752: gcc -E conftest.c conftest.c:26:10: fatal error: TargetConfig.h: No such file or directory #include ^~~~~~~~~~~~~~~~ compilation terminated. configure:16752: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "EMBOSS" | #define PACKAGE_TARNAME "EMBOSS" | #define PACKAGE_VERSION "6.6.0" | #define PACKAGE_STRING "EMBOSS 6.6.0" | #define PACKAGE_BUGREPORT "emboss-bug@emboss.open-bio.org" | #define PACKAGE_URL "http://emboss.open-bio.org/" | #define PACKAGE "EMBOSS" | #define VERSION "6.6.0" | #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_DLFCN_H 1 | #define LT_OBJDIR ".libs/" | #define HAVE_DIRENT_H 1 | #define STDC_HEADERS 1 | #define HAVE_UNISTD_H 1 | /* end confdefs.h. */ | #include configure:16752: result: no configure:16752: checking for TargetConfig.h configure:16752: result: no configure:16765: checking whether byte ordering is bigendian configure:16780: gcc -c -O2 conftest.c >&5 conftest.c:27:9: error: unknown type name 'not' not a universal capable compiler ^~~ conftest.c:27:15: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'universal' not a universal capable compiler ^~~~~~~~~ conftest.c:27:15: error: unknown type name 'universal' configure:16780: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "EMBOSS" | #define PACKAGE_TARNAME "EMBOSS" | #define PACKAGE_VERSION "6.6.0" | #define PACKAGE_STRING "EMBOSS 6.6.0" | #define PACKAGE_BUGREPORT "emboss-bug@emboss.open-bio.org" | #define PACKAGE_URL "http://emboss.open-bio.org/" | #define PACKAGE "EMBOSS" | #define VERSION "6.6.0" | #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_DLFCN_H 1 | #define LT_OBJDIR ".libs/" | #define HAVE_DIRENT_H 1 | #define STDC_HEADERS 1 | #define HAVE_UNISTD_H 1 | /* end confdefs.h. */ | #ifndef __APPLE_CC__ | not a universal capable compiler | #endif | typedef int dummy; | configure:16825: gcc -c -O2 conftest.c >&5 configure:16825: $? = 0 configure:16843: gcc -c -O2 conftest.c >&5 conftest.c: In function 'main': conftest.c:33:4: error: unknown type name 'not'; did you mean 'ino_t'? not big endian ^~~ ino_t conftest.c:33:12: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'endian' not big endian ^~~~~~ configure:16843: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "EMBOSS" | #define PACKAGE_TARNAME "EMBOSS" | #define PACKAGE_VERSION "6.6.0" | #define PACKAGE_STRING "EMBOSS 6.6.0" | #define PACKAGE_BUGREPORT "emboss-bug@emboss.open-bio.org" | #define PACKAGE_URL "http://emboss.open-bio.org/" | #define PACKAGE "EMBOSS" | #define VERSION "6.6.0" | #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_DLFCN_H 1 | #define LT_OBJDIR ".libs/" | #define HAVE_DIRENT_H 1 | #define STDC_HEADERS 1 | #define HAVE_UNISTD_H 1 | /* end confdefs.h. */ | #include | #include | | int | main () | { | #if BYTE_ORDER != BIG_ENDIAN | not big endian | #endif | | ; | return 0; | } configure:16971: result: no configure:16989: checking for an ANSI C-conforming const configure:17055: gcc -c -O2 conftest.c >&5 configure:17055: $? = 0 configure:17062: result: yes configure:17070: checking for inline configure:17086: gcc -c -O2 conftest.c >&5 configure:17086: $? = 0 configure:17094: result: inline configure:17112: checking for pid_t configure:17112: gcc -c -O2 conftest.c >&5 configure:17112: $? = 0 configure:17112: gcc -c -O2 conftest.c >&5 conftest.c: In function 'main': conftest.c:62:20: error: expected expression before ')' token if (sizeof ((pid_t))) ^ configure:17112: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "EMBOSS" | #define PACKAGE_TARNAME "EMBOSS" | #define PACKAGE_VERSION "6.6.0" | #define PACKAGE_STRING "EMBOSS 6.6.0" | #define PACKAGE_BUGREPORT "emboss-bug@emboss.open-bio.org" | #define PACKAGE_URL "http://emboss.open-bio.org/" | #define PACKAGE "EMBOSS" | #define VERSION "6.6.0" | #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_DLFCN_H 1 | #define LT_OBJDIR ".libs/" | #define HAVE_DIRENT_H 1 | #define STDC_HEADERS 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 ((pid_t))) | return 0; | ; | return 0; | } configure:17112: result: yes configure:17123: checking for size_t configure:17123: gcc -c -O2 conftest.c >&5 configure:17123: $? = 0 configure:17123: gcc -c -O2 conftest.c >&5 conftest.c: In function 'main': conftest.c:62:21: error: expected expression before ')' token if (sizeof ((size_t))) ^ configure:17123: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "EMBOSS" | #define PACKAGE_TARNAME "EMBOSS" | #define PACKAGE_VERSION "6.6.0" | #define PACKAGE_STRING "EMBOSS 6.6.0" | #define PACKAGE_BUGREPORT "emboss-bug@emboss.open-bio.org" | #define PACKAGE_URL "http://emboss.open-bio.org/" | #define PACKAGE "EMBOSS" | #define VERSION "6.6.0" | #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_DLFCN_H 1 | #define LT_OBJDIR ".libs/" | #define HAVE_DIRENT_H 1 | #define STDC_HEADERS 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 ((size_t))) | return 0; | ; | return 0; | } configure:17123: result: yes configure:17134: checking whether struct tm is in sys/time.h or time.h configure:17154: gcc -c -O2 conftest.c >&5 configure:17154: $? = 0 configure:17161: result: time.h configure:17172: checking whether getpgrp requires zero arguments configure:17189: gcc -c -O2 conftest.c >&5 conftest.c: In function 'main': conftest.c:62:1: error: too many arguments to function 'getpgrp' getpgrp (0); ^~~~~~~ In file included from conftest.c:57: /usr/include/unistd.h:634:16: note: declared here extern __pid_t getpgrp (void) __THROW; ^~~~~~~ configure:17189: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "EMBOSS" | #define PACKAGE_TARNAME "EMBOSS" | #define PACKAGE_VERSION "6.6.0" | #define PACKAGE_STRING "EMBOSS 6.6.0" | #define PACKAGE_BUGREPORT "emboss-bug@emboss.open-bio.org" | #define PACKAGE_URL "http://emboss.open-bio.org/" | #define PACKAGE "EMBOSS" | #define VERSION "6.6.0" | #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_DLFCN_H 1 | #define LT_OBJDIR ".libs/" | #define HAVE_DIRENT_H 1 | #define STDC_HEADERS 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 () | { | getpgrp (0); | ; | return 0; | } configure:17197: result: yes configure:17207: checking for strftime configure:17207: gcc -o conftest -O2 conftest.c >&5 conftest.c:50:6: warning: conflicting types for built-in function 'strftime' [-Wbuiltin-declaration-mismatch] char strftime (); ^~~~~~~~ configure:17207: $? = 0 configure:17207: result: yes configure:17262: checking vfork.h usability configure:17262: gcc -c -O2 conftest.c >&5 conftest.c:61:10: fatal error: vfork.h: No such file or directory #include ^~~~~~~~~ compilation terminated. configure:17262: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "EMBOSS" | #define PACKAGE_TARNAME "EMBOSS" | #define PACKAGE_VERSION "6.6.0" | #define PACKAGE_STRING "EMBOSS 6.6.0" | #define PACKAGE_BUGREPORT "emboss-bug@emboss.open-bio.org" | #define PACKAGE_URL "http://emboss.open-bio.org/" | #define PACKAGE "EMBOSS" | #define VERSION "6.6.0" | #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_DLFCN_H 1 | #define LT_OBJDIR ".libs/" | #define HAVE_DIRENT_H 1 | #define STDC_HEADERS 1 | #define HAVE_UNISTD_H 1 | #define GETPGRP_VOID 1 | #define HAVE_STRFTIME 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 | #include configure:17262: result: no configure:17262: checking vfork.h presence configure:17262: gcc -E conftest.c conftest.c:28:10: fatal error: vfork.h: No such file or directory #include ^~~~~~~~~ compilation terminated. configure:17262: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "EMBOSS" | #define PACKAGE_TARNAME "EMBOSS" | #define PACKAGE_VERSION "6.6.0" | #define PACKAGE_STRING "EMBOSS 6.6.0" | #define PACKAGE_BUGREPORT "emboss-bug@emboss.open-bio.org" | #define PACKAGE_URL "http://emboss.open-bio.org/" | #define PACKAGE "EMBOSS" | #define VERSION "6.6.0" | #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_DLFCN_H 1 | #define LT_OBJDIR ".libs/" | #define HAVE_DIRENT_H 1 | #define STDC_HEADERS 1 | #define HAVE_UNISTD_H 1 | #define GETPGRP_VOID 1 | #define HAVE_STRFTIME 1 | /* end confdefs.h. */ | #include configure:17262: result: no configure:17262: checking for vfork.h configure:17262: result: no configure:17275: checking for fork configure:17275: gcc -o conftest -O2 conftest.c >&5 conftest.c:51:6: warning: conflicting types for built-in function 'fork' [-Wbuiltin-declaration-mismatch] char fork (); ^~~~ configure:17275: $? = 0 configure:17275: result: yes configure:17275: checking for vfork configure:17275: gcc -o conftest -O2 conftest.c >&5 configure:17275: $? = 0 configure:17275: result: yes configure:17285: checking for working fork configure:17307: gcc -o conftest -O2 conftest.c >&5 configure:17307: $? = 0 configure:17307: ./conftest configure:17307: $? = 0 configure:17317: result: yes configure:17338: checking for working vfork configure:17448: result: yes configure:17475: checking for vprintf configure:17475: gcc -o conftest -O2 conftest.c >&5 conftest.c:55:6: warning: conflicting types for built-in function 'vprintf' [-Wbuiltin-declaration-mismatch] char vprintf (); ^~~~~~~ configure:17475: $? = 0 configure:17475: result: yes configure:17481: checking for _doprnt configure:17481: gcc -o conftest -O2 conftest.c >&5 /tmp/cc3p7akj.o: In function `main': conftest.c:(.text.startup+0x7): undefined reference to `_doprnt' collect2: error: ld returned 1 exit status configure:17481: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "EMBOSS" | #define PACKAGE_TARNAME "EMBOSS" | #define PACKAGE_VERSION "6.6.0" | #define PACKAGE_STRING "EMBOSS 6.6.0" | #define PACKAGE_BUGREPORT "emboss-bug@emboss.open-bio.org" | #define PACKAGE_URL "http://emboss.open-bio.org/" | #define PACKAGE "EMBOSS" | #define VERSION "6.6.0" | #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_DLFCN_H 1 | #define LT_OBJDIR ".libs/" | #define HAVE_DIRENT_H 1 | #define STDC_HEADERS 1 | #define HAVE_UNISTD_H 1 | #define GETPGRP_VOID 1 | #define HAVE_STRFTIME 1 | #define HAVE_FORK 1 | #define HAVE_VFORK 1 | #define HAVE_WORKING_VFORK 1 | #define HAVE_WORKING_FORK 1 | #define HAVE_VPRINTF 1 | /* end confdefs.h. */ | /* Define _doprnt to an innocuous variant, in case declares _doprnt. | For example, HP-UX 11i declares gettimeofday. */ | #define _doprnt innocuous__doprnt | | /* System header to define __stub macros and hopefully few prototypes, | which can conflict with char _doprnt (); below. | Prefer to if __STDC__ is defined, since | exists even on freestanding compilers. */ | | #ifdef __STDC__ | # include | #else | # include | #endif | | #undef _doprnt | | /* 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 _doprnt (); | /* 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__doprnt || defined __stub____doprnt | choke me | #endif | | int | main () | { | return _doprnt (); | ; | return 0; | } configure:17481: result: no configure:17495: checking for memmove configure:17495: gcc -o conftest -O2 conftest.c >&5 conftest.c:56:6: warning: conflicting types for built-in function 'memmove' [-Wbuiltin-declaration-mismatch] char memmove (); ^~~~~~~ configure:17495: $? = 0 configure:17495: result: yes configure:17520: checking X11/Xlib.h usability configure:17520: gcc -c -O2 conftest.c >&5 configure:17520: $? = 0 configure:17520: result: yes configure:17520: checking X11/Xlib.h presence configure:17520: gcc -E conftest.c configure:17520: $? = 0 configure:17520: result: yes configure:17520: checking for X11/Xlib.h configure:17520: result: yes configure:17558: checking for socket in -lc configure:17583: gcc -o conftest -O2 conftest.c -lc >&5 configure:17583: $? = 0 configure:17592: result: yes configure:17600: checking for main in -lm configure:17619: gcc -o conftest -O2 conftest.c -lm >&5 configure:17619: $? = 0 configure:17628: result: yes configure:17712: checking if docroot is given configure:17724: result: no configure:17733: checking if gcc profiling is selected configure:17746: result: no configure:17755: checking if gcov coverage is selected configure:17767: result: no configure:17776: checking for EMBOSS pre-indexed databases configure:17781: result: yes configure:17802: checking for Java JNI configure:17817: result: no configure:17838: checking for Java JNI OS configure:17864: result: no configure:17872: checking for authorisation type configure:18055: result: no configure:18068: checking for threading type configure:18146: result: no configure:18375: checking whether to look for pdf support configure:18390: result: yes configure:18419: checking for HPDF_New in -lhpdf configure:18444: gcc -o conftest -O2 -I/usr/include -L/usr/lib conftest.c -lhpdf -L/usr/lib -lm >&5 /usr/bin/ld: cannot find -lhpdf collect2: error: ld returned 1 exit status configure:18444: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "EMBOSS" | #define PACKAGE_TARNAME "EMBOSS" | #define PACKAGE_VERSION "6.6.0" | #define PACKAGE_STRING "EMBOSS 6.6.0" | #define PACKAGE_BUGREPORT "emboss-bug@emboss.open-bio.org" | #define PACKAGE_URL "http://emboss.open-bio.org/" | #define PACKAGE "EMBOSS" | #define VERSION "6.6.0" | #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_DLFCN_H 1 | #define LT_OBJDIR ".libs/" | #define HAVE_DIRENT_H 1 | #define STDC_HEADERS 1 | #define HAVE_UNISTD_H 1 | #define GETPGRP_VOID 1 | #define HAVE_STRFTIME 1 | #define HAVE_FORK 1 | #define HAVE_VFORK 1 | #define HAVE_WORKING_VFORK 1 | #define HAVE_WORKING_FORK 1 | #define HAVE_VPRINTF 1 | #define HAVE_MEMMOVE 1 | #define PLD_xwin 1 | #define HAVE_LIBM 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 HPDF_New (); | int | main () | { | return HPDF_New (); | ; | return 0; | } configure:18453: result: no configure:18567: checking for pkg-config configure:18585: found /usr/bin/pkg-config configure:18597: result: /usr/bin/pkg-config configure:18622: checking pkg-config is at least version 0.9.0 configure:18625: result: yes configure:18634: checking whether to look for axis2c support configure:18809: result: no configure:18823: checking if png driver is wanted configure:18838: result: yes configure:18923: checking for inflateEnd in -lz configure:18948: gcc -o conftest -O2 -I/usr/include -L/usr/lib conftest.c -lz -L/usr/lib -lz -lm >&5 configure:18948: $? = 0 configure:18957: result: yes configure:18971: checking for png_destroy_read_struct in -lpng configure:18996: gcc -o conftest -O2 -I/usr/include -L/usr/lib conftest.c -lpng -L/usr/lib -lz -lm >&5 configure:18996: $? = 0 configure:19005: result: yes configure:19022: checking for gdImageCreateFromPng in -lgd configure:19047: gcc -o conftest -O2 -I/usr/include -L/usr/lib conftest.c -lgd -L/usr/lib -lgd -lpng -lz -lm -lm >&5 /usr/bin/ld: cannot find -lgd /usr/bin/ld: cannot find -lgd collect2: error: ld returned 1 exit status configure:19047: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "EMBOSS" | #define PACKAGE_TARNAME "EMBOSS" | #define PACKAGE_VERSION "6.6.0" | #define PACKAGE_STRING "EMBOSS 6.6.0" | #define PACKAGE_BUGREPORT "emboss-bug@emboss.open-bio.org" | #define PACKAGE_URL "http://emboss.open-bio.org/" | #define PACKAGE "EMBOSS" | #define VERSION "6.6.0" | #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_DLFCN_H 1 | #define LT_OBJDIR ".libs/" | #define HAVE_DIRENT_H 1 | #define STDC_HEADERS 1 | #define HAVE_UNISTD_H 1 | #define GETPGRP_VOID 1 | #define HAVE_STRFTIME 1 | #define HAVE_FORK 1 | #define HAVE_VFORK 1 | #define HAVE_WORKING_VFORK 1 | #define HAVE_WORKING_FORK 1 | #define HAVE_VPRINTF 1 | #define HAVE_MEMMOVE 1 | #define PLD_xwin 1 | #define HAVE_LIBM 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 gdImageCreateFromPng (); | int | main () | { | return gdImageCreateFromPng (); | ; | return 0; | } configure:19056: result: no configure:19164: checking for mysql_config configure:19195: result: no configure:19358: checking for pg_config configure:19389: result: no configure:19574: checking for large file support configure:19630: result: yes configure:19667: checking for purify configure:19679: result: no configure:19722: checking for cygwin configure:19732: result: no configure:19857: checking for savestats configure:19870: result: no configure:19990: checking that generated files are newer than configure configure:19996: result: done configure:20080: creating ./config.status ## ---------------------- ## ## Running config.status. ## ## ---------------------- ## This file was extended by EMBOSS config.status 6.6.0, which was generated by GNU Autoconf 2.69. Invocation command line was CONFIG_FILES = CONFIG_HEADERS = CONFIG_LINKS = CONFIG_COMMANDS = $ ./config.status on orchid.rnet.missouri.edu config.status:1268: creating Makefile config.status:1268: creating ajax/Makefile config.status:1268: creating ajax/acd/Makefile config.status:1268: creating ajax/ajaxdb/Makefile config.status:1268: creating ajax/core/Makefile config.status:1268: creating ajax/ensembl/Makefile config.status:1268: creating ajax/expat/Makefile config.status:1268: creating ajax/graphics/Makefile config.status:1268: creating ajax/pcre/Makefile config.status:1268: creating ajax/zlib/Makefile config.status:1268: creating doc/Makefile config.status:1268: creating doc/manuals/Makefile config.status:1268: creating doc/programs/Makefile config.status:1268: creating doc/programs/html/Makefile config.status:1268: creating doc/programs/text/Makefile config.status:1268: creating doc/tutorials/Makefile config.status:1268: creating emboss/Makefile config.status:1268: creating emboss/acd/Makefile config.status:1268: creating emboss/data/AAINDEX/Makefile config.status:1268: creating emboss/data/CODONS/Makefile config.status:1268: creating emboss/data/JASPAR_CNE/Makefile config.status:1268: creating emboss/data/JASPAR_CORE/Makefile config.status:1268: creating emboss/data/JASPAR_FAM/Makefile config.status:1268: creating emboss/data/JASPAR_PBM/Makefile config.status:1268: creating emboss/data/JASPAR_PBM_HLH/Makefile config.status:1268: creating emboss/data/JASPAR_PBM_HOMEO/Makefile config.status:1268: creating emboss/data/JASPAR_PHYLOFACTS/Makefile config.status:1268: creating emboss/data/JASPAR_POLII/Makefile config.status:1268: creating emboss/data/JASPAR_SPLICE/Makefile config.status:1268: creating emboss/data/Makefile config.status:1268: creating emboss/data/OBO/Makefile config.status:1268: creating emboss/data/PRINTS/Makefile config.status:1268: creating emboss/data/PROSITE/Makefile config.status:1268: creating emboss/data/REBASE/Makefile config.status:1268: creating emboss/data/TAXONOMY/Makefile config.status:1268: creating emboss/index/Makefile config.status:1268: creating jemboss/Makefile config.status:1268: creating jemboss/runJemboss.sh config.status:1268: creating jemboss/images/Makefile config.status:1268: creating jemboss/lib/Makefile config.status:1268: creating jemboss/lib/axis/Makefile config.status:1268: creating jemboss/resources/Makefile config.status:1268: creating jemboss/utils/Makefile config.status:1268: creating nucleus/Makefile config.status:1268: creating plplot/Makefile config.status:1268: creating plplot/lib/Makefile config.status:1268: creating test/Makefile config.status:1268: creating test/data/Makefile config.status:1268: creating test/embl/Makefile config.status:1268: creating test/genbank/Makefile config.status:1268: creating test/pir/Makefile config.status:1268: creating test/swiss/Makefile config.status:1268: creating test/swnew/Makefile config.status:1268: creating test/testdb/Makefile config.status:1268: creating ajax/core/config.h config.status:1449: ajax/core/config.h is unchanged config.status:1497: executing depfiles commands config.status:1497: executing libtool commands ## ---------------- ## ## Cache variables. ## ## ---------------- ## ac_cv_build=x86_64-unknown-linux-gnu ac_cv_c_bigendian=no 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_ANT_set= ac_cv_env_ANT_value= ac_cv_env_AXIS2C_CFLAGS_set= ac_cv_env_AXIS2C_CFLAGS_value= ac_cv_env_AXIS2C_LIBS_set= ac_cv_env_AXIS2C_LIBS_value= 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_JAR_set= ac_cv_env_JAR_value= ac_cv_env_JAVAC_set= ac_cv_env_JAVAC_value= ac_cv_env_JAVA_set= ac_cv_env_JAVA_value= ac_cv_env_LDFLAGS_set= ac_cv_env_LDFLAGS_value= ac_cv_env_LIBS_set= ac_cv_env_LIBS_value= ac_cv_env_PKG_CONFIG_LIBDIR_set= ac_cv_env_PKG_CONFIG_LIBDIR_value= ac_cv_env_PKG_CONFIG_PATH_set= ac_cv_env_PKG_CONFIG_PATH_value= ac_cv_env_PKG_CONFIG_set= ac_cv_env_PKG_CONFIG_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__doprnt=no ac_cv_func_connect=yes ac_cv_func_fork=yes ac_cv_func_fork_works=yes ac_cv_func_gethostbyname=yes ac_cv_func_getpgrp_void=yes ac_cv_func_memmove=yes ac_cv_func_remove=yes ac_cv_func_shmat=yes ac_cv_func_strftime=yes ac_cv_func_vfork=yes ac_cv_func_vfork_works=yes ac_cv_func_vprintf=yes ac_cv_have_x='have_x=yes ac_x_includes='\'''\'' ac_x_libraries='\'''\''' ac_cv_header_TargetConfig_h=no ac_cv_header_X11_Xlib_h=yes ac_cv_header_dirent_dirent_h=yes ac_cv_header_dlfcn_h=yes ac_cv_header_inttypes_h=yes ac_cv_header_memory_h=yes ac_cv_header_stdc=yes ac_cv_header_stdint_h=yes ac_cv_header_stdlib_h=yes ac_cv_header_string_h=yes ac_cv_header_strings_h=yes ac_cv_header_sys_stat_h=yes ac_cv_header_sys_types_h=yes ac_cv_header_unistd_h=yes ac_cv_header_vfork_h=no ac_cv_host=x86_64-unknown-linux-gnu ac_cv_lib_ICE_IceConnectionNumber=yes ac_cv_lib_c_socket=yes ac_cv_lib_gd_gdImageCreateFromPng=no ac_cv_lib_hpdf_HPDF_New=no ac_cv_lib_m_main=yes ac_cv_lib_png_png_destroy_read_struct=yes ac_cv_lib_z_inflateEnd=yes ac_cv_objext=o ac_cv_path_EGREP='/usr/bin/grep -E' ac_cv_path_FGREP='/usr/bin/grep -F' ac_cv_path_GREP=/usr/bin/grep ac_cv_path_MYSQL_CONFIG=no ac_cv_path_POSTGRESQL_CONFIG=no ac_cv_path_SED=/usr/bin/sed ac_cv_path_ac_pt_PKG_CONFIG=/usr/bin/pkg-config ac_cv_path_install='/usr/bin/install -c' ac_cv_path_mkdir=/usr/bin/mkdir ac_cv_prog_AWK=gawk ac_cv_prog_CPP='gcc -E' 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_OBJDUMP=objdump ac_cv_prog_ac_ct_RANLIB=ranlib ac_cv_prog_ac_ct_STRIP=strip 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_search_opendir='none required' ac_cv_struct_tm=time.h ac_cv_type_pid_t=yes ac_cv_type_size_t=yes am_cv_CC_dependencies_compiler_type=gcc3 am_cv_CXX_dependencies_compiler_type=gcc3 lt_cv_ar_at_file=@ lt_cv_archive_cmds_need_lc=no lt_cv_deplibs_check_method=pass_all lt_cv_file_magic_cmd='$MAGIC_CMD' lt_cv_file_magic_test_file= lt_cv_ld_reload_flag=-r lt_cv_nm_interface='BSD nm' lt_cv_objdir=.libs lt_cv_path_LD=/usr/bin/ld lt_cv_path_LDCXX='/usr/bin/ld -m elf_x86_64' lt_cv_path_NM='/usr/bin/nm -B' lt_cv_path_mainfest_tool=no lt_cv_prog_compiler_c_o=yes lt_cv_prog_compiler_c_o_CXX=yes lt_cv_prog_compiler_pic='-fPIC -DPIC' lt_cv_prog_compiler_pic_CXX='-fPIC -DPIC' lt_cv_prog_compiler_pic_works=yes lt_cv_prog_compiler_pic_works_CXX=yes lt_cv_prog_compiler_rtti_exceptions=no lt_cv_prog_compiler_static_works=no lt_cv_prog_compiler_static_works_CXX=no lt_cv_prog_gnu_ld=yes lt_cv_prog_gnu_ldcxx=yes lt_cv_sharedlib_from_linklib_cmd='printf %s\n' lt_cv_shlibpath_overrides_runpath=no lt_cv_sys_global_symbol_pipe='sed -n -e '\''s/^.*[ ]\([ABCDGIRSTW][ABCDGIRSTW]*\)[ ][ ]*\([_A-Za-z][_A-Za-z0-9]*\)$/\1 \2 \2/p'\'' | sed '\''/ __gnu_lto/d'\''' lt_cv_sys_global_symbol_to_c_name_address='sed -n -e '\''s/^: \([^ ]*\)[ ]*$/ {\"\1\", (void *) 0},/p'\'' -e '\''s/^[ABCDGIRSTW]* \([^ ]*\) \([^ ]*\)$/ {"\2", (void *) \&\2},/p'\''' lt_cv_sys_global_symbol_to_c_name_address_lib_prefix='sed -n -e '\''s/^: \([^ ]*\)[ ]*$/ {\"\1\", (void *) 0},/p'\'' -e '\''s/^[ABCDGIRSTW]* \([^ ]*\) \(lib[^ ]*\)$/ {"\2", (void *) \&\2},/p'\'' -e '\''s/^[ABCDGIRSTW]* \([^ ]*\) \([^ ]*\)$/ {"lib\2", (void *) \&\2},/p'\''' lt_cv_sys_global_symbol_to_cdecl='sed -n -e '\''s/^T .* \(.*\)$/extern int \1();/p'\'' -e '\''s/^[ABCDGIRSTW]* .* \(.*\)$/extern char \1;/p'\''' lt_cv_sys_max_cmd_len=1572864 lt_cv_to_host_file_cmd=func_convert_file_noop lt_cv_to_tool_file_cmd=func_convert_file_noop ## ----------------- ## ## Output variables. ## ## ----------------- ## ACLOCAL='${SHELL} /bmlfast/bml_casp15/tools/casp14/casp14_qa/tools/EMBOSS-6.6.0/missing --run aclocal-1.12' AJAX_FIXED_ROOT='\"/bmlfast/bml_casp15/tools/casp14/casp14_qa/tools/EMBOSS-6.6.0/emboss\"' AJAX_SYSTEM='\"Linux\"' AMDEPBACKSLASH='\' AMDEP_FALSE='#' AMDEP_TRUE='' AMPDF_FALSE='' AMPDF_TRUE='#' AMPNG_FALSE='' AMPNG_TRUE='#' AMTAR='$${TAR-tar}' ANT='' AR='ar' AUTOCONF='${SHELL} /bmlfast/bml_casp15/tools/casp14/casp14_qa/tools/EMBOSS-6.6.0/missing --run autoconf' AUTOHEADER='${SHELL} /bmlfast/bml_casp15/tools/casp14/casp14_qa/tools/EMBOSS-6.6.0/missing --run autoheader' AUTOMAKE='${SHELL} /bmlfast/bml_casp15/tools/casp14/casp14_qa/tools/EMBOSS-6.6.0/missing --run automake-1.12' AWK='gawk' AXIS2C_CFLAGS='' AXIS2C_CPPFLAGS='' AXIS2C_LDFLAGS='' AXIS2C_LIBS='' CC='gcc' CCDEPMODE='depmode=gcc3' CFLAGS=' -O2 ' CPP='gcc -E' CPPFLAGS=' -DAJ_LinuxLF -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64' CXX='g++' CXXCPP='g++ -E' CXXDEPMODE='depmode=gcc3' CXXFLAGS='-g -O2' CYGPATH_W='echo' DEFS='-DHAVE_CONFIG_H' DEPDIR='.deps' DEVWARN_CFLAGS='' DLLTOOL='false' DSYMUTIL='' DUMPBIN='' ECHO_C='' ECHO_N='-n' ECHO_T='' EGREP='/usr/bin/grep -E' EMBOSS_TOP='/bmlfast/bml_casp15/tools/casp14/casp14_qa/tools/EMBOSS-6.6.0' ESYSTEMLIBS_FALSE='' ESYSTEMLIBS_TRUE='#' EXEEXT='' FGREP='/usr/bin/grep -F' GREP='/usr/bin/grep' HAVE_MEMMOVE='' HAVE_STRERROR='' INSTALL_DATA='${INSTALL} -m 644' INSTALL_PROGRAM='${INSTALL}' INSTALL_SCRIPT='${INSTALL}' INSTALL_STRIP_PROGRAM='$(install_sh) -c -s' ISAIXIA64_FALSE='' ISAIXIA64_TRUE='#' ISCYGWIN_FALSE='' ISCYGWIN_TRUE='#' ISSHARED_FALSE='#' ISSHARED_TRUE='' JAR='' JAVA='' JAVAC='' JAVA_BUILD_FALSE='' JAVA_BUILD_TRUE='#' JAVA_CFLAGS='' JAVA_CPPFLAGS=' -DNO_AUTH' JAVA_LDFLAGS='' LD='/usr/bin/ld -m elf_x86_64' LDFLAGS='' LIBOBJS='' LIBS='-lm ' LIBTOOL='$(SHELL) $(top_builddir)/libtool' LIPO='' LN_S='ln -s' LTLIBOBJS='' MAKEINFO='${SHELL} /bmlfast/bml_casp15/tools/casp14/casp14_qa/tools/EMBOSS-6.6.0/missing --run makeinfo' MANIFEST_TOOL=':' MKDIR_P='/usr/bin/mkdir -p' MYSQL_CFLAGS='' MYSQL_CONFIG='no' MYSQL_CPPFLAGS='' MYSQL_LDFLAGS='' MYSQL_VERSION='' NEEDAJAX_FALSE='' NEEDAJAX_TRUE='#' NM='/usr/bin/nm -B' NMEDIT='' OBJDUMP='objdump' OBJEXT='o' OTOOL64='' OTOOL='' PACKAGE='EMBOSS' PACKAGE_BUGREPORT='emboss-bug@emboss.open-bio.org' PACKAGE_NAME='EMBOSS' PACKAGE_STRING='EMBOSS 6.6.0' PACKAGE_TARNAME='EMBOSS' PACKAGE_URL='http://emboss.open-bio.org/' PACKAGE_VERSION='6.6.0' PATH_SEPARATOR=':' PCRE_DATE='11-Apr-2009' PCRE_LIB_VERSION='0:1:0' PCRE_MAJOR='7' PCRE_MINOR='9' PCRE_POSIXLIB_VERSION='0:0:0' PCRE_VERSION='7.9' PKG_CONFIG='/usr/bin/pkg-config' PKG_CONFIG_LIBDIR='' PKG_CONFIG_PATH='' POSIX_MALLOC_THRESHOLD='-DPOSIX_MALLOC_THRESHOLD=10' POSTGRESQL_CFLAGS='' POSTGRESQL_CONFIG='no' POSTGRESQL_CPPFLAGS='' POSTGRESQL_LDFLAGS='' POSTGRESQL_VERSION='' PURIFY_FALSE='' PURIFY_TRUE='#' RANLIB='ranlib' SED='/usr/bin/sed' SET_MAKE='' SHELL='/bin/sh' STRIP='strip' VERSION='6.6.0' WARN_CFLAGS='' XLIB=' -lX11 ' XMKMF='' X_CFLAGS='' X_EXTRA_LIBS='' X_LIBS='' X_PRE_LIBS=' -lSM -lICE' ac_ct_AR='ar' ac_ct_CC='gcc' ac_ct_CXX='g++' ac_ct_DUMPBIN='' 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='${exec_prefix}/bin' build='x86_64-unknown-linux-gnu' build_alias='' build_cpu='x86_64' build_os='linux-gnu' build_vendor='unknown' datadir='${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='${SHELL} /bmlfast/bml_casp15/tools/casp14/casp14_qa/tools/EMBOSS-6.6.0/install-sh' libdir='${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='/bmlfast/bml_casp15/tools/casp14/casp14_qa/tools/EMBOSS-6.6.0' 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 "EMBOSS" #define PACKAGE_TARNAME "EMBOSS" #define PACKAGE_VERSION "6.6.0" #define PACKAGE_STRING "EMBOSS 6.6.0" #define PACKAGE_BUGREPORT "emboss-bug@emboss.open-bio.org" #define PACKAGE_URL "http://emboss.open-bio.org/" #define PACKAGE "EMBOSS" #define VERSION "6.6.0" #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_DLFCN_H 1 #define LT_OBJDIR ".libs/" #define HAVE_DIRENT_H 1 #define STDC_HEADERS 1 #define HAVE_UNISTD_H 1 #define GETPGRP_VOID 1 #define HAVE_STRFTIME 1 #define HAVE_FORK 1 #define HAVE_VFORK 1 #define HAVE_WORKING_VFORK 1 #define HAVE_WORKING_FORK 1 #define HAVE_VPRINTF 1 #define HAVE_MEMMOVE 1 #define PLD_xwin 1 #define HAVE_LIBM 1 configure: exit 0 ## ---------------------- ## ## Running config.status. ## ## ---------------------- ## This file was extended by EMBOSS config.status 6.6.0, which was generated by GNU Autoconf 2.69. Invocation command line was CONFIG_FILES = CONFIG_HEADERS = CONFIG_LINKS = CONFIG_COMMANDS = $ ./config.status ajax/core/config.h on orchid.rnet.missouri.edu config.status:1268: creating ajax/core/config.h config.status:1449: ajax/core/config.h is unchanged