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=/usr --build=x86_64-pc-linux-gnu --host=x86_64-pc-linux-gnu --mandir=/usr/share/man --infodir=/usr/share/info --datadir=/usr/share --sysconfdir=/etc --localstatedir=/var/lib --disable-dependency-tracking --disable-silent-rules --docdir=/usr/share/doc/emboss-6.6.0-r1 --htmldir=/usr/share/doc/emboss-6.6.0-r1/html --libdir=/usr/lib64 --enable-shared --disable-static --with-x --with-pngdriver=/usr --with-hpdf=/usr --without-mysql --without-postgresql --enable-large --without-java --enable-systemlibs ## --------- ## ## Platform. ## ## --------- ## hostname = mr-fox uname -m = x86_64 uname -r = 4.9.10-hardened uname -s = Linux uname -v = #1 SMP Sat Feb 18 17:04:06 CET 2017 /usr/bin/uname -p = Intel(R) Core(TM) i7-3930K CPU @ 3.20GHz /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: /usr/lib/portage/python3.4/ebuild-helpers/xattr PATH: /usr/lib/portage/python3.4/ebuild-helpers PATH: /usr/local/sbin PATH: /usr/local/bin PATH: /usr/sbin PATH: /usr/bin PATH: /sbin PATH: /bin PATH: /opt/bin PATH: /usr/x86_64-pc-linux-gnu/gcc-bin/6.3.0 PATH: /opt/aws-elb-tools/bin PATH: /opt/aws-iam-tools/bin ## ----------- ## ## Core tests. ## ## ----------- ## configure:2597: checking for gawk configure:2613: found /usr/bin/gawk configure:2624: result: gawk configure:2645: checking for x86_64-pc-linux-gnu-icc configure:2675: result: no configure:2645: checking for x86_64-pc-linux-gnu-gcc configure:2661: found /usr/bin/x86_64-pc-linux-gnu-gcc configure:2672: result: x86_64-pc-linux-gnu-gcc configure:2747: checking for C compiler version configure:2756: x86_64-pc-linux-gnu-gcc --version >&5 x86_64-pc-linux-gnu-gcc (Gentoo 6.3.0 p1.0) 6.3.0 Copyright (C) 2016 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:2767: $? = 0 configure:2756: x86_64-pc-linux-gnu-gcc -v >&5 Using built-in specs. COLLECT_GCC=/usr/x86_64-pc-linux-gnu/gcc-bin/6.3.0/x86_64-pc-linux-gnu-gcc COLLECT_LTO_WRAPPER=/usr/libexec/gcc/x86_64-pc-linux-gnu/6.3.0/lto-wrapper Target: x86_64-pc-linux-gnu Configured with: /var/tmp/portage/sys-devel/gcc-6.3.0/work/gcc-6.3.0/configure --host=x86_64-pc-linux-gnu --build=x86_64-pc-linux-gnu --prefix=/usr --bindir=/usr/x86_64-pc-linux-gnu/gcc-bin/6.3.0 --includedir=/usr/lib/gcc/x86_64-pc-linux-gnu/6.3.0/include --datadir=/usr/share/gcc-data/x86_64-pc-linux-gnu/6.3.0 --mandir=/usr/share/gcc-data/x86_64-pc-linux-gnu/6.3.0/man --infodir=/usr/share/gcc-data/x86_64-pc-linux-gnu/6.3.0/info --with-gxx-include-dir=/usr/lib/gcc/x86_64-pc-linux-gnu/6.3.0/include/g++-v6 --with-python-dir=/share/gcc-data/x86_64-pc-linux-gnu/6.3.0/python --enable-languages=c,c++,fortran --enable-obsolete --enable-secureplt --disable-werror --with-system-zlib --enable-nls --without-included-gettext --enable-checking=release --with-bugurl=https://bugs.gentoo.org/ --with-pkgversion='Gentoo 6.3.0 p1.0' --disable-esp --enable-libstdcxx-time --enable-shared --enable-threads=posix --enable-__cxa_atexit --enable-clocale=gnu --enable-multilib --with-multilib-list=m32,m64 --disable-altivec --disable-fixed-point --enable-targets=all --disable-libgcj --enable-libgomp --disable-libmudflap --disable-libssp --disable-libcilkrts --disable-libmpx --enable-vtable-verify --enable-libvtv --enable-lto --without-isl --enable-libsanitizer --disable-default-pie --enable-default-ssp Thread model: posix gcc version 6.3.0 (Gentoo 6.3.0 p1.0) configure:2767: $? = 0 configure:2756: x86_64-pc-linux-gnu-gcc -V >&5 x86_64-pc-linux-gnu-gcc: error: unrecognized command line option '-V' x86_64-pc-linux-gnu-gcc: fatal error: no input files compilation terminated. configure:2767: $? = 1 configure:2756: x86_64-pc-linux-gnu-gcc -qversion >&5 x86_64-pc-linux-gnu-gcc: error: unrecognized command line option '-qversion'; did you mean '--version'? x86_64-pc-linux-gnu-gcc: fatal error: no input files compilation terminated. configure:2767: $? = 1 configure:2787: checking whether the C compiler works configure:2809: x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -Wall -Wl,-O1 -Wl,--as-needed conftest.c >&5 configure:2813: $? = 0 configure:2861: result: yes configure:2864: checking for C compiler default output file name configure:2866: result: a.out configure:2872: checking for suffix of executables configure:2879: x86_64-pc-linux-gnu-gcc -o conftest -O2 -pipe -march=native -Wall -Wl,-O1 -Wl,--as-needed conftest.c >&5 configure:2883: $? = 0 configure:2905: result: configure:2927: checking whether we are cross compiling configure:2935: x86_64-pc-linux-gnu-gcc -o conftest -O2 -pipe -march=native -Wall -Wl,-O1 -Wl,--as-needed conftest.c >&5 configure:2939: $? = 0 configure:2946: ./conftest configure:2950: $? = 0 configure:2965: result: no configure:2970: checking for suffix of object files configure:2992: x86_64-pc-linux-gnu-gcc -c -O2 -pipe -march=native -Wall conftest.c >&5 configure:2996: $? = 0 configure:3017: result: o configure:3021: checking whether we are using the GNU C compiler configure:3040: x86_64-pc-linux-gnu-gcc -c -O2 -pipe -march=native -Wall conftest.c >&5 configure:3040: $? = 0 configure:3049: result: yes configure:3058: checking whether x86_64-pc-linux-gnu-gcc accepts -g configure:3078: x86_64-pc-linux-gnu-gcc -c -g conftest.c >&5 configure:3078: $? = 0 configure:3119: result: yes configure:3136: checking for x86_64-pc-linux-gnu-gcc option to accept ISO C89 configure:3199: x86_64-pc-linux-gnu-gcc -c -O2 -pipe -march=native -Wall conftest.c >&5 configure:3199: $? = 0 configure:3212: result: none needed configure:3269: checking whether x86_64-pc-linux-gnu-gcc understands -c and -o together configure:3291: x86_64-pc-linux-gnu-gcc -c conftest.c -o conftest2.o configure:3294: $? = 0 configure:3291: x86_64-pc-linux-gnu-gcc -c conftest.c -o conftest2.o configure:3294: $? = 0 configure:3306: result: yes configure:3337: checking for x86_64-pc-linux-gnu-icpc configure:3367: result: no configure:3337: checking for x86_64-pc-linux-gnu-g++ configure:3353: found /usr/bin/x86_64-pc-linux-gnu-g++ configure:3364: result: x86_64-pc-linux-gnu-g++ configure:3435: checking for C++ compiler version configure:3444: x86_64-pc-linux-gnu-g++ --version >&5 x86_64-pc-linux-gnu-g++ (Gentoo 6.3.0 p1.0) 6.3.0 Copyright (C) 2016 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:3455: $? = 0 configure:3444: x86_64-pc-linux-gnu-g++ -v >&5 Using built-in specs. COLLECT_GCC=/usr/x86_64-pc-linux-gnu/gcc-bin/6.3.0/x86_64-pc-linux-gnu-g++ COLLECT_LTO_WRAPPER=/usr/libexec/gcc/x86_64-pc-linux-gnu/6.3.0/lto-wrapper Target: x86_64-pc-linux-gnu Configured with: /var/tmp/portage/sys-devel/gcc-6.3.0/work/gcc-6.3.0/configure --host=x86_64-pc-linux-gnu --build=x86_64-pc-linux-gnu --prefix=/usr --bindir=/usr/x86_64-pc-linux-gnu/gcc-bin/6.3.0 --includedir=/usr/lib/gcc/x86_64-pc-linux-gnu/6.3.0/include --datadir=/usr/share/gcc-data/x86_64-pc-linux-gnu/6.3.0 --mandir=/usr/share/gcc-data/x86_64-pc-linux-gnu/6.3.0/man --infodir=/usr/share/gcc-data/x86_64-pc-linux-gnu/6.3.0/info --with-gxx-include-dir=/usr/lib/gcc/x86_64-pc-linux-gnu/6.3.0/include/g++-v6 --with-python-dir=/share/gcc-data/x86_64-pc-linux-gnu/6.3.0/python --enable-languages=c,c++,fortran --enable-obsolete --enable-secureplt --disable-werror --with-system-zlib --enable-nls --without-included-gettext --enable-checking=release --with-bugurl=https://bugs.gentoo.org/ --with-pkgversion='Gentoo 6.3.0 p1.0' --disable-esp --enable-libstdcxx-time --enable-shared --enable-threads=posix --enable-__cxa_atexit --enable-clocale=gnu --enable-multilib --with-multilib-list=m32,m64 --disable-altivec --disable-fixed-point --enable-targets=all --disable-libgcj --enable-libgomp --disable-libmudflap --disable-libssp --disable-libcilkrts --disable-libmpx --enable-vtable-verify --enable-libvtv --enable-lto --without-isl --enable-libsanitizer --disable-default-pie --enable-default-ssp Thread model: posix gcc version 6.3.0 (Gentoo 6.3.0 p1.0) configure:3455: $? = 0 configure:3444: x86_64-pc-linux-gnu-g++ -V >&5 x86_64-pc-linux-gnu-g++: error: unrecognized command line option '-V' x86_64-pc-linux-gnu-g++: fatal error: no input files compilation terminated. configure:3455: $? = 1 configure:3444: x86_64-pc-linux-gnu-g++ -qversion >&5 x86_64-pc-linux-gnu-g++: error: unrecognized command line option '-qversion'; did you mean '--version'? x86_64-pc-linux-gnu-g++: fatal error: no input files compilation terminated. configure:3455: $? = 1 configure:3459: checking whether we are using the GNU C++ compiler configure:3478: x86_64-pc-linux-gnu-g++ -c -Werror=terminate -O2 -pipe -march=native conftest.cpp >&5 configure:3478: $? = 0 configure:3487: result: yes configure:3496: checking whether x86_64-pc-linux-gnu-g++ accepts -g configure:3516: x86_64-pc-linux-gnu-g++ -c -g conftest.cpp >&5 configure:3516: $? = 0 configure:3557: result: yes configure:3585: checking how to run the C preprocessor configure:3616: x86_64-pc-linux-gnu-gcc -E conftest.c configure:3616: $? = 0 configure:3630: x86_64-pc-linux-gnu-gcc -E conftest.c conftest.c:9:28: fatal error: ac_nonexistent.h: No such file or directory #include ^ compilation terminated. configure:3630: $? = 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:3655: result: x86_64-pc-linux-gnu-gcc -E configure:3675: x86_64-pc-linux-gnu-gcc -E conftest.c configure:3675: $? = 0 configure:3689: x86_64-pc-linux-gnu-gcc -E conftest.c conftest.c:9:28: fatal error: ac_nonexistent.h: No such file or directory #include ^ compilation terminated. configure:3689: $? = 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:3731: checking for a BSD-compatible install configure:3799: result: /usr/lib/portage/python3.4/ebuild-helpers/xattr/install -c configure:3810: checking whether ln -s works configure:3814: result: yes configure:3821: checking whether make sets $(MAKE) configure:3843: result: yes configure:3852: checking for a thread-safe mkdir -p configure:3891: result: /bin/mkdir -p configure:3897: checking whether build environment is sane configure:3952: result: yes configure:4121: checking for style of include used by make configure:4149: result: GNU configure:4183: checking whether make supports nested variables configure:4200: result: yes configure:4285: checking dependency style of x86_64-pc-linux-gnu-gcc configure:4396: result: none configure:4413: checking dependency style of x86_64-pc-linux-gnu-g++ configure:4524: result: none configure:4613: checking build system type configure:4627: result: x86_64-pc-linux-gnu configure:4647: checking host system type configure:4660: result: x86_64-pc-linux-gnu configure:4701: checking how to print strings configure:4728: result: printf configure:4749: checking for a sed that does not truncate output configure:4813: result: /bin/sed configure:4831: checking for grep that handles long lines and -e configure:4889: result: /bin/grep configure:4894: checking for egrep configure:4956: result: /bin/grep -E configure:4961: checking for fgrep configure:5023: result: /bin/grep -F configure:5058: checking for ld used by x86_64-pc-linux-gnu-gcc configure:5125: result: /usr/x86_64-pc-linux-gnu/bin/ld configure:5132: checking if the linker (/usr/x86_64-pc-linux-gnu/bin/ld) is GNU ld configure:5147: result: yes configure:5159: checking for BSD- or MS-compatible name lister (nm) configure:5213: result: /usr/bin/x86_64-pc-linux-gnu-nm -B configure:5343: checking the name lister (/usr/bin/x86_64-pc-linux-gnu-nm -B) interface configure:5350: x86_64-pc-linux-gnu-gcc -c -O2 -pipe -march=native -Wall conftest.c >&5 configure:5353: /usr/bin/x86_64-pc-linux-gnu-nm -B "conftest.o" configure:5356: output 0000000000000000 B some_variable configure:5363: result: BSD nm configure:5367: checking the maximum length of command line arguments configure:5498: result: 1572864 configure:5546: checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format configure:5586: result: func_convert_file_noop configure:5593: checking how to convert x86_64-pc-linux-gnu file names to toolchain format configure:5613: result: func_convert_file_noop configure:5620: checking for /usr/x86_64-pc-linux-gnu/bin/ld option to reload object files configure:5627: result: -r configure:5661: checking for x86_64-pc-linux-gnu-objdump configure:5677: found /usr/bin/x86_64-pc-linux-gnu-objdump configure:5688: result: x86_64-pc-linux-gnu-objdump configure:5760: checking how to recognize dependent libraries configure:5960: result: pass_all configure:6005: checking for x86_64-pc-linux-gnu-dlltool configure:6035: result: no configure:6045: checking for dlltool configure:6075: result: no configure:6105: checking how to associate runtime and link libraries configure:6132: result: printf %s\n configure:6149: checking for x86_64-pc-linux-gnu-ar configure:6165: found /usr/bin/x86_64-pc-linux-gnu-ar configure:6176: result: x86_64-pc-linux-gnu-ar configure:6257: checking for archiver @FILE support configure:6274: x86_64-pc-linux-gnu-gcc -c -O2 -pipe -march=native -Wall conftest.c >&5 configure:6274: $? = 0 configure:6277: x86_64-pc-linux-gnu-ar cru libconftest.a @conftest.lst >&5 configure:6280: $? = 0 configure:6285: x86_64-pc-linux-gnu-ar cru libconftest.a @conftest.lst >&5 x86_64-pc-linux-gnu-ar: conftest.o: No such file or directory configure:6288: $? = 1 configure:6300: result: @ configure:6318: checking for x86_64-pc-linux-gnu-strip configure:6334: found /usr/bin/x86_64-pc-linux-gnu-strip configure:6345: result: x86_64-pc-linux-gnu-strip configure:6417: checking for x86_64-pc-linux-gnu-ranlib configure:6433: found /usr/bin/x86_64-pc-linux-gnu-ranlib configure:6444: result: x86_64-pc-linux-gnu-ranlib configure:6586: checking command to parse /usr/bin/x86_64-pc-linux-gnu-nm -B output from x86_64-pc-linux-gnu-gcc object configure:6739: x86_64-pc-linux-gnu-gcc -c -O2 -pipe -march=native -Wall conftest.c >&5 configure:6742: $? = 0 configure:6746: /usr/bin/x86_64-pc-linux-gnu-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:6749: $? = 0 configure:6815: x86_64-pc-linux-gnu-gcc -o conftest -O2 -pipe -march=native -Wall -Wl,-O1 -Wl,--as-needed conftest.c conftstm.o >&5 configure:6818: $? = 0 configure:6856: result: ok configure:6903: checking for sysroot configure:6933: result: no configure:6940: checking for a working dd configure:6978: result: /bin/dd configure:6982: checking how to truncate binary pipes configure:6997: result: /bin/dd bs=4096 count=1 configure:7133: x86_64-pc-linux-gnu-gcc -c -O2 -pipe -march=native -Wall conftest.c >&5 configure:7136: $? = 0 configure:7286: checking for x86_64-pc-linux-gnu-mt configure:7316: result: no configure:7326: checking for mt configure:7356: result: no configure:7376: checking if : is a manifest tool configure:7382: : '-?' configure:7390: result: no configure:8063: checking for ANSI C header files configure:8083: x86_64-pc-linux-gnu-gcc -c -O2 -pipe -march=native -Wall conftest.c >&5 configure:8083: $? = 0 configure:8156: x86_64-pc-linux-gnu-gcc -o conftest -O2 -pipe -march=native -Wall -Wl,-O1 -Wl,--as-needed conftest.c >&5 configure:8156: $? = 0 configure:8156: ./conftest configure:8156: $? = 0 configure:8167: result: yes configure:8180: checking for sys/types.h configure:8180: x86_64-pc-linux-gnu-gcc -c -O2 -pipe -march=native -Wall conftest.c >&5 configure:8180: $? = 0 configure:8180: result: yes configure:8180: checking for sys/stat.h configure:8180: x86_64-pc-linux-gnu-gcc -c -O2 -pipe -march=native -Wall conftest.c >&5 configure:8180: $? = 0 configure:8180: result: yes configure:8180: checking for stdlib.h configure:8180: x86_64-pc-linux-gnu-gcc -c -O2 -pipe -march=native -Wall conftest.c >&5 configure:8180: $? = 0 configure:8180: result: yes configure:8180: checking for string.h configure:8180: x86_64-pc-linux-gnu-gcc -c -O2 -pipe -march=native -Wall conftest.c >&5 configure:8180: $? = 0 configure:8180: result: yes configure:8180: checking for memory.h configure:8180: x86_64-pc-linux-gnu-gcc -c -O2 -pipe -march=native -Wall conftest.c >&5 configure:8180: $? = 0 configure:8180: result: yes configure:8180: checking for strings.h configure:8180: x86_64-pc-linux-gnu-gcc -c -O2 -pipe -march=native -Wall conftest.c >&5 configure:8180: $? = 0 configure:8180: result: yes configure:8180: checking for inttypes.h configure:8180: x86_64-pc-linux-gnu-gcc -c -O2 -pipe -march=native -Wall conftest.c >&5 configure:8180: $? = 0 configure:8180: result: yes configure:8180: checking for stdint.h configure:8180: x86_64-pc-linux-gnu-gcc -c -O2 -pipe -march=native -Wall conftest.c >&5 configure:8180: $? = 0 configure:8180: result: yes configure:8180: checking for unistd.h configure:8180: x86_64-pc-linux-gnu-gcc -c -O2 -pipe -march=native -Wall conftest.c >&5 configure:8180: $? = 0 configure:8180: result: yes configure:8194: checking for dlfcn.h configure:8194: x86_64-pc-linux-gnu-gcc -c -O2 -pipe -march=native -Wall conftest.c >&5 configure:8194: $? = 0 configure:8194: result: yes configure:8461: checking for objdir configure:8476: result: .libs configure:8740: checking if x86_64-pc-linux-gnu-gcc supports -fno-rtti -fno-exceptions configure:8758: x86_64-pc-linux-gnu-gcc -c -O2 -pipe -march=native -Wall -fno-rtti -fno-exceptions conftest.c >&5 cc1: warning: command line option '-fno-rtti' is valid for C++/ObjC++ but not for C configure:8762: $? = 0 configure:8775: result: no configure:9133: checking for x86_64-pc-linux-gnu-gcc option to produce PIC configure:9140: result: -fPIC -DPIC configure:9148: checking if x86_64-pc-linux-gnu-gcc PIC flag -fPIC -DPIC works configure:9166: x86_64-pc-linux-gnu-gcc -c -O2 -pipe -march=native -Wall -fPIC -DPIC -DPIC conftest.c >&5 configure:9170: $? = 0 configure:9183: result: yes configure:9212: checking if x86_64-pc-linux-gnu-gcc static flag -static works configure:9240: result: yes configure:9255: checking if x86_64-pc-linux-gnu-gcc supports -c -o file.o configure:9276: x86_64-pc-linux-gnu-gcc -c -O2 -pipe -march=native -Wall -o out/conftest2.o conftest.c >&5 configure:9280: $? = 0 configure:9302: result: yes configure:9310: checking if x86_64-pc-linux-gnu-gcc supports -c -o file.o configure:9357: result: yes configure:9390: checking whether the x86_64-pc-linux-gnu-gcc linker (/usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64) supports shared libraries configure:10649: result: yes configure:10686: checking whether -lc should be explicitly linked in configure:10694: x86_64-pc-linux-gnu-gcc -c -O2 -pipe -march=native -Wall conftest.c >&5 configure:10697: $? = 0 configure:10712: x86_64-pc-linux-gnu-gcc -shared -fPIC -DPIC conftest.o -v -Wl,-soname -Wl,conftest -o conftest 2\>\&1 \| /bin/grep -lc \>/dev/null 2\>\&1 configure:10715: $? = 0 configure:10729: result: no configure:10889: checking dynamic linker characteristics configure:11483: x86_64-pc-linux-gnu-gcc -o conftest -O2 -pipe -march=native -Wall -Wl,-O1 -Wl,--as-needed -Wl,-rpath -Wl,/foo conftest.c >&5 configure:11483: $? = 0 configure:11720: result: GNU/Linux ld.so configure:11842: checking how to hardcode library paths into programs configure:11867: result: immediate configure:12415: checking whether stripping libraries is possible configure:12420: result: yes configure:12455: checking if libtool supports shared libraries configure:12457: result: yes configure:12460: checking whether to build shared libraries configure:12485: result: yes configure:12488: checking whether to build static libraries configure:12492: result: no configure:12515: checking how to run the C++ preprocessor configure:12542: x86_64-pc-linux-gnu-g++ -E conftest.cpp configure:12542: $? = 0 configure:12556: x86_64-pc-linux-gnu-g++ -E conftest.cpp conftest.cpp:23:28: fatal error: ac_nonexistent.h: No such file or directory #include ^ compilation terminated. configure:12556: $? = 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:12581: result: x86_64-pc-linux-gnu-g++ -E configure:12601: x86_64-pc-linux-gnu-g++ -E conftest.cpp configure:12601: $? = 0 configure:12615: x86_64-pc-linux-gnu-g++ -E conftest.cpp conftest.cpp:23:28: fatal error: ac_nonexistent.h: No such file or directory #include ^ compilation terminated. configure:12615: $? = 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:12777: checking for ld used by x86_64-pc-linux-gnu-g++ configure:12844: result: /usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64 configure:12851: checking if the linker (/usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64) is GNU ld configure:12866: result: yes configure:12921: checking whether the x86_64-pc-linux-gnu-g++ linker (/usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64) supports shared libraries configure:13994: result: yes configure:14030: x86_64-pc-linux-gnu-g++ -c -Werror=terminate -O2 -pipe -march=native conftest.cpp >&5 configure:14033: $? = 0 configure:14514: checking for x86_64-pc-linux-gnu-g++ option to produce PIC configure:14521: result: -fPIC -DPIC configure:14529: checking if x86_64-pc-linux-gnu-g++ PIC flag -fPIC -DPIC works configure:14547: x86_64-pc-linux-gnu-g++ -c -Werror=terminate -O2 -pipe -march=native -fPIC -DPIC -DPIC conftest.cpp >&5 configure:14551: $? = 0 configure:14564: result: yes configure:14587: checking if x86_64-pc-linux-gnu-g++ static flag -static works configure:14615: result: yes configure:14627: checking if x86_64-pc-linux-gnu-g++ supports -c -o file.o configure:14648: x86_64-pc-linux-gnu-g++ -c -Werror=terminate -O2 -pipe -march=native -o out/conftest2.o conftest.cpp >&5 configure:14652: $? = 0 configure:14674: result: yes configure:14679: checking if x86_64-pc-linux-gnu-g++ supports -c -o file.o configure:14726: result: yes configure:14756: checking whether the x86_64-pc-linux-gnu-g++ linker (/usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64) supports shared libraries configure:14796: result: yes configure:14937: checking dynamic linker characteristics configure:15695: result: GNU/Linux ld.so configure:15760: checking how to hardcode library paths into programs configure:15785: result: immediate configure:16586: checking for X configure:16725: x86_64-pc-linux-gnu-gcc -o conftest -O2 -pipe -march=native -Wall -O2 -Wl,-O1 -Wl,--as-needed conftest.c -lX11 >&5 configure:16725: $? = 0 configure:16775: result: libraries , headers configure:16874: x86_64-pc-linux-gnu-gcc -o conftest -O2 -pipe -march=native -Wall -O2 -Wl,-O1 -Wl,--as-needed conftest.c -lX11 >&5 configure:16874: $? = 0 configure:16972: checking for gethostbyname configure:16972: x86_64-pc-linux-gnu-gcc -o conftest -O2 -pipe -march=native -Wall -O2 -Wl,-O1 -Wl,--as-needed conftest.c >&5 configure:16972: $? = 0 configure:16972: result: yes configure:17069: checking for connect configure:17069: x86_64-pc-linux-gnu-gcc -o conftest -O2 -pipe -march=native -Wall -O2 -Wl,-O1 -Wl,--as-needed conftest.c >&5 configure:17069: $? = 0 configure:17069: result: yes configure:17118: checking for remove configure:17118: x86_64-pc-linux-gnu-gcc -o conftest -O2 -pipe -march=native -Wall -O2 -Wl,-O1 -Wl,--as-needed conftest.c >&5 configure:17118: $? = 0 configure:17118: result: yes configure:17167: checking for shmat configure:17167: x86_64-pc-linux-gnu-gcc -o conftest -O2 -pipe -march=native -Wall -O2 -Wl,-O1 -Wl,--as-needed conftest.c >&5 configure:17167: $? = 0 configure:17167: result: yes configure:17225: checking for IceConnectionNumber in -lICE configure:17250: x86_64-pc-linux-gnu-gcc -o conftest -O2 -pipe -march=native -Wall -O2 -Wl,-O1 -Wl,--as-needed conftest.c -lICE >&5 configure:17250: $? = 0 configure:17259: result: yes configure:17272: checking for dirent.h that defines DIR configure:17291: x86_64-pc-linux-gnu-gcc -c -O2 -pipe -march=native -Wall -O2 conftest.c >&5 configure:17291: $? = 0 configure:17299: result: yes configure:17312: checking for library containing opendir configure:17343: x86_64-pc-linux-gnu-gcc -o conftest -O2 -pipe -march=native -Wall -O2 -Wl,-O1 -Wl,--as-needed conftest.c >&5 configure:17343: $? = 0 configure:17360: result: none required configure:17427: checking for ANSI C header files configure:17531: result: yes configure:17543: checking for unistd.h configure:17543: result: yes configure:17543: checking TargetConfig.h usability configure:17543: x86_64-pc-linux-gnu-gcc -c -O2 -pipe -march=native -Wall -O2 conftest.c >&5 conftest.c:59:26: fatal error: TargetConfig.h: No such file or directory #include ^ compilation terminated. configure:17543: $? = 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:17543: result: no configure:17543: checking TargetConfig.h presence configure:17543: x86_64-pc-linux-gnu-gcc -E conftest.c conftest.c:26:26: fatal error: TargetConfig.h: No such file or directory #include ^ compilation terminated. configure:17543: $? = 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:17543: result: no configure:17543: checking for TargetConfig.h configure:17543: result: no configure:17556: checking whether byte ordering is bigendian configure:17571: x86_64-pc-linux-gnu-gcc -c -O2 -pipe -march=native -Wall -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:17571: $? = 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:17616: x86_64-pc-linux-gnu-gcc -c -O2 -pipe -march=native -Wall -O2 conftest.c >&5 configure:17616: $? = 0 configure:17634: x86_64-pc-linux-gnu-gcc -c -O2 -pipe -march=native -Wall -O2 conftest.c >&5 conftest.c: In function 'main': conftest.c:33:4: error: unknown type name 'not' not big endian ^~~ conftest.c:33:12: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'endian' not big endian ^~~~~~ configure:17634: $? = 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:17762: result: no configure:17780: checking for an ANSI C-conforming const configure:17846: x86_64-pc-linux-gnu-gcc -c -O2 -pipe -march=native -Wall -O2 conftest.c >&5 configure:17846: $? = 0 configure:17853: result: yes configure:17861: checking for inline configure:17877: x86_64-pc-linux-gnu-gcc -c -O2 -pipe -march=native -Wall -O2 conftest.c >&5 configure:17877: $? = 0 configure:17885: result: inline configure:17903: checking for pid_t configure:17903: x86_64-pc-linux-gnu-gcc -c -O2 -pipe -march=native -Wall -O2 conftest.c >&5 configure:17903: $? = 0 configure:17903: x86_64-pc-linux-gnu-gcc -c -O2 -pipe -march=native -Wall -O2 conftest.c >&5 conftest.c: In function 'main': conftest.c:62:20: error: expected expression before ')' token if (sizeof ((pid_t))) ^ configure:17903: $? = 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:17903: result: yes configure:17914: checking for size_t configure:17914: x86_64-pc-linux-gnu-gcc -c -O2 -pipe -march=native -Wall -O2 conftest.c >&5 configure:17914: $? = 0 configure:17914: x86_64-pc-linux-gnu-gcc -c -O2 -pipe -march=native -Wall -O2 conftest.c >&5 conftest.c: In function 'main': conftest.c:62:21: error: expected expression before ')' token if (sizeof ((size_t))) ^ configure:17914: $? = 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:17914: result: yes configure:17925: checking whether struct tm is in sys/time.h or time.h configure:17945: x86_64-pc-linux-gnu-gcc -c -O2 -pipe -march=native -Wall -O2 conftest.c >&5 configure:17945: $? = 0 configure:17952: result: time.h configure:17963: checking whether getpgrp requires zero arguments configure:17980: x86_64-pc-linux-gnu-gcc -c -O2 -pipe -march=native -Wall -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:57:0: /usr/include/unistd.h:637:16: note: declared here extern __pid_t getpgrp (void) __THROW; ^~~~~~~ configure:17980: $? = 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:17988: result: yes configure:17998: checking for strftime configure:17998: x86_64-pc-linux-gnu-gcc -o conftest -O2 -pipe -march=native -Wall -O2 -Wl,-O1 -Wl,--as-needed conftest.c >&5 conftest.c:50:6: warning: conflicting types for built-in function 'strftime' char strftime (); ^~~~~~~~ configure:17998: $? = 0 configure:17998: result: yes configure:18053: checking vfork.h usability configure:18053: x86_64-pc-linux-gnu-gcc -c -O2 -pipe -march=native -Wall -O2 conftest.c >&5 conftest.c:61:19: fatal error: vfork.h: No such file or directory #include ^ compilation terminated. configure:18053: $? = 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:18053: result: no configure:18053: checking vfork.h presence configure:18053: x86_64-pc-linux-gnu-gcc -E conftest.c conftest.c:28:19: fatal error: vfork.h: No such file or directory #include ^ compilation terminated. configure:18053: $? = 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:18053: result: no configure:18053: checking for vfork.h configure:18053: result: no configure:18066: checking for fork configure:18066: x86_64-pc-linux-gnu-gcc -o conftest -O2 -pipe -march=native -Wall -O2 -Wl,-O1 -Wl,--as-needed conftest.c >&5 conftest.c:51:6: warning: conflicting types for built-in function 'fork' char fork (); ^~~~ configure:18066: $? = 0 configure:18066: result: yes configure:18066: checking for vfork configure:18066: x86_64-pc-linux-gnu-gcc -o conftest -O2 -pipe -march=native -Wall -O2 -Wl,-O1 -Wl,--as-needed conftest.c >&5 configure:18066: $? = 0 configure:18066: result: yes configure:18076: checking for working fork configure:18098: x86_64-pc-linux-gnu-gcc -o conftest -O2 -pipe -march=native -Wall -O2 -Wl,-O1 -Wl,--as-needed conftest.c >&5 configure:18098: $? = 0 configure:18098: ./conftest configure:18098: $? = 0 configure:18108: result: yes configure:18129: checking for working vfork configure:18239: result: yes configure:18266: checking for vprintf configure:18266: x86_64-pc-linux-gnu-gcc -o conftest -O2 -pipe -march=native -Wall -O2 -Wl,-O1 -Wl,--as-needed conftest.c >&5 conftest.c:55:6: warning: conflicting types for built-in function 'vprintf' char vprintf (); ^~~~~~~ configure:18266: $? = 0 configure:18266: result: yes configure:18272: checking for _doprnt configure:18272: x86_64-pc-linux-gnu-gcc -o conftest -O2 -pipe -march=native -Wall -O2 -Wl,-O1 -Wl,--as-needed conftest.c >&5 /var/tmp/portage/sci-biology/emboss-6.6.0-r1/temp/ccEj6kMV.o: In function `main': conftest.c:(.text.startup+0x7): undefined reference to `_doprnt' collect2: error: ld returned 1 exit status configure:18272: $? = 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:18272: result: no configure:18286: checking for memmove configure:18286: x86_64-pc-linux-gnu-gcc -o conftest -O2 -pipe -march=native -Wall -O2 -Wl,-O1 -Wl,--as-needed conftest.c >&5 conftest.c:56:6: warning: conflicting types for built-in function 'memmove' char memmove (); ^~~~~~~ configure:18286: $? = 0 configure:18286: result: yes configure:18311: checking X11/Xlib.h usability configure:18311: x86_64-pc-linux-gnu-gcc -c -O2 -pipe -march=native -Wall -O2 conftest.c >&5 configure:18311: $? = 0 configure:18311: result: yes configure:18311: checking X11/Xlib.h presence configure:18311: x86_64-pc-linux-gnu-gcc -E conftest.c configure:18311: $? = 0 configure:18311: result: yes configure:18311: checking for X11/Xlib.h configure:18311: result: yes configure:18349: checking for socket in -lc configure:18374: x86_64-pc-linux-gnu-gcc -o conftest -O2 -pipe -march=native -Wall -O2 -Wl,-O1 -Wl,--as-needed conftest.c -lc >&5 configure:18374: $? = 0 configure:18383: result: yes configure:18391: checking for main in -lm configure:18410: x86_64-pc-linux-gnu-gcc -o conftest -O2 -pipe -march=native -Wall -O2 -Wl,-O1 -Wl,--as-needed conftest.c -lm >&5 configure:18410: $? = 0 configure:18419: result: yes configure:18503: checking if docroot is given configure:18515: result: no configure:18524: checking if gcc profiling is selected configure:18537: result: no configure:18546: checking if gcov coverage is selected configure:18558: result: no configure:18567: checking for EMBOSS pre-indexed databases configure:18571: checking for ./emboss/index/edam.xac configure:18585: result: yes configure:18602: checking for Java JNI configure:18609: result: no configure:18638: checking for Java JNI OS configure:18664: result: no configure:18672: checking for authorisation type configure:18855: result: no configure:18868: checking for threading type configure:18946: result: no configure:19175: checking whether to look for pdf support configure:19181: result: yes configure:19219: checking for HPDF_New in -lhpdf configure:19244: x86_64-pc-linux-gnu-gcc -o conftest -O2 -pipe -march=native -Wall -O2 -I/usr/include -Wl,-O1 -Wl,--as-needed -L/usr/lib conftest.c -lhpdf -L/usr/lib -lm >&5 configure:19244: $? = 0 configure:19253: result: yes configure:19324: checking for x86_64-pc-linux-gnu-pkg-config configure:19342: found /usr/bin/x86_64-pc-linux-gnu-pkg-config configure:19354: result: /usr/bin/x86_64-pc-linux-gnu-pkg-config configure:19422: checking pkg-config is at least version 0.9.0 configure:19425: result: yes configure:19434: checking whether to look for axis2c support configure:19609: result: no configure:19623: checking if png driver is wanted configure:19629: result: yes configure:19723: checking for inflateEnd in -lz configure:19748: x86_64-pc-linux-gnu-gcc -o conftest -O2 -pipe -march=native -Wall -O2 -I/usr/include -Wl,-O1 -Wl,--as-needed -L/usr/lib conftest.c -lz -L/usr/lib -lz -lm -lhpdf >&5 configure:19748: $? = 0 configure:19757: result: yes configure:19771: checking for png_destroy_read_struct in -lpng configure:19796: x86_64-pc-linux-gnu-gcc -o conftest -O2 -pipe -march=native -Wall -O2 -I/usr/include -Wl,-O1 -Wl,--as-needed -L/usr/lib conftest.c -lpng -L/usr/lib -lz -lm -lhpdf >&5 configure:19796: $? = 0 configure:19805: result: yes configure:19822: checking for gdImageCreateFromPng in -lgd configure:19847: x86_64-pc-linux-gnu-gcc -o conftest -O2 -pipe -march=native -Wall -O2 -I/usr/include -Wl,-O1 -Wl,--as-needed -L/usr/lib conftest.c -lgd -L/usr/lib -lgd -lpng -lz -lm -lm -lhpdf >&5 configure:19847: $? = 0 configure:19856: result: yes configure:20365: checking for large file support configure:20421: result: yes configure:20451: checking for PCRE configure:20458: $PKG_CONFIG --exists --print-errors "libpcre" configure:20461: $? = 0 configure:20474: $PKG_CONFIG --exists --print-errors "libpcre" configure:20477: $? = 0 configure:20536: result: yes configure:20542: checking for EXPAT configure:20549: $PKG_CONFIG --exists --print-errors "expat" configure:20552: $? = 0 configure:20565: $PKG_CONFIG --exists --print-errors "expat" configure:20568: $? = 0 configure:20627: result: yes configure:20633: checking for ZLIB configure:20640: $PKG_CONFIG --exists --print-errors "zlib" configure:20643: $? = 0 configure:20656: $PKG_CONFIG --exists --print-errors "zlib" configure:20659: $? = 0 configure:20718: result: yes configure:20724: checking for PLPLOT configure:20731: $PKG_CONFIG --exists --print-errors "plplotd" Package plplotd was not found in the pkg-config search path. Perhaps you should add the directory containing `plplotd.pc' to the PKG_CONFIG_PATH environment variable No package 'plplotd' found configure:20734: $? = 1 configure:20747: $PKG_CONFIG --exists --print-errors "plplotd" Package plplotd was not found in the pkg-config search path. Perhaps you should add the directory containing `plplotd.pc' to the PKG_CONFIG_PATH environment variable No package 'plplotd' found configure:20750: $? = 1 configure:20763: result: no No package 'plplotd' found configure:20781: checking for PLPLOT configure:20788: $PKG_CONFIG --exists --print-errors "plplot" configure:20791: $? = 0 configure:20804: $PKG_CONFIG --exists --print-errors "plplot" configure:20807: $? = 0 configure:20866: result: yes configure:21011: checking for purify configure:21023: result: no configure:21066: checking for cygwin configure:21076: result: no configure:21201: checking for savestats configure:21214: result: no configure:21334: checking that generated files are newer than configure configure:21340: result: done configure:21424: 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 mr-fox config.status:1285: creating Makefile config.status:1285: creating ajax/Makefile config.status:1285: creating ajax/acd/Makefile config.status:1285: creating ajax/ajaxdb/Makefile config.status:1285: creating ajax/core/Makefile config.status:1285: creating ajax/ensembl/Makefile config.status:1285: creating ajax/expat/Makefile config.status:1285: creating ajax/graphics/Makefile config.status:1285: creating ajax/pcre/Makefile config.status:1285: creating ajax/zlib/Makefile config.status:1285: creating doc/Makefile config.status:1285: creating doc/manuals/Makefile config.status:1285: creating doc/programs/Makefile config.status:1285: creating doc/programs/html/Makefile config.status:1285: creating doc/programs/text/Makefile config.status:1285: creating doc/tutorials/Makefile config.status:1285: creating emboss/Makefile config.status:1285: creating emboss/acd/Makefile config.status:1285: creating emboss/data/AAINDEX/Makefile config.status:1285: creating emboss/data/CODONS/Makefile config.status:1285: creating emboss/data/JASPAR_CNE/Makefile config.status:1285: creating emboss/data/JASPAR_CORE/Makefile config.status:1285: creating emboss/data/JASPAR_FAM/Makefile config.status:1285: creating emboss/data/JASPAR_PBM/Makefile config.status:1285: creating emboss/data/JASPAR_PBM_HLH/Makefile config.status:1285: creating emboss/data/JASPAR_PBM_HOMEO/Makefile config.status:1285: creating emboss/data/JASPAR_PHYLOFACTS/Makefile config.status:1285: creating emboss/data/JASPAR_POLII/Makefile config.status:1285: creating emboss/data/JASPAR_SPLICE/Makefile config.status:1285: creating emboss/data/Makefile config.status:1285: creating emboss/data/OBO/Makefile config.status:1285: creating emboss/data/PRINTS/Makefile config.status:1285: creating emboss/data/PROSITE/Makefile config.status:1285: creating emboss/data/REBASE/Makefile config.status:1285: creating emboss/data/TAXONOMY/Makefile config.status:1285: creating emboss/index/Makefile config.status:1285: creating jemboss/Makefile config.status:1285: creating jemboss/runJemboss.sh config.status:1285: creating jemboss/images/Makefile config.status:1285: creating jemboss/lib/Makefile config.status:1285: creating jemboss/lib/axis/Makefile config.status:1285: creating jemboss/resources/Makefile config.status:1285: creating jemboss/utils/Makefile config.status:1285: creating nucleus/Makefile config.status:1285: creating plplot/Makefile config.status:1285: creating plplot/lib/Makefile config.status:1285: creating test/Makefile config.status:1285: creating test/data/Makefile config.status:1285: creating test/embl/Makefile config.status:1285: creating test/genbank/Makefile config.status:1285: creating test/pir/Makefile config.status:1285: creating test/swiss/Makefile config.status:1285: creating test/swnew/Makefile config.status:1285: creating test/testdb/Makefile config.status:1285: creating ajax/core/config.h config.status:1514: executing depfiles commands config.status:1514: executing libtool commands ## ---------------- ## ## Cache variables. ## ## ---------------- ## ac_cv_build=x86_64-pc-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=set ac_cv_env_CFLAGS_value='-O2 -pipe -march=native -Wall' 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=set ac_cv_env_CXXFLAGS_value='-Werror=terminate -O2 -pipe -march=native' ac_cv_env_CXX_set= ac_cv_env_CXX_value= ac_cv_env_EXPAT_CFLAGS_set= ac_cv_env_EXPAT_CFLAGS_value= ac_cv_env_EXPAT_LIBS_set= ac_cv_env_EXPAT_LIBS_value= ac_cv_env_JAR_set= ac_cv_env_JAR_value= ac_cv_env_JAVAC_set=set ac_cv_env_JAVAC_value=/etc/java-config-2/current-system-vm/bin/javac ac_cv_env_JAVA_set= ac_cv_env_JAVA_value= ac_cv_env_LDFLAGS_set=set ac_cv_env_LDFLAGS_value='-Wl,-O1 -Wl,--as-needed' ac_cv_env_LIBS_set= ac_cv_env_LIBS_value= ac_cv_env_LT_SYS_LIBRARY_PATH_set= ac_cv_env_LT_SYS_LIBRARY_PATH_value= ac_cv_env_PCRE_CFLAGS_set= ac_cv_env_PCRE_CFLAGS_value= ac_cv_env_PCRE_LIBS_set= ac_cv_env_PCRE_LIBS_value= ac_cv_env_PKG_CONFIG_LIBDIR_set= ac_cv_env_PKG_CONFIG_LIBDIR_value= ac_cv_env_PKG_CONFIG_PATH_set=set ac_cv_env_PKG_CONFIG_PATH_value=/usr/lib64/pkgconfig ac_cv_env_PKG_CONFIG_set= ac_cv_env_PKG_CONFIG_value= ac_cv_env_PLPLOT_CFLAGS_set= ac_cv_env_PLPLOT_CFLAGS_value= ac_cv_env_PLPLOT_LIBS_set= ac_cv_env_PLPLOT_LIBS_value= ac_cv_env_XMKMF_set= ac_cv_env_XMKMF_value= ac_cv_env_ZLIB_CFLAGS_set= ac_cv_env_ZLIB_CFLAGS_value= ac_cv_env_ZLIB_LIBS_set= ac_cv_env_ZLIB_LIBS_value= ac_cv_env_build_alias_set=set ac_cv_env_build_alias_value=x86_64-pc-linux-gnu ac_cv_env_host_alias_set=set ac_cv_env_host_alias_value=x86_64-pc-linux-gnu ac_cv_env_target_alias_set= ac_cv_env_target_alias_value= ac_cv_file___emboss_index_edam_xac=yes 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-pc-linux-gnu ac_cv_lib_ICE_IceConnectionNumber=yes ac_cv_lib_c_socket=yes ac_cv_lib_gd_gdImageCreateFromPng=yes ac_cv_lib_hpdf_HPDF_New=yes 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='/bin/grep -E' ac_cv_path_FGREP='/bin/grep -F' ac_cv_path_GREP=/bin/grep ac_cv_path_PKG_CONFIG=/usr/bin/x86_64-pc-linux-gnu-pkg-config ac_cv_path_SED=/bin/sed ac_cv_path_install='/usr/lib/portage/python3.4/ebuild-helpers/xattr/install -c' ac_cv_path_lt_DD=/bin/dd ac_cv_path_mkdir=/bin/mkdir ac_cv_prog_AR=x86_64-pc-linux-gnu-ar ac_cv_prog_AWK=gawk ac_cv_prog_CC=x86_64-pc-linux-gnu-gcc ac_cv_prog_CPP='x86_64-pc-linux-gnu-gcc -E' ac_cv_prog_CXX=x86_64-pc-linux-gnu-g++ ac_cv_prog_CXXCPP='x86_64-pc-linux-gnu-g++ -E' ac_cv_prog_OBJDUMP=x86_64-pc-linux-gnu-objdump ac_cv_prog_RANLIB=x86_64-pc-linux-gnu-ranlib ac_cv_prog_STRIP=x86_64-pc-linux-gnu-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=none am_cv_CXX_dependencies_compiler_type=none am_cv_make_support_nested_variables=yes am_cv_prog_cc_c_o=yes 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/x86_64-pc-linux-gnu/bin/ld lt_cv_path_LDCXX='/usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64' lt_cv_path_NM='/usr/bin/x86_64-pc-linux-gnu-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=yes lt_cv_prog_compiler_static_works_CXX=yes 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=yes 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][ABCDGIRSTW]* .* \(.*\)$/ {"\1", (void *) \&\1},/p'\''' lt_cv_sys_global_symbol_to_c_name_address_lib_prefix='sed -n -e '\''s/^: \(.*\) .*$/ {"\1", (void *) 0},/p'\'' -e '\''s/^[ABCDGIRSTW][ABCDGIRSTW]* .* \(lib.*\)$/ {"\1", (void *) \&\1},/p'\'' -e '\''s/^[ABCDGIRSTW][ABCDGIRSTW]* .* \(.*\)$/ {"lib\1", (void *) \&\1},/p'\''' lt_cv_sys_global_symbol_to_cdecl='sed -n -e '\''s/^T .* \(.*\)$/extern int \1();/p'\'' -e '\''s/^[ABCDGIRSTW][ABCDGIRSTW]* .* \(.*\)$/extern char \1;/p'\''' lt_cv_sys_global_symbol_to_import= lt_cv_sys_max_cmd_len=1572864 lt_cv_to_host_file_cmd=func_convert_file_noop lt_cv_to_tool_file_cmd=func_convert_file_noop lt_cv_truncate_bin='/bin/dd bs=4096 count=1' pkg_cv_EXPAT_CFLAGS= pkg_cv_EXPAT_LIBS=-lexpat pkg_cv_PCRE_CFLAGS= pkg_cv_PCRE_LIBS=-lpcre pkg_cv_PLPLOT_CFLAGS=-I/usr/include/plplot pkg_cv_PLPLOT_LIBS='-Llib64 -lplplot' pkg_cv_ZLIB_CFLAGS= pkg_cv_ZLIB_LIBS=-lz ## ----------------- ## ## Output variables. ## ## ----------------- ## ACLOCAL='${SHELL} /var/tmp/portage/sci-biology/emboss-6.6.0-r1/work/EMBOSS-6.6.0/missing aclocal-1.15' AJAX_FIXED_ROOT='\"/var/tmp/portage/sci-biology/emboss-6.6.0-r1/work/EMBOSS-6.6.0/emboss\"' AJAX_SYSTEM='\"Linux\"' AMDEPBACKSLASH='' AMDEP_FALSE='' AMDEP_TRUE='#' AMPDF_FALSE='#' AMPDF_TRUE='' AMPNG_FALSE='#' AMPNG_TRUE='' AMTAR='$${TAR-tar}' AM_BACKSLASH='\' AM_DEFAULT_V='$(AM_DEFAULT_VERBOSITY)' AM_DEFAULT_VERBOSITY='1' AM_V='$(V)' ANT='' AR='x86_64-pc-linux-gnu-ar' AUTOCONF='${SHELL} /var/tmp/portage/sci-biology/emboss-6.6.0-r1/work/EMBOSS-6.6.0/missing autoconf' AUTOHEADER='${SHELL} /var/tmp/portage/sci-biology/emboss-6.6.0-r1/work/EMBOSS-6.6.0/missing autoheader' AUTOMAKE='${SHELL} /var/tmp/portage/sci-biology/emboss-6.6.0-r1/work/EMBOSS-6.6.0/missing automake-1.15' AWK='gawk' AXIS2C_CFLAGS='' AXIS2C_CPPFLAGS='' AXIS2C_LDFLAGS='' AXIS2C_LIBS='' CC='x86_64-pc-linux-gnu-gcc' CCDEPMODE='depmode=none' CFLAGS='-O2 -pipe -march=native -Wall -O2 ' CPP='x86_64-pc-linux-gnu-gcc -E' CPPFLAGS=' -DAJ_LinuxLF -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64' CXX='x86_64-pc-linux-gnu-g++' CXXCPP='x86_64-pc-linux-gnu-g++ -E' CXXDEPMODE='depmode=none' CXXFLAGS='-Werror=terminate -O2 -pipe -march=native' CYGPATH_W='echo' DEFS='-DHAVE_CONFIG_H' DEPDIR='.deps' DEVWARN_CFLAGS='' DLLTOOL='false' DSYMUTIL='' DUMPBIN='' ECHO_C='' ECHO_N='-n' ECHO_T='' EGREP='/bin/grep -E' EMBOSS_TOP='/var/tmp/portage/sci-biology/emboss-6.6.0-r1/work/EMBOSS-6.6.0' ESYSTEMLIBS_FALSE='#' ESYSTEMLIBS_TRUE='' EXEEXT='' EXPAT_CFLAGS='' EXPAT_LIBS='-lexpat' FGREP='/bin/grep -F' GREP='/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='/etc/java-config-2/current-system-vm/bin/javac' JAVA_BUILD_FALSE='' JAVA_BUILD_TRUE='#' JAVA_CFLAGS='' JAVA_CPPFLAGS=' -DNO_AUTH' JAVA_LDFLAGS='' LD='/usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64' LDFLAGS='-Wl,-O1 -Wl,--as-needed' LIBOBJS='' LIBS='-lm -lhpdf -lgd -lpng -lz -lm' LIBTOOL='$(SHELL) $(top_builddir)/libtool' LIPO='' LN_S='ln -s' LTLIBOBJS='' LT_SYS_LIBRARY_PATH='' MAKEINFO='${SHELL} /var/tmp/portage/sci-biology/emboss-6.6.0-r1/work/EMBOSS-6.6.0/missing makeinfo' MANIFEST_TOOL=':' MKDIR_P='/bin/mkdir -p' MYSQL_CFLAGS='' MYSQL_CONFIG='' MYSQL_CPPFLAGS='' MYSQL_LDFLAGS='' MYSQL_VERSION='' NEEDAJAX_FALSE='' NEEDAJAX_TRUE='#' NM='/usr/bin/x86_64-pc-linux-gnu-nm -B' NMEDIT='' OBJDUMP='x86_64-pc-linux-gnu-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_CFLAGS='' PCRE_DATE='' PCRE_LIBS='-lpcre' PCRE_LIB_VERSION='' PCRE_MAJOR='' PCRE_MINOR='' PCRE_POSIXLIB_VERSION='' PCRE_VERSION='' PKG_CONFIG='/usr/bin/x86_64-pc-linux-gnu-pkg-config' PKG_CONFIG_LIBDIR='' PKG_CONFIG_PATH='/usr/lib64/pkgconfig' PLPLOT_CFLAGS='-I/usr/include/plplot' PLPLOT_LIBS='-Llib64 -lplplot' POSIX_MALLOC_THRESHOLD='' POSTGRESQL_CFLAGS='' POSTGRESQL_CONFIG='' POSTGRESQL_CPPFLAGS='' POSTGRESQL_LDFLAGS='' POSTGRESQL_VERSION='' PURIFY_FALSE='' PURIFY_TRUE='#' RANLIB='x86_64-pc-linux-gnu-ranlib' SED='/bin/sed' SET_MAKE='' SHELL='/bin/sh' STRIP='x86_64-pc-linux-gnu-strip' VERSION='6.6.0' WARN_CFLAGS='' XLIB=' -lX11 ' XMKMF='' X_CFLAGS='' X_EXTRA_LIBS='' X_LIBS='' X_PRE_LIBS=' -lSM -lICE' ZLIB_CFLAGS='' ZLIB_LIBS='-lz' ac_ct_AR='' ac_ct_CC='' ac_ct_CXX='' 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='' am__quote='' am__tar='$${TAR-tar} chof - "$$tardir"' am__untar='$${TAR-tar} xf -' bindir='${exec_prefix}/bin' build='x86_64-pc-linux-gnu' build_alias='x86_64-pc-linux-gnu' build_cpu='x86_64' build_os='linux-gnu' build_vendor='pc' datadir='/usr/share' datarootdir='${prefix}/share' docdir='/usr/share/doc/emboss-6.6.0-r1' dvidir='${docdir}' exec_prefix='${prefix}' host='x86_64-pc-linux-gnu' host_alias='x86_64-pc-linux-gnu' host_cpu='x86_64' host_os='linux-gnu' host_vendor='pc' htmldir='/usr/share/doc/emboss-6.6.0-r1/html' includedir='${prefix}/include' infodir='/usr/share/info' install_sh='${SHELL} /var/tmp/portage/sci-biology/emboss-6.6.0-r1/work/EMBOSS-6.6.0/install-sh' libdir='/usr/lib64' libexecdir='${exec_prefix}/libexec' localedir='${datarootdir}/locale' localstatedir='/var/lib' mandir='/usr/share/man' mkdir_p='$(MKDIR_P)' oldincludedir='/usr/include' pdfdir='${docdir}' prefix='/usr' program_transform_name='s,x,x,' psdir='${docdir}' sbindir='${exec_prefix}/sbin' sharedstatedir='${prefix}/com' sysconfdir='/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 #define PLD_pdf 1 #define PLD_png 1 configure: exit 0