This file contains any messages produced by compilers while running configure, to aid debugging if configure makes a mistake. It was created by jellyfish configure 2.2.7, which was generated by GNU Autoconf 2.69. Invocation command line was $ ./configure --prefix=/home/psgendb/BIRCHDEV/pkg/jellyfish ## --------- ## ## Platform. ## ## --------- ## hostname = venus uname -m = x86_64 uname -r = 2.6.32-696.18.7.el6.x86_64 uname -s = Linux uname -v = #1 SMP Thu Dec 28 20:15:47 EST 2017 /usr/bin/uname -p = unknown /bin/uname -X = unknown /bin/arch = x86_64 /usr/bin/arch -k = unknown /usr/convex/getsysinfo = unknown /usr/bin/hostinfo = unknown /bin/machine = unknown /usr/bin/oslevel = unknown /bin/universe = unknown PATH: /home/psgendb/BIRCHDEV/local/script PATH: /home/psgendb/BIRCHDEV/local/bin-linux-x86_64 PATH: /usr/lib64/qt-3.3/bin PATH: /usr/local/bin PATH: /bin PATH: /usr/bin PATH: /opt/thinlinc/bin PATH: /usr/local/bin PATH: /usr/bin/X11 PATH: /usr/dt/bin PATH: /usr/openwin/bin PATH: /sbin PATH: /usr/sbin PATH: /usr/local/sbin PATH: /var/cfengine/bin PATH: /home/psgendb/BIRCHDEV/script PATH: /home/psgendb/BIRCHDEV/bin-linux-x86_64 PATH: /home/psgendb/BIRCHDEV/local/pkg/EMBOSS/linux-x86_64/bin PATH: /home/psgendb/bin ## ----------- ## ## Core tests. ## ## ----------- ## configure:2555: checking build system type configure:2569: result: x86_64-pc-linux-gnu configure:2589: checking host system type configure:2602: result: x86_64-pc-linux-gnu configure:2639: checking for a BSD-compatible install configure:2707: result: /usr/bin/install -c configure:2718: checking whether build environment is sane configure:2773: result: yes configure:2924: checking for a thread-safe mkdir -p configure:2963: result: /bin/mkdir -p configure:2970: checking for gawk configure:2986: found /bin/gawk configure:2997: result: gawk configure:3008: checking whether make sets $(MAKE) configure:3030: result: yes configure:3059: checking whether make supports nested variables configure:3076: result: yes configure:3213: checking whether make supports nested variables configure:3230: result: yes configure:3290: checking how to print strings configure:3317: result: printf configure:3350: checking for style of include used by make configure:3378: result: GNU configure:3449: checking for gcc configure:3465: found /usr/bin/gcc configure:3476: result: gcc configure:3705: checking for C compiler version configure:3714: gcc --version >&5 gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-18) Copyright (C) 2010 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:3725: $? = 0 configure:3714: gcc -v >&5 Using built-in specs. Target: x86_64-redhat-linux Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --with-bugurl=http://bugzilla.redhat.com/bugzilla --enable-bootstrap --enable-shared --enable-threads=posix --enable-checking=release --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-gnu-unique-object --enable-languages=c,c++,objc,obj-c++,java,fortran,ada --enable-java-awt=gtk --disable-dssi --with-java-home=/usr/lib/jvm/java-1.5.0-gcj-1.5.0.0/jre --enable-libgcj-multifile --enable-java-maintainer-mode --with-ecj-jar=/usr/share/java/eclipse-ecj.jar --disable-libjava-multilib --with-ppl --with-cloog --with-tune=generic --with-arch_32=i686 --build=x86_64-redhat-linux Thread model: posix gcc version 4.4.7 20120313 (Red Hat 4.4.7-18) (GCC) configure:3725: $? = 0 configure:3714: gcc -V >&5 gcc: '-V' option must have argument configure:3725: $? = 1 configure:3714: gcc -qversion >&5 gcc: unrecognized option '-qversion' gcc: no input files configure:3725: $? = 1 configure:3745: checking whether the C compiler works configure:3767: gcc conftest.c >&5 configure:3771: $? = 0 configure:3819: result: yes configure:3822: checking for C compiler default output file name configure:3824: result: a.out configure:3830: checking for suffix of executables configure:3837: gcc -o conftest conftest.c >&5 configure:3841: $? = 0 configure:3863: result: configure:3885: checking whether we are cross compiling configure:3893: gcc -o conftest conftest.c >&5 configure:3897: $? = 0 configure:3904: ./conftest configure:3908: $? = 0 configure:3923: result: no configure:3928: checking for suffix of object files configure:3950: gcc -c conftest.c >&5 configure:3954: $? = 0 configure:3975: result: o configure:3979: checking whether we are using the GNU C compiler configure:3998: gcc -c conftest.c >&5 configure:3998: $? = 0 configure:4007: result: yes configure:4016: checking whether gcc accepts -g configure:4036: gcc -c -g conftest.c >&5 configure:4036: $? = 0 configure:4077: result: yes configure:4094: checking for gcc option to accept ISO C89 configure:4157: gcc -c -g -O2 conftest.c >&5 configure:4157: $? = 0 configure:4170: result: none needed configure:4195: checking whether gcc understands -c and -o together configure:4217: gcc -c conftest.c -o conftest2.o configure:4220: $? = 0 configure:4217: gcc -c conftest.c -o conftest2.o configure:4220: $? = 0 configure:4232: result: yes configure:4251: checking dependency style of gcc configure:4362: result: gcc3 configure:4377: checking for a sed that does not truncate output configure:4441: result: /bin/sed configure:4459: checking for grep that handles long lines and -e configure:4517: result: /bin/grep configure:4522: checking for egrep configure:4584: result: /bin/grep -E configure:4589: checking for fgrep configure:4651: result: /bin/grep -F configure:4686: checking for ld used by gcc configure:4753: result: /usr/bin/ld configure:4760: checking if the linker (/usr/bin/ld) is GNU ld configure:4775: result: yes configure:4787: checking for BSD- or MS-compatible name lister (nm) configure:4841: result: /usr/bin/nm -B configure:4971: checking the name lister (/usr/bin/nm -B) interface configure:4978: gcc -c -g -O2 conftest.c >&5 configure:4981: /usr/bin/nm -B "conftest.o" configure:4984: output 0000000000000000 B some_variable configure:4991: result: BSD nm configure:4994: checking whether ln -s works configure:4998: result: yes configure:5006: checking the maximum length of command line arguments configure:5137: result: 1966080 configure:5185: checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format configure:5225: result: func_convert_file_noop configure:5232: checking how to convert x86_64-pc-linux-gnu file names to toolchain format configure:5252: result: func_convert_file_noop configure:5259: checking for /usr/bin/ld option to reload object files configure:5266: result: -r configure:5340: checking for objdump configure:5356: found /usr/bin/objdump configure:5367: result: objdump configure:5399: checking how to recognize dependent libraries configure:5599: result: pass_all configure:5684: checking for dlltool configure:5714: result: no configure:5744: checking how to associate runtime and link libraries configure:5771: result: printf %s\n configure:5832: checking for ar configure:5848: found /usr/bin/ar configure:5859: result: ar configure:5912: checking for archiver @FILE support configure:5929: gcc -c -g -O2 conftest.c >&5 configure:5929: $? = 0 configure:5932: ar cr libconftest.a @conftest.lst >&5 configure:5935: $? = 0 configure:5940: ar cr libconftest.a @conftest.lst >&5 ar: conftest.o: No such file or directory configure:5943: $? = 1 configure:5955: result: @ configure:6013: checking for strip configure:6029: found /usr/bin/strip configure:6040: result: strip configure:6112: checking for ranlib configure:6128: found /usr/bin/ranlib configure:6139: result: ranlib configure:6241: checking command to parse /usr/bin/nm -B output from gcc object configure:6394: gcc -c -g -O2 conftest.c >&5 configure:6397: $? = 0 configure:6401: /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:6404: $? = 0 configure:6470: gcc -o conftest -g -O2 conftest.c conftstm.o >&5 configure:6473: $? = 0 configure:6511: result: ok configure:6558: checking for sysroot configure:6588: result: no configure:6595: checking for a working dd configure:6633: result: /bin/dd configure:6637: checking how to truncate binary pipes configure:6652: result: /bin/dd bs=4096 count=1 configure:6788: gcc -c -g -O2 conftest.c >&5 configure:6791: $? = 0 configure:6981: checking for mt configure:7011: result: no configure:7031: checking if : is a manifest tool configure:7037: : '-?' configure:7045: result: no configure:7722: checking how to run the C preprocessor configure:7753: gcc -E conftest.c configure:7753: $? = 0 configure:7767: gcc -E conftest.c conftest.c:11:28: error: ac_nonexistent.h: No such file or directory configure:7767: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "jellyfish" | #define PACKAGE_TARNAME "jellyfish" | #define PACKAGE_VERSION "2.2.7" | #define PACKAGE_STRING "jellyfish 2.2.7" | #define PACKAGE_BUGREPORT "gmarcais@umd.edu" | #define PACKAGE_URL "" | #define PACKAGE "jellyfish" | #define VERSION "2.2.7" | /* end confdefs.h. */ | #include configure:7792: result: gcc -E configure:7812: gcc -E conftest.c configure:7812: $? = 0 configure:7826: gcc -E conftest.c conftest.c:11:28: error: ac_nonexistent.h: No such file or directory configure:7826: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "jellyfish" | #define PACKAGE_TARNAME "jellyfish" | #define PACKAGE_VERSION "2.2.7" | #define PACKAGE_STRING "jellyfish 2.2.7" | #define PACKAGE_BUGREPORT "gmarcais@umd.edu" | #define PACKAGE_URL "" | #define PACKAGE "jellyfish" | #define VERSION "2.2.7" | /* end confdefs.h. */ | #include configure:7855: checking for ANSI C header files configure:7875: gcc -c -g -O2 conftest.c >&5 configure:7875: $? = 0 configure:7948: gcc -o conftest -g -O2 conftest.c >&5 configure:7948: $? = 0 configure:7948: ./conftest configure:7948: $? = 0 configure:7959: result: yes configure:7972: checking for sys/types.h configure:7972: gcc -c -g -O2 conftest.c >&5 configure:7972: $? = 0 configure:7972: result: yes configure:7972: checking for sys/stat.h configure:7972: gcc -c -g -O2 conftest.c >&5 configure:7972: $? = 0 configure:7972: result: yes configure:7972: checking for stdlib.h configure:7972: gcc -c -g -O2 conftest.c >&5 configure:7972: $? = 0 configure:7972: result: yes configure:7972: checking for string.h configure:7972: gcc -c -g -O2 conftest.c >&5 configure:7972: $? = 0 configure:7972: result: yes configure:7972: checking for memory.h configure:7972: gcc -c -g -O2 conftest.c >&5 configure:7972: $? = 0 configure:7972: result: yes configure:7972: checking for strings.h configure:7972: gcc -c -g -O2 conftest.c >&5 configure:7972: $? = 0 configure:7972: result: yes configure:7972: checking for inttypes.h configure:7972: gcc -c -g -O2 conftest.c >&5 configure:7972: $? = 0 configure:7972: result: yes configure:7972: checking for stdint.h configure:7972: gcc -c -g -O2 conftest.c >&5 configure:7972: $? = 0 configure:7972: result: yes configure:7972: checking for unistd.h configure:7972: gcc -c -g -O2 conftest.c >&5 configure:7972: $? = 0 configure:7972: result: yes configure:7986: checking for dlfcn.h configure:7986: gcc -c -g -O2 conftest.c >&5 configure:7986: $? = 0 configure:7986: result: yes configure:8242: checking for objdir configure:8257: result: .libs configure:8521: checking if gcc supports -fno-rtti -fno-exceptions configure:8539: gcc -c -g -O2 -fno-rtti -fno-exceptions conftest.c >&5 cc1: warning: command line option "-fno-rtti" is valid for C++/ObjC++ but not for C configure:8543: $? = 0 configure:8556: result: no configure:8914: checking for gcc option to produce PIC configure:8921: result: -fPIC -DPIC configure:8929: checking if gcc PIC flag -fPIC -DPIC works configure:8947: gcc -c -g -O2 -fPIC -DPIC -DPIC conftest.c >&5 configure:8951: $? = 0 configure:8964: result: yes configure:8993: checking if gcc static flag -static works configure:9021: result: yes configure:9036: checking if gcc supports -c -o file.o configure:9057: gcc -c -g -O2 -o out/conftest2.o conftest.c >&5 configure:9061: $? = 0 configure:9083: result: yes configure:9091: checking if gcc supports -c -o file.o configure:9138: result: yes configure:9171: checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries configure:10432: result: yes configure:10469: checking whether -lc should be explicitly linked in configure:10477: gcc -c -g -O2 conftest.c >&5 configure:10480: $? = 0 configure:10495: gcc -shared -fPIC -DPIC conftest.o -v -Wl,-soname -Wl,conftest -o conftest 2\>\&1 \| /bin/grep -lc \>/dev/null 2\>\&1 configure:10498: $? = 0 configure:10512: result: no configure:10672: checking dynamic linker characteristics configure:11253: gcc -o conftest -g -O2 -Wl,-rpath -Wl,/foo conftest.c >&5 configure:11253: $? = 0 configure:11490: result: GNU/Linux ld.so configure:11612: checking how to hardcode library paths into programs configure:11637: result: immediate configure:12185: checking whether stripping libraries is possible configure:12194: result: yes configure:12236: checking if libtool supports shared libraries configure:12238: result: yes configure:12241: checking whether to build shared libraries configure:12266: result: yes configure:12269: checking whether to build static libraries configure:12273: result: yes configure:12335: checking for ld used by gcc configure:12402: result: /usr/bin/ld -m elf_x86_64 configure:12409: checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld configure:12424: result: yes configure:12431: checking for shared library run path origin configure:12444: result: done configure:12517: checking for pkg-config configure:12535: found /usr/bin/pkg-config configure:12547: result: /usr/bin/pkg-config configure:12572: checking pkg-config is at least version 0.9.0 configure:12575: result: yes configure:12652: checking for g++ configure:12668: found /usr/bin/g++ configure:12679: result: g++ configure:12706: checking for C++ compiler version configure:12715: g++ --version >&5 g++ (GCC) 4.4.7 20120313 (Red Hat 4.4.7-18) Copyright (C) 2010 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:12726: $? = 0 configure:12715: g++ -v >&5 Using built-in specs. Target: x86_64-redhat-linux Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --with-bugurl=http://bugzilla.redhat.com/bugzilla --enable-bootstrap --enable-shared --enable-threads=posix --enable-checking=release --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-gnu-unique-object --enable-languages=c,c++,objc,obj-c++,java,fortran,ada --enable-java-awt=gtk --disable-dssi --with-java-home=/usr/lib/jvm/java-1.5.0-gcj-1.5.0.0/jre --enable-libgcj-multifile --enable-java-maintainer-mode --with-ecj-jar=/usr/share/java/eclipse-ecj.jar --disable-libjava-multilib --with-ppl --with-cloog --with-tune=generic --with-arch_32=i686 --build=x86_64-redhat-linux Thread model: posix gcc version 4.4.7 20120313 (Red Hat 4.4.7-18) (GCC) configure:12726: $? = 0 configure:12715: g++ -V >&5 g++: '-V' option must have argument configure:12726: $? = 1 configure:12715: g++ -qversion >&5 g++: unrecognized option '-qversion' g++: no input files configure:12726: $? = 1 configure:12730: checking whether we are using the GNU C++ compiler configure:12749: g++ -c -std=c++0x conftest.cpp >&5 configure:12749: $? = 0 configure:12758: result: yes configure:12767: checking whether g++ accepts -g configure:12787: g++ -c -g conftest.cpp >&5 configure:12787: $? = 0 configure:12828: result: yes configure:12853: checking dependency style of g++ configure:12964: result: gcc3 configure:12997: checking how to run the C++ preprocessor configure:13024: g++ -E conftest.cpp configure:13024: $? = 0 configure:13038: g++ -E conftest.cpp conftest.cpp:23:28: error: ac_nonexistent.h: No such file or directory configure:13038: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "jellyfish" | #define PACKAGE_TARNAME "jellyfish" | #define PACKAGE_VERSION "2.2.7" | #define PACKAGE_STRING "jellyfish 2.2.7" | #define PACKAGE_BUGREPORT "gmarcais@umd.edu" | #define PACKAGE_URL "" | #define PACKAGE "jellyfish" | #define VERSION "2.2.7" | #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:13063: result: g++ -E configure:13083: g++ -E conftest.cpp configure:13083: $? = 0 configure:13097: g++ -E conftest.cpp conftest.cpp:23:28: error: ac_nonexistent.h: No such file or directory configure:13097: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "jellyfish" | #define PACKAGE_TARNAME "jellyfish" | #define PACKAGE_VERSION "2.2.7" | #define PACKAGE_STRING "jellyfish 2.2.7" | #define PACKAGE_BUGREPORT "gmarcais@umd.edu" | #define PACKAGE_URL "" | #define PACKAGE "jellyfish" | #define VERSION "2.2.7" | #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:13259: checking for ld used by g++ configure:13326: result: /usr/bin/ld -m elf_x86_64 configure:13333: checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld configure:13348: result: yes configure:13403: checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries configure:14477: result: yes configure:14513: g++ -c -std=c++0x conftest.cpp >&5 configure:14516: $? = 0 configure:14997: checking for g++ option to produce PIC configure:15004: result: -fPIC -DPIC configure:15012: checking if g++ PIC flag -fPIC -DPIC works configure:15030: g++ -c -std=c++0x -fPIC -DPIC -DPIC conftest.cpp >&5 configure:15034: $? = 0 configure:15047: result: yes configure:15070: checking if g++ static flag -static works configure:15098: result: yes configure:15110: checking if g++ supports -c -o file.o configure:15131: g++ -c -std=c++0x -o out/conftest2.o conftest.cpp >&5 configure:15135: $? = 0 configure:15157: result: yes configure:15162: checking if g++ supports -c -o file.o configure:15209: result: yes configure:15239: checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries configure:15279: result: yes configure:15420: checking dynamic linker characteristics configure:16165: result: GNU/Linux ld.so configure:16230: checking how to hardcode library paths into programs configure:16255: result: immediate configure:16374: checking for htslib configure:16381: $PKG_CONFIG --exists --print-errors "htslib" Package htslib was not found in the pkg-config search path. Perhaps you should add the directory containing `htslib.pc' to the PKG_CONFIG_PATH environment variable No package 'htslib' found configure:16384: $? = 1 configure:16398: $PKG_CONFIG --exists --print-errors "htslib" Package htslib was not found in the pkg-config search path. Perhaps you should add the directory containing `htslib.pc' to the PKG_CONFIG_PATH environment variable No package 'htslib' found configure:16401: $? = 1 configure:16415: result: no No package 'htslib' found configure:16511: checking for samtools configure:16544: result: no configure:16556: checking for md5sum configure:16572: found /usr/bin/md5sum configure:16583: result: md5sum configure:16640: checking for yaggo configure:16671: result: false configure:16701: checking for x86 cpuid output configure:16733: gcc -o conftest -g -O2 conftest.c >&5 conftest.c: In function 'main': conftest.c:28: error: expected expression before ',' token configure:16733: $? = 1 configure: program exited with status 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "jellyfish" | #define PACKAGE_TARNAME "jellyfish" | #define PACKAGE_VERSION "2.2.7" | #define PACKAGE_STRING "jellyfish 2.2.7" | #define PACKAGE_BUGREPORT "gmarcais@umd.edu" | #define PACKAGE_URL "" | #define PACKAGE "jellyfish" | #define VERSION "2.2.7" | #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 | int | main () | { | | int op = , level = 0, eax, ebx, ecx, edx; | FILE *f; | __asm__ __volatile__ ("xchg %%ebx, %1\n" | "cpuid\n" | "xchg %%ebx, %1\n" | : "=a" (eax), "=r" (ebx), "=c" (ecx), "=d" (edx) | : "a" (op), "2" (level)); | | f = fopen("conftest_cpuid", "w"); if (!f) return 1; | fprintf(f, "%x:%x:%x:%x\n", eax, ebx, ecx, edx); | fclose(f); | return 0; | | ; | return 0; | } configure:16743: result: unknown configure:16760: checking for x86-AVX xgetbv output configure:16790: gcc -o conftest -g -O2 conftest.c >&5 conftest.c: In function 'main': conftest.c:28: error: expected expression before ',' token configure:16790: $? = 1 configure: program exited with status 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "jellyfish" | #define PACKAGE_TARNAME "jellyfish" | #define PACKAGE_VERSION "2.2.7" | #define PACKAGE_STRING "jellyfish 2.2.7" | #define PACKAGE_BUGREPORT "gmarcais@umd.edu" | #define PACKAGE_URL "" | #define PACKAGE "jellyfish" | #define VERSION "2.2.7" | #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 | int | main () | { | | int op = , eax, edx; | FILE *f; | /* Opcodes for xgetbv */ | __asm__ __volatile__ (".byte 0x0f, 0x01, 0xd0" | : "=a" (eax), "=d" (edx) | : "c" (op)); | f = fopen("conftest_xgetbv", "w"); if (!f) return 1; | fprintf(f, "%x:%x\n", eax, edx); | fclose(f); | return 0; | | ; | return 0; | } configure:16800: result: unknown configure:16891: checking for x86 cpuid 0x00000000 output configure:16923: gcc -o conftest -g -O2 conftest.c >&5 configure:16923: $? = 0 configure:16923: ./conftest configure:16923: $? = 0 configure:16933: result: d:68747541:444d4163:69746e65 configure:16956: checking for x86 cpuid 0x80000000 output configure:16988: gcc -o conftest -g -O2 conftest.c >&5 configure:16988: $? = 0 configure:16988: ./conftest configure:16988: $? = 0 configure:16998: result: 8000001e:68747541:444d4163:69746e65 configure:17023: checking for x86 cpuid 0x00000001 output configure:17055: gcc -o conftest -g -O2 conftest.c >&5 configure:17055: $? = 0 configure:17055: ./conftest configure:17055: $? = 0 configure:17065: result: 600f20:23100800:3e98320b:178bfbff configure:17092: checking for x86 cpuid 0x00000007 output configure:17124: gcc -o conftest -g -O2 conftest.c >&5 configure:17124: $? = 0 configure:17124: ./conftest configure:17124: $? = 0 configure:17134: result: 0:8:0:0 configure:17160: checking for x86 cpuid 0x80000001 output configure:17192: gcc -o conftest -g -O2 conftest.c >&5 configure:17192: $? = 0 configure:17192: ./conftest configure:17192: $? = 0 configure:17202: result: 600f20:30000000:1ebbfff:2fd3fbff configure:17261: gcc -o conftest -g -O2 conftest.c >&5 configure:17261: $? = 0 configure:17261: ./conftest configure:17261: $? = 0 configure:17290: checking for x86-AVX xgetbv 0x00000000 output configure:17320: gcc -o conftest -g -O2 conftest.c >&5 configure:17320: $? = 0 configure:17320: ./conftest configure:17320: $? = 0 configure:17330: result: 7:0 configure:17384: checking whether RDRND is supported by the processor configure:17397: result: no configure:17384: checking whether BMI1 is supported by the processor configure:17397: result: yes configure:17401: checking whether BMI1 is supported by the processor and OS configure:17414: result: yes configure:17419: checking whether C++ compiler accepts -mbmi configure:17438: g++ -c -std=c++0x -mbmi conftest.cpp >&5 configure:17438: $? = 0 configure:17447: result: yes configure:17384: checking whether BMI2 is supported by the processor configure:17397: result: no configure:17384: checking whether ADX is supported by the processor configure:17397: result: no configure:17384: checking whether MPX is supported by the processor configure:17397: result: no configure:17384: checking whether PREFETCHWT1 is supported by the processor configure:17397: result: no configure:17384: checking whether ABM is supported by the processor configure:17397: result: yes configure:17401: checking whether ABM is supported by the processor and OS configure:17414: result: yes configure:17419: checking whether C++ compiler accepts -mabm configure:17438: g++ -c -std=c++0x -mabm conftest.cpp >&5 configure:17438: $? = 0 configure:17447: result: yes configure:17384: checking whether MMX is supported by the processor configure:17397: result: yes configure:17401: checking whether MMX is supported by the processor and OS configure:17414: result: yes configure:17419: checking whether C++ compiler accepts -mmmx configure:17438: g++ -c -std=c++0x -mmmx conftest.cpp >&5 configure:17438: $? = 0 configure:17447: result: yes configure:17384: checking whether SSE is supported by the processor configure:17397: result: yes configure:17401: checking whether SSE is supported by the processor and OS configure:17414: result: yes configure:17419: checking whether C++ compiler accepts -msse configure:17438: g++ -c -std=c++0x -msse conftest.cpp >&5 configure:17438: $? = 0 configure:17447: result: yes configure:17384: checking whether SSE2 is supported by the processor configure:17397: result: yes configure:17401: checking whether SSE2 is supported by the processor and OS configure:17414: result: yes configure:17419: checking whether C++ compiler accepts -msse2 configure:17438: g++ -c -std=c++0x -msse2 conftest.cpp >&5 configure:17438: $? = 0 configure:17447: result: yes configure:17384: checking whether SSE3 is supported by the processor configure:17397: result: yes configure:17401: checking whether SSE3 is supported by the processor and OS configure:17414: result: yes configure:17419: checking whether C++ compiler accepts -msse3 configure:17438: g++ -c -std=c++0x -msse3 conftest.cpp >&5 configure:17438: $? = 0 configure:17447: result: yes configure:17384: checking whether SSSE3 is supported by the processor configure:17397: result: yes configure:17401: checking whether SSSE3 is supported by the processor and OS configure:17414: result: yes configure:17419: checking whether C++ compiler accepts -mssse3 configure:17438: g++ -c -std=c++0x -mssse3 conftest.cpp >&5 configure:17438: $? = 0 configure:17447: result: yes configure:17384: checking whether SSE4.1 is supported by the processor configure:17397: result: yes configure:17401: checking whether SSE4.1 is supported by the processor and OS configure:17414: result: yes configure:17419: checking whether C++ compiler accepts -msse4.1 configure:17438: g++ -c -std=c++0x -msse4.1 conftest.cpp >&5 configure:17438: $? = 0 configure:17447: result: yes configure:17384: checking whether SSE4.2 is supported by the processor configure:17397: result: yes configure:17401: checking whether SSE4.2 is supported by the processor and OS configure:17414: result: yes configure:17419: checking whether C++ compiler accepts -msse4.2 configure:17438: g++ -c -std=c++0x -msse4.2 conftest.cpp >&5 configure:17438: $? = 0 configure:17447: result: yes configure:17384: checking whether SSE4a is supported by the processor configure:17397: result: yes configure:17401: checking whether SSE4a is supported by the processor and OS configure:17414: result: yes configure:17419: checking whether C++ compiler accepts -msse4a configure:17438: g++ -c -std=c++0x -msse4a conftest.cpp >&5 configure:17438: $? = 0 configure:17447: result: yes configure:17384: checking whether SHA is supported by the processor configure:17397: result: no configure:17384: checking whether AES is supported by the processor configure:17397: result: yes configure:17401: checking whether AES is supported by the processor and OS configure:17414: result: yes configure:17419: checking whether C++ compiler accepts -maes configure:17438: g++ -c -std=c++0x -maes conftest.cpp >&5 configure:17438: $? = 0 configure:17447: result: yes configure:17384: checking whether AVX is supported by the processor configure:17397: result: yes configure:17401: checking whether AVX is supported by the processor and OS configure:17414: result: yes configure:17419: checking whether C++ compiler accepts -mavx configure:17438: g++ -c -std=c++0x -mavx conftest.cpp >&5 configure:17438: $? = 0 configure:17447: result: yes configure:17384: checking whether FMA3 is supported by the processor configure:17397: result: yes configure:17401: checking whether FMA3 is supported by the processor and OS configure:17414: result: yes configure:17419: checking whether C++ compiler accepts -mfma configure:17438: g++ -c -std=c++0x -mfma conftest.cpp >&5 configure:17438: $? = 0 configure:17447: result: yes configure:17384: checking whether FMA4 is supported by the processor configure:17397: result: yes configure:17401: checking whether FMA4 is supported by the processor and OS configure:17414: result: yes configure:17419: checking whether C++ compiler accepts -mfma4 configure:17438: g++ -c -std=c++0x -mfma4 conftest.cpp >&5 configure:17438: $? = 0 configure:17447: result: yes configure:17384: checking whether XOP is supported by the processor configure:17397: result: yes configure:17401: checking whether XOP is supported by the processor and OS configure:17414: result: yes configure:17419: checking whether C++ compiler accepts -mxop configure:17438: g++ -c -std=c++0x -mxop conftest.cpp >&5 configure:17438: $? = 0 configure:17447: result: yes configure:17384: checking whether AVX2 is supported by the processor configure:17397: result: no configure:17384: checking whether AVX512-F is supported by the processor configure:17397: result: no configure:17384: checking whether AVX512-CD is supported by the processor configure:17397: result: no configure:17384: checking whether AVX512-PF is supported by the processor configure:17397: result: no configure:17384: checking whether AVX512-ER is supported by the processor configure:17397: result: no configure:17384: checking whether AVX512-VL is supported by the processor configure:17397: result: no configure:17384: checking whether AVX512-BW is supported by the processor configure:17397: result: no configure:17384: checking whether AVX512-DQ is supported by the processor configure:17397: result: no configure:17384: checking whether AVX512-IFMA is supported by the processor configure:17397: result: no configure:17384: checking whether AVX512-VBMI is supported by the processor configure:17397: result: no configure:17645: checking for __int128 configure:17645: g++ -c -std=c++0x conftest.cpp >&5 conftest.cpp: In function 'int main()': conftest.cpp:74: error: '__int128' was not declared in this scope configure:17645: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "jellyfish" | #define PACKAGE_TARNAME "jellyfish" | #define PACKAGE_VERSION "2.2.7" | #define PACKAGE_STRING "jellyfish 2.2.7" | #define PACKAGE_BUGREPORT "gmarcais@umd.edu" | #define PACKAGE_URL "" | #define PACKAGE "jellyfish" | #define VERSION "2.2.7" | #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_BMI1 1 | #define HAVE_ABM 1 | #define HAVE_MMX 1 | #define HAVE_SSE 1 | #define HAVE_SSE2 1 | #define HAVE_SSE3 1 | #define HAVE_SSSE3 1 | #define HAVE_SSE4_1 1 | #define HAVE_SSE4_2 1 | #define HAVE_SSE4a 1 | #define HAVE_AES 1 | #define HAVE_AVX 1 | #define HAVE_FMA3 1 | #define HAVE_FMA4 1 | #define HAVE_XOP 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 (__int128)) | return 0; | ; | return 0; | } configure:17645: result: no configure:17652: checking for std::numeric_limits<__int128> configure:17666: g++ -c -std=c++0x conftest.cpp >&5 conftest.cpp: In function 'int main()': conftest.cpp:43: error: '__int128' was not declared in this scope conftest.cpp:43: error: template argument 1 is invalid conftest.cpp:43: error: template argument 1 is invalid conftest.cpp:43: error: invalid type in declaration before ';' token configure:17666: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "jellyfish" | #define PACKAGE_TARNAME "jellyfish" | #define PACKAGE_VERSION "2.2.7" | #define PACKAGE_STRING "jellyfish 2.2.7" | #define PACKAGE_BUGREPORT "gmarcais@umd.edu" | #define PACKAGE_URL "" | #define PACKAGE "jellyfish" | #define VERSION "2.2.7" | #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_BMI1 1 | #define HAVE_ABM 1 | #define HAVE_MMX 1 | #define HAVE_SSE 1 | #define HAVE_SSE2 1 | #define HAVE_SSE3 1 | #define HAVE_SSSE3 1 | #define HAVE_SSE4_1 1 | #define HAVE_SSE4_2 1 | #define HAVE_SSE4a 1 | #define HAVE_AES 1 | #define HAVE_AVX 1 | #define HAVE_FMA3 1 | #define HAVE_FMA4 1 | #define HAVE_XOP 1 | /* end confdefs.h. */ | #include | template struct StaticAssert; template<> struct StaticAssert { static void assert() { } }; | int | main () | { | StaticAssert::is_specialized>::assert(); | ; | return 0; | } configure:17673: result: no configure:17680: checking for _NSGetExecutablePath configure:17693: g++ -o conftest -std=c++0x conftest.cpp >&5 conftest.cpp:38:25: error: mach-o/dyld.h: No such file or directory conftest.cpp: In function 'int main()': conftest.cpp:42: error: '_NSGetExecutablePath' was not declared in this scope configure:17693: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "jellyfish" | #define PACKAGE_TARNAME "jellyfish" | #define PACKAGE_VERSION "2.2.7" | #define PACKAGE_STRING "jellyfish 2.2.7" | #define PACKAGE_BUGREPORT "gmarcais@umd.edu" | #define PACKAGE_URL "" | #define PACKAGE "jellyfish" | #define VERSION "2.2.7" | #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_BMI1 1 | #define HAVE_ABM 1 | #define HAVE_MMX 1 | #define HAVE_SSE 1 | #define HAVE_SSE2 1 | #define HAVE_SSE3 1 | #define HAVE_SSSE3 1 | #define HAVE_SSE4_1 1 | #define HAVE_SSE4_2 1 | #define HAVE_SSE4a 1 | #define HAVE_AES 1 | #define HAVE_AVX 1 | #define HAVE_FMA3 1 | #define HAVE_FMA4 1 | #define HAVE_XOP 1 | /* end confdefs.h. */ | #include | int | main () | { | _NSGetExecutablePath(0, 0); | ; | return 0; | } configure:17700: result: no configure:17713: checking for execinfo.h configure:17713: g++ -c -std=c++0x conftest.cpp >&5 configure:17713: $? = 0 configure:17713: result: yes configure:17713: checking for ext/stdio_filebuf.h configure:17713: g++ -c -std=c++0x conftest.cpp >&5 configure:17713: $? = 0 configure:17713: result: yes configure:17729: checking for siginfo_t.si_int configure:17729: g++ -c -std=c++0x conftest.cpp >&5 configure:17729: $? = 0 configure:17729: result: yes configure:18690: checking that generated files are newer than configure configure:18696: result: done configure:18739: creating ./config.status ## ---------------------- ## ## Running config.status. ## ## ---------------------- ## This file was extended by jellyfish config.status 2.2.7, which was generated by GNU Autoconf 2.69. Invocation command line was CONFIG_FILES = CONFIG_HEADERS = CONFIG_LINKS = CONFIG_COMMANDS = $ ./config.status on venus config.status:1212: creating Makefile config.status:1212: creating tests/compat.sh config.status:1212: creating jellyfish-2.0.pc config.status:1212: creating config.h config.status:1441: executing depfiles commands config.status:1441: executing libtool commands ## ---------------- ## ## Cache variables. ## ## ---------------- ## ac_cv_build=x86_64-pc-linux-gnu ac_cv_c_compiler_gnu=yes ac_cv_cxx_compiler_gnu=yes ac_cv_env_CCC_set= ac_cv_env_CCC_value= ac_cv_env_CC_set= ac_cv_env_CC_value= ac_cv_env_CFLAGS_set= ac_cv_env_CFLAGS_value= ac_cv_env_CPPFLAGS_set= ac_cv_env_CPPFLAGS_value= ac_cv_env_CPP_set= ac_cv_env_CPP_value= ac_cv_env_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_HTSLIB_CFLAGS_set= ac_cv_env_HTSLIB_CFLAGS_value= ac_cv_env_HTSLIB_LIBS_set= ac_cv_env_HTSLIB_LIBS_value= ac_cv_env_LDFLAGS_set= ac_cv_env_LDFLAGS_value= 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_MD5_set= ac_cv_env_MD5_value= ac_cv_env_PERL_EXT_CPPFLAGS_set= ac_cv_env_PERL_EXT_CPPFLAGS_value= ac_cv_env_PERL_EXT_INC_set= ac_cv_env_PERL_EXT_INC_value= ac_cv_env_PERL_EXT_LDFLAGS_set= ac_cv_env_PERL_EXT_LDFLAGS_value= ac_cv_env_PERL_EXT_LIB_set= ac_cv_env_PERL_EXT_LIB_value= ac_cv_env_PERL_EXT_PREFIX_set= ac_cv_env_PERL_EXT_PREFIX_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_PYTHON_VERSION_set= ac_cv_env_PYTHON_VERSION_value= ac_cv_env_RUBY_set= ac_cv_env_RUBY_value= ac_cv_env_SAMTOOLS_set= ac_cv_env_SAMTOOLS_value= ac_cv_env_VALGRIND_CFLAGS_set= ac_cv_env_VALGRIND_CFLAGS_value= ac_cv_env_VALGRIND_LIBS_set= ac_cv_env_VALGRIND_LIBS_value= ac_cv_env_YAGGO_set= ac_cv_env_YAGGO_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_header_dlfcn_h=yes ac_cv_header_execinfo_h=yes ac_cv_header_ext_stdio_filebuf_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_host=x86_64-pc-linux-gnu ac_cv_member_siginfo_t_si_int=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_SED=/bin/sed ac_cv_path_YAGGO=false ac_cv_path_ac_pt_PKG_CONFIG=/usr/bin/pkg-config ac_cv_path_install='/usr/bin/install -c' ac_cv_path_lt_DD=/bin/dd ac_cv_path_mkdir=/bin/mkdir ac_cv_prog_AWK=gawk ac_cv_prog_CPP='gcc -E' ac_cv_prog_CXXCPP='g++ -E' ac_cv_prog_MD5=md5sum 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_type___int128=no acl_cv_hardcode_direct=no acl_cv_hardcode_libdir_flag_spec='${wl}-rpath ${wl}$libdir' acl_cv_hardcode_libdir_separator= acl_cv_hardcode_minus_L=no acl_cv_libext=a acl_cv_path_LD='/usr/bin/ld -m elf_x86_64' acl_cv_prog_gnu_ld=yes acl_cv_rpath=done acl_cv_shlibext=so acl_cv_wl=-Wl, am_cv_CC_dependencies_compiler_type=gcc3 am_cv_CXX_dependencies_compiler_type=gcc3 am_cv_make_support_nested_variables=yes am_cv_prog_cc_c_o=yes ax_cv_check_cxxflags___mabm=yes ax_cv_check_cxxflags___maes=yes ax_cv_check_cxxflags___mavx=yes ax_cv_check_cxxflags___mbmi=yes ax_cv_check_cxxflags___mfma4=yes ax_cv_check_cxxflags___mfma=yes ax_cv_check_cxxflags___mmmx=yes ax_cv_check_cxxflags___msse2=yes ax_cv_check_cxxflags___msse3=yes ax_cv_check_cxxflags___msse4_1=yes ax_cv_check_cxxflags___msse4_2=yes ax_cv_check_cxxflags___msse4a=yes ax_cv_check_cxxflags___msse=yes ax_cv_check_cxxflags___mssse3=yes ax_cv_check_cxxflags___mxop=yes ax_cv_gcc_x86_avx_xgetbv_0x00000000=7:0 ax_cv_gcc_x86_avx_xgetbv_=unknown ax_cv_gcc_x86_cpuid_0x00000000=d:68747541:444d4163:69746e65 ax_cv_gcc_x86_cpuid_0x00000001=600f20:23100800:3e98320b:178bfbff ax_cv_gcc_x86_cpuid_0x00000007=0:8:0:0 ax_cv_gcc_x86_cpuid_0x80000000=8000001e:68747541:444d4163:69746e65 ax_cv_gcc_x86_cpuid_0x80000001=600f20:30000000:1ebbfff:2fd3fbff ax_cv_gcc_x86_cpuid_=unknown ax_cv_have_abm_cpu_ext=yes ax_cv_have_abm_ext=yes ax_cv_have_adx_cpu_ext=no ax_cv_have_adx_ext=no ax_cv_have_aes_cpu_ext=yes ax_cv_have_aes_ext=yes ax_cv_have_avx2_cpu_ext=no ax_cv_have_avx2_ext=no ax_cv_have_avx512_os_support_ext=no ax_cv_have_avx512bw_cpu_ext=no ax_cv_have_avx512bw_ext=no ax_cv_have_avx512cd_cpu_ext=no ax_cv_have_avx512cd_ext=no ax_cv_have_avx512dq_cpu_ext=no ax_cv_have_avx512dq_ext=no ax_cv_have_avx512er_cpu_ext=no ax_cv_have_avx512er_ext=no ax_cv_have_avx512f_cpu_ext=no ax_cv_have_avx512f_ext=no ax_cv_have_avx512ifma_cpu_ext=no ax_cv_have_avx512ifma_ext=no ax_cv_have_avx512pf_cpu_ext=no ax_cv_have_avx512pf_ext=no ax_cv_have_avx512vbmi_cpu_ext=no ax_cv_have_avx512vbmi_ext=no ax_cv_have_avx512vl_cpu_ext=no ax_cv_have_avx512vl_ext=no ax_cv_have_avx_cpu_ext=yes ax_cv_have_avx_ext=yes ax_cv_have_avx_os_support_ext=yes ax_cv_have_bmi1_cpu_ext=yes ax_cv_have_bmi1_ext=yes ax_cv_have_bmi2_cpu_ext=no ax_cv_have_bmi2_ext=no ax_cv_have_fma3_cpu_ext=yes ax_cv_have_fma3_ext=yes ax_cv_have_fma4_cpu_ext=yes ax_cv_have_fma4_ext=yes ax_cv_have_mmx_cpu_ext=yes ax_cv_have_mmx_ext=yes ax_cv_have_mmx_os_support_ext=yes ax_cv_have_mpx_cpu_ext=no ax_cv_have_mpx_ext=no ax_cv_have_none_os_support_ext=yes ax_cv_have_prefetchwt1_cpu_ext=no ax_cv_have_prefetchwt1_ext=no ax_cv_have_rdrnd_cpu_ext=no ax_cv_have_rdrnd_ext=no ax_cv_have_sha_cpu_ext=no ax_cv_have_sha_ext=no ax_cv_have_sse2_cpu_ext=yes ax_cv_have_sse2_ext=yes ax_cv_have_sse3_cpu_ext=yes ax_cv_have_sse3_ext=yes ax_cv_have_sse41_cpu_ext=yes ax_cv_have_sse41_ext=yes ax_cv_have_sse42_cpu_ext=yes ax_cv_have_sse42_ext=yes ax_cv_have_sse4a_cpu_ext=yes ax_cv_have_sse4a_ext=yes ax_cv_have_sse_cpu_ext=yes ax_cv_have_sse_ext=yes ax_cv_have_sse_os_support_ext=yes ax_cv_have_ssse3_cpu_ext=yes ax_cv_have_ssse3_ext=yes ax_cv_have_xop_cpu_ext=yes ax_cv_have_xop_ext=yes ax_cv_support_abm_ext=yes ax_cv_support_adx_ext=no ax_cv_support_aes_ext=yes ax_cv_support_avx2_ext=no ax_cv_support_avx512bw_ext=no ax_cv_support_avx512cd_ext=no ax_cv_support_avx512dq_ext=no ax_cv_support_avx512er_ext=no ax_cv_support_avx512f_ext=no ax_cv_support_avx512ifma_ext=no ax_cv_support_avx512pf_ext=no ax_cv_support_avx512vbmi_ext=no ax_cv_support_avx512vl_ext=no ax_cv_support_avx_ext=yes ax_cv_support_bmi1_ext=yes ax_cv_support_bmi2_ext=no ax_cv_support_fma3_ext=yes ax_cv_support_fma4_ext=yes ax_cv_support_mmx_ext=yes ax_cv_support_mpx_ext=no ax_cv_support_prefetchwt1_ext=no ax_cv_support_rdrnd_ext=no ax_cv_support_sha_ext=no ax_cv_support_sse2_ext=yes ax_cv_support_sse3_ext=yes ax_cv_support_sse41_ext=yes ax_cv_support_sse42_ext=yes ax_cv_support_sse4a_ext=yes ax_cv_support_sse_ext=yes ax_cv_support_ssse3_ext=yes ax_cv_support_xop_ext=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/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=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=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][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]* .* \(.*\)$/extern char \1;/p'\''' lt_cv_sys_global_symbol_to_import= lt_cv_sys_max_cmd_len=1966080 lt_cv_to_host_file_cmd=func_convert_file_noop lt_cv_to_tool_file_cmd=func_convert_file_noop lt_cv_truncate_bin='/bin/dd bs=4096 count=1' ## ----------------- ## ## Output variables. ## ## ----------------- ## ACLOCAL='${SHELL} /home/psgendb/BIRCHDEV/install/jellyfish-2.2.7/missing aclocal-1.15' ALL_CXXFLAGS='-std=c++0x' AMDEPBACKSLASH='\' AMDEP_FALSE='#' AMDEP_TRUE='' AMTAR='$${TAR-tar}' AM_BACKSLASH='\' AM_DEFAULT_V='$(AM_DEFAULT_VERBOSITY)' AM_DEFAULT_VERBOSITY='0' AM_V='$(V)' AR='ar' AUTOCONF='${SHELL} /home/psgendb/BIRCHDEV/install/jellyfish-2.2.7/missing autoconf' AUTOHEADER='${SHELL} /home/psgendb/BIRCHDEV/install/jellyfish-2.2.7/missing autoheader' AUTOMAKE='${SHELL} /home/psgendb/BIRCHDEV/install/jellyfish-2.2.7/missing automake-1.15' AWK='gawk' CC='gcc' CCDEPMODE='depmode=gcc3' CFLAGS='-g -O2' CPP='gcc -E' CPPFLAGS='' CPUEXT_FLAGS=' -mbmi -mabm' CXX='g++' CXXCPP='g++ -E' CXXDEPMODE='depmode=gcc3' CXXFLAGS='-std=c++0x ' CYGPATH_W='echo' DEFS='-DHAVE_CONFIG_H' DEPDIR='.deps' DLLTOOL='false' DSYMUTIL='' DUMPBIN='' ECHO_C='' ECHO_N='-n' ECHO_T='' EGREP='/bin/grep -E' EXEEXT='' FGREP='/bin/grep -F' GREP='/bin/grep' HAVE_SWIG_FALSE='' HAVE_SWIG_TRUE='#' HTSLIB_CFLAGS='' HTSLIB_LIBS='' HTSLIB_RPATH='' INSTALL_DATA='${INSTALL} -m 644' INSTALL_PROGRAM='${INSTALL}' INSTALL_SCRIPT='${INSTALL}' INSTALL_STRIP_PROGRAM='$(install_sh) -c -s' LD='/usr/bin/ld -m elf_x86_64' LDFLAGS='' LIBOBJS='' LIBS='' LIBTOOL='$(SHELL) $(top_builddir)/libtool' LIPO='' LN_S='ln -s' LTLIBOBJS='' LT_SYS_LIBRARY_PATH='' MAKEINFO='${SHELL} /home/psgendb/BIRCHDEV/install/jellyfish-2.2.7/missing makeinfo' MANIFEST_TOOL=':' MD5='md5sum' MKDIR_P='/bin/mkdir -p' NM='/usr/bin/nm -B' NMEDIT='' OBJDUMP='objdump' OBJEXT='o' OTOOL64='' OTOOL='' PACKAGE='jellyfish' PACKAGE_BUGREPORT='gmarcais@umd.edu' PACKAGE_LIB='2.0' PACKAGE_NAME='jellyfish' PACKAGE_STRING='jellyfish 2.2.7' PACKAGE_TARNAME='jellyfish' PACKAGE_URL='' PACKAGE_VERSION='2.2.7' PATH_SEPARATOR=':' PERL='' PERL_BINDING_FALSE='' PERL_BINDING_TRUE='#' PERL_EXT_CPPFLAGS='' PERL_EXT_INC='' PERL_EXT_LDFLAGS='' PERL_EXT_LIB='' PERL_EXT_PREFIX='' PKG_CONFIG='/usr/bin/pkg-config' PKG_CONFIG_LIBDIR='' PKG_CONFIG_PATH='' PYTHON='' PYTHON_BINDING_FALSE='' PYTHON_BINDING_TRUE='#' PYTHON_CPPFLAGS='' PYTHON_EXTRA_LDFLAGS='' PYTHON_EXTRA_LIBS='' PYTHON_LDFLAGS='' PYTHON_SITE_PKG='' PYTHON_VERSION='' RANLIB='ranlib' RUBY='' RUBY_BINDING_FALSE='' RUBY_BINDING_TRUE='#' RUBY_EXT_CFLAGS='' RUBY_EXT_LDFLAGS='' RUBY_EXT_LIB='' RUBY_EXT_LIBS='' RUBY_VERSION='' SAMTOOLS='' SED='/bin/sed' SET_MAKE='' SHELL='/bin/sh' SIMD_FLAGS=' -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -msse4a -maes -mavx -mfma -mfma4 -mxop' STATIC_FLAGS='' STRIP='strip' SWIG='' SWIG_LIB='' VALGRIND_CFLAGS='' VALGRIND_LIBS='' VERSION='2.2.7' YAGGO='false' 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='${exec_prefix}/bin' build='x86_64-pc-linux-gnu' build_alias='' build_cpu='x86_64' build_os='linux-gnu' build_vendor='pc' datadir='${datarootdir}' datarootdir='${prefix}/share' docdir='${datarootdir}/doc/${PACKAGE_TARNAME}' dvidir='${docdir}' exec_prefix='${prefix}' host='x86_64-pc-linux-gnu' host_alias='' host_cpu='x86_64' host_os='linux-gnu' host_vendor='pc' htmldir='${docdir}' includedir='${prefix}/include' infodir='${datarootdir}/info' install_sh='${SHELL} /home/psgendb/BIRCHDEV/install/jellyfish-2.2.7/install-sh' libdir='${exec_prefix}/lib' libexecdir='${exec_prefix}/libexec' localedir='${datarootdir}/locale' localstatedir='${prefix}/var' mandir='${datarootdir}/man' mkdir_p='$(MKDIR_P)' oldincludedir='/usr/include' pdfdir='${docdir}' prefix='/home/psgendb/BIRCHDEV/pkg/jellyfish' 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 "jellyfish" #define PACKAGE_TARNAME "jellyfish" #define PACKAGE_VERSION "2.2.7" #define PACKAGE_STRING "jellyfish 2.2.7" #define PACKAGE_BUGREPORT "gmarcais@umd.edu" #define PACKAGE_URL "" #define PACKAGE "jellyfish" #define VERSION "2.2.7" #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_BMI1 1 #define HAVE_ABM 1 #define HAVE_MMX 1 #define HAVE_SSE 1 #define HAVE_SSE2 1 #define HAVE_SSE3 1 #define HAVE_SSSE3 1 #define HAVE_SSE4_1 1 #define HAVE_SSE4_2 1 #define HAVE_SSE4a 1 #define HAVE_AES 1 #define HAVE_AVX 1 #define HAVE_FMA3 1 #define HAVE_FMA4 1 #define HAVE_XOP 1 #define HAVE_EXECINFO_H 1 #define HAVE_EXT_STDIO_FILEBUF_H 1 #define HAVE_SI_INT 1 configure: exit 0