This file contains any messages produced by compilers while running configure, to aid debugging if configure makes a mistake. It was created by HTSlib configure 1.17, which was generated by GNU Autoconf 2.69. Invocation command line was $ ./configure --disable-option-checking --prefix=/usr/local --cache-file=/dev/null --srcdir=. ## --------- ## ## Platform. ## ## --------- ## hostname = venus.cc.umanitoba.ca uname -m = x86_64 uname -r = 3.10.0-1160.88.1.el7.x86_64 uname -s = Linux uname -v = #1 SMP Sat Feb 18 13:27:00 UTC 2023 /usr/bin/uname -p = x86_64 /bin/uname -X = unknown /bin/arch = x86_64 /usr/bin/arch -k = unknown /usr/convex/getsysinfo = unknown /usr/bin/hostinfo = unknown /bin/machine = unknown /usr/bin/oslevel = unknown /bin/universe = unknown PATH: /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: /usr/bin PATH: /bin PATH: /opt/thinlinc/bin PATH: /usr/bin/X11 PATH: /usr/local/sbin PATH: /usr/sbin PATH: /sbin PATH: /opt/puppetlabs/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:2279: checking for gcc configure:2295: found /usr/bin/gcc configure:2306: result: gcc configure:2535: checking for C compiler version configure:2544: gcc --version >&5 gcc (GCC) 4.8.5 20150623 (Red Hat 4.8.5-44) Copyright (C) 2015 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. configure:2555: $? = 0 configure:2544: gcc -v >&5 Using built-in specs. COLLECT_GCC=gcc COLLECT_LTO_WRAPPER=/usr/libexec/gcc/x86_64-redhat-linux/4.8.5/lto-wrapper 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-linker-build-id --with-linker-hash-style=gnu --enable-languages=c,c++,objc,obj-c++,java,fortran,ada,go,lto --enable-plugin --enable-initfini-array --disable-libgcj --with-isl=/builddir/build/BUILD/gcc-4.8.5-20150702/obj-x86_64-redhat-linux/isl-install --with-cloog=/builddir/build/BUILD/gcc-4.8.5-20150702/obj-x86_64-redhat-linux/cloog-install --enable-gnu-indirect-function --with-tune=generic --with-arch_32=x86-64 --build=x86_64-redhat-linux Thread model: posix gcc version 4.8.5 20150623 (Red Hat 4.8.5-44) (GCC) configure:2555: $? = 0 configure:2544: gcc -V >&5 gcc: error: unrecognized command line option '-V' gcc: fatal error: no input files compilation terminated. configure:2555: $? = 4 configure:2544: gcc -qversion >&5 gcc: error: unrecognized command line option '-qversion' gcc: fatal error: no input files compilation terminated. configure:2555: $? = 4 configure:2575: checking whether the C compiler works configure:2597: gcc conftest.c >&5 configure:2601: $? = 0 configure:2649: result: yes configure:2652: checking for C compiler default output file name configure:2654: result: a.out configure:2660: checking for suffix of executables configure:2667: gcc -o conftest conftest.c >&5 configure:2671: $? = 0 configure:2693: result: configure:2715: checking whether we are cross compiling configure:2723: gcc -o conftest conftest.c >&5 configure:2727: $? = 0 configure:2734: ./conftest configure:2738: $? = 0 configure:2753: result: no configure:2758: checking for suffix of object files configure:2780: gcc -c conftest.c >&5 configure:2784: $? = 0 configure:2805: result: o configure:2809: checking whether we are using the GNU C compiler configure:2828: gcc -c conftest.c >&5 configure:2828: $? = 0 configure:2837: result: yes configure:2846: checking whether gcc accepts -g configure:2866: gcc -c -g conftest.c >&5 configure:2866: $? = 0 configure:2907: result: yes configure:2924: checking for gcc option to accept ISO C89 configure:2987: gcc -c -g -O2 conftest.c >&5 configure:2987: $? = 0 configure:3000: result: none needed configure:3063: checking for ranlib configure:3079: found /usr/bin/ranlib configure:3090: result: ranlib configure:3113: checking for grep that handles long lines and -e configure:3171: result: /usr/bin/grep configure:3196: checking for C compiler warning flags configure:3309: result: -Wall configure:3397: checking whether C compiler accepts -mssse3 -mpopcnt -msse4.1 configure:3424: gcc -o conftest -Wall -g -O2 -mssse3 -mpopcnt -msse4.1 conftest.c >&5 configure:3424: $? = 0 configure:3433: result: yes configure:3457: checking whether C compiler accepts -mavx2 configure:3483: gcc -o conftest -Wall -g -O2 -mavx2 conftest.c >&5 configure:3483: $? = 0 configure:3492: result: yes configure:3507: checking whether C compiler accepts -mavx512f configure:3532: gcc -o conftest -Wall -g -O2 -mavx512f conftest.c >&5 gcc: error: unrecognized command line option '-mavx512f' configure:3532: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "HTSlib" | #define PACKAGE_TARNAME "htslib" | #define PACKAGE_VERSION "1.17" | #define PACKAGE_STRING "HTSlib 1.17" | #define PACKAGE_BUGREPORT "samtools-help@lists.sourceforge.net" | #define PACKAGE_URL "http://www.htslib.org/" | #define HAVE_SSSE3 1 | #define HAVE_POPCNT 1 | #define HAVE_SSE4_1 1 | #define UBSAN 1 | #define HAVE_AVX2 1 | /* end confdefs.h. */ | | #include "x86intrin.h" | | int | main () | { | | __m512i a = _mm512_set1_epi32(1); | __m512i b = _mm512_add_epi32(a, a); | return *((char *) &b); | | ; | return 0; | } configure:3541: result: no configure:3556: checking whether C compiler supports ARM Neon configure:3580: gcc -c -Wall -g -O2 conftest.c >&5 conftest.c:16:28: fatal error: arm_neon.h: No such file or directory #include "arm_neon.h" ^ compilation terminated. configure:3580: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "HTSlib" | #define PACKAGE_TARNAME "htslib" | #define PACKAGE_VERSION "1.17" | #define PACKAGE_STRING "HTSlib 1.17" | #define PACKAGE_BUGREPORT "samtools-help@lists.sourceforge.net" | #define PACKAGE_URL "http://www.htslib.org/" | #define HAVE_SSSE3 1 | #define HAVE_POPCNT 1 | #define HAVE_SSE4_1 1 | #define UBSAN 1 | #define HAVE_AVX2 1 | /* end confdefs.h. */ | | | #include "arm_neon.h" | | int | main () | { | | int32x4_t a = vdupq_n_s32(1); | int32x4_t b = vaddq_s32(a, a); | return *((char *) &b); | | ; | return 0; | } configure:3587: result: no configure:3649: checking for pkg-config configure:3667: found /usr/bin/pkg-config configure:3679: result: /usr/bin/pkg-config configure:3704: checking pkg-config is at least version 0.9.0 configure:3707: result: yes configure:3753: checking for special C compiler options needed for large files configure:3798: result: no configure:3804: checking for _FILE_OFFSET_BITS value needed for large files configure:3829: gcc -c -Wall -g -O2 conftest.c >&5 configure:3829: $? = 0 configure:3861: result: no configure:4037: checking shared library type for unknown-Linux configure:4065: result: plain .so configure:4070: checking whether the linker supports versioned symbols configure:4089: gcc -o conftest -Wall -g -O2 -Wl,-version-script,./htslib.map conftest.c >&5 configure:4089: $? = 0 configure:4099: result: yes configure:4116: checking whether the compiler accepts -fvisibility=hidden configure:4136: gcc -o conftest -Wall -g -O2 -fvisibility=hidden -fvisibility=hidden conftest.c >&5 configure:4136: $? = 0 configure:4149: result: yes configure:4203: checking how to run the C preprocessor configure:4234: gcc -E conftest.c configure:4234: $? = 0 configure:4248: gcc -E conftest.c conftest.c:14:28: fatal error: ac_nonexistent.h: No such file or directory #include ^ compilation terminated. configure:4248: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "HTSlib" | #define PACKAGE_TARNAME "htslib" | #define PACKAGE_VERSION "1.17" | #define PACKAGE_STRING "HTSlib 1.17" | #define PACKAGE_BUGREPORT "samtools-help@lists.sourceforge.net" | #define PACKAGE_URL "http://www.htslib.org/" | #define HAVE_SSSE3 1 | #define HAVE_POPCNT 1 | #define HAVE_SSE4_1 1 | #define UBSAN 1 | #define HAVE_AVX2 1 | /* end confdefs.h. */ | #include configure:4273: result: gcc -E configure:4293: gcc -E conftest.c configure:4293: $? = 0 configure:4307: gcc -E conftest.c conftest.c:14:28: fatal error: ac_nonexistent.h: No such file or directory #include ^ compilation terminated. configure:4307: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "HTSlib" | #define PACKAGE_TARNAME "htslib" | #define PACKAGE_VERSION "1.17" | #define PACKAGE_STRING "HTSlib 1.17" | #define PACKAGE_BUGREPORT "samtools-help@lists.sourceforge.net" | #define PACKAGE_URL "http://www.htslib.org/" | #define HAVE_SSSE3 1 | #define HAVE_POPCNT 1 | #define HAVE_SSE4_1 1 | #define UBSAN 1 | #define HAVE_AVX2 1 | /* end confdefs.h. */ | #include configure:4336: checking for egrep configure:4398: result: /usr/bin/grep -E configure:4403: checking for ANSI C header files configure:4423: gcc -c -Wall -g -O2 -fvisibility=hidden conftest.c >&5 configure:4423: $? = 0 configure:4496: gcc -o conftest -Wall -g -O2 -fvisibility=hidden -fvisibility=hidden conftest.c >&5 configure:4496: $? = 0 configure:4496: ./conftest configure:4496: $? = 0 configure:4507: result: yes configure:4520: checking for sys/types.h configure:4520: gcc -c -Wall -g -O2 -fvisibility=hidden conftest.c >&5 configure:4520: $? = 0 configure:4520: result: yes configure:4520: checking for sys/stat.h configure:4520: gcc -c -Wall -g -O2 -fvisibility=hidden conftest.c >&5 configure:4520: $? = 0 configure:4520: result: yes configure:4520: checking for stdlib.h configure:4520: gcc -c -Wall -g -O2 -fvisibility=hidden conftest.c >&5 configure:4520: $? = 0 configure:4520: result: yes configure:4520: checking for string.h configure:4520: gcc -c -Wall -g -O2 -fvisibility=hidden conftest.c >&5 configure:4520: $? = 0 configure:4520: result: yes configure:4520: checking for memory.h configure:4520: gcc -c -Wall -g -O2 -fvisibility=hidden conftest.c >&5 configure:4520: $? = 0 configure:4520: result: yes configure:4520: checking for strings.h configure:4520: gcc -c -Wall -g -O2 -fvisibility=hidden conftest.c >&5 configure:4520: $? = 0 configure:4520: result: yes configure:4520: checking for inttypes.h configure:4520: gcc -c -Wall -g -O2 -fvisibility=hidden conftest.c >&5 configure:4520: $? = 0 configure:4520: result: yes configure:4520: checking for stdint.h configure:4520: gcc -c -Wall -g -O2 -fvisibility=hidden conftest.c >&5 configure:4520: $? = 0 configure:4520: result: yes configure:4520: checking for unistd.h configure:4520: gcc -c -Wall -g -O2 -fvisibility=hidden conftest.c >&5 configure:4520: $? = 0 configure:4520: result: yes configure:4538: checking for stdlib.h configure:4538: result: yes configure:4538: checking for unistd.h configure:4538: result: yes configure:4538: checking for sys/param.h configure:4538: gcc -c -Wall -g -O2 -fvisibility=hidden conftest.c >&5 configure:4538: $? = 0 configure:4538: result: yes configure:4558: checking for getpagesize configure:4558: gcc -o conftest -Wall -g -O2 -fvisibility=hidden -fvisibility=hidden conftest.c >&5 configure:4558: $? = 0 configure:4558: result: yes configure:4567: checking for working mmap configure:4716: gcc -o conftest -Wall -g -O2 -fvisibility=hidden -fvisibility=hidden conftest.c >&5 configure:4716: $? = 0 configure:4716: ./conftest configure:4716: $? = 0 configure:4726: result: yes configure:4738: checking for gmtime_r configure:4738: gcc -o conftest -Wall -g -O2 -fvisibility=hidden -fvisibility=hidden conftest.c >&5 configure:4738: $? = 0 configure:4738: result: yes configure:4738: checking for fsync configure:4738: gcc -o conftest -Wall -g -O2 -fvisibility=hidden -fvisibility=hidden conftest.c >&5 configure:4738: $? = 0 configure:4738: result: yes configure:4738: checking for drand48 configure:4738: gcc -o conftest -Wall -g -O2 -fvisibility=hidden -fvisibility=hidden conftest.c >&5 configure:4738: $? = 0 configure:4738: result: yes configure:4738: checking for srand48_deterministic configure:4738: gcc -o conftest -Wall -g -O2 -fvisibility=hidden -fvisibility=hidden conftest.c >&5 /tmp/cc0y55FW.o: In function `main': /home/psgendb/BIRCHDEV/install/samtools-1.17/htslib-1.17/conftest.c:66: undefined reference to `srand48_deterministic' collect2: error: ld returned 1 exit status configure:4738: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "HTSlib" | #define PACKAGE_TARNAME "htslib" | #define PACKAGE_VERSION "1.17" | #define PACKAGE_STRING "HTSlib 1.17" | #define PACKAGE_BUGREPORT "samtools-help@lists.sourceforge.net" | #define PACKAGE_URL "http://www.htslib.org/" | #define HAVE_SSSE3 1 | #define HAVE_POPCNT 1 | #define HAVE_SSE4_1 1 | #define UBSAN 1 | #define HAVE_AVX2 1 | #define STDC_HEADERS 1 | #define HAVE_SYS_TYPES_H 1 | #define HAVE_SYS_STAT_H 1 | #define HAVE_STDLIB_H 1 | #define HAVE_STRING_H 1 | #define HAVE_MEMORY_H 1 | #define HAVE_STRINGS_H 1 | #define HAVE_INTTYPES_H 1 | #define HAVE_STDINT_H 1 | #define HAVE_UNISTD_H 1 | #define HAVE_STDLIB_H 1 | #define HAVE_UNISTD_H 1 | #define HAVE_SYS_PARAM_H 1 | #define HAVE_GETPAGESIZE 1 | #define HAVE_MMAP 1 | #define HAVE_GMTIME_R 1 | #define HAVE_FSYNC 1 | #define HAVE_DRAND48 1 | /* end confdefs.h. */ | /* Define srand48_deterministic to an innocuous variant, in case declares srand48_deterministic. | For example, HP-UX 11i declares gettimeofday. */ | #define srand48_deterministic innocuous_srand48_deterministic | | /* System header to define __stub macros and hopefully few prototypes, | which can conflict with char srand48_deterministic (); below. | Prefer to if __STDC__ is defined, since | exists even on freestanding compilers. */ | | #ifdef __STDC__ | # include | #else | # include | #endif | | #undef srand48_deterministic | | /* 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 srand48_deterministic (); | /* 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_srand48_deterministic || defined __stub___srand48_deterministic | choke me | #endif | | int | main () | { | return srand48_deterministic (); | ; | return 0; | } configure:4738: result: no configure:4750: checking whether fdatasync is declared configure:4750: gcc -c -Wall -g -O2 -fvisibility=hidden conftest.c >&5 configure:4750: $? = 0 configure:4750: result: yes configure:4754: checking for fdatasync configure:4754: gcc -o conftest -Wall -g -O2 -fvisibility=hidden -fvisibility=hidden conftest.c >&5 configure:4754: $? = 0 configure:4754: result: yes configure:4889: checking for library containing log configure:4920: gcc -o conftest -Wall -g -O2 -fvisibility=hidden -fvisibility=hidden conftest.c >&5 conftest.c:40:6: warning: conflicting types for built-in function 'log' [enabled by default] char log (); ^ /tmp/cceT6bpi.o: In function `main': /home/psgendb/BIRCHDEV/install/samtools-1.17/htslib-1.17/conftest.c:44: undefined reference to `log' collect2: error: ld returned 1 exit status configure:4920: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "HTSlib" | #define PACKAGE_TARNAME "htslib" | #define PACKAGE_VERSION "1.17" | #define PACKAGE_STRING "HTSlib 1.17" | #define PACKAGE_BUGREPORT "samtools-help@lists.sourceforge.net" | #define PACKAGE_URL "http://www.htslib.org/" | #define HAVE_SSSE3 1 | #define HAVE_POPCNT 1 | #define HAVE_SSE4_1 1 | #define UBSAN 1 | #define HAVE_AVX2 1 | #define STDC_HEADERS 1 | #define HAVE_SYS_TYPES_H 1 | #define HAVE_SYS_STAT_H 1 | #define HAVE_STDLIB_H 1 | #define HAVE_STRING_H 1 | #define HAVE_MEMORY_H 1 | #define HAVE_STRINGS_H 1 | #define HAVE_INTTYPES_H 1 | #define HAVE_STDINT_H 1 | #define HAVE_UNISTD_H 1 | #define HAVE_STDLIB_H 1 | #define HAVE_UNISTD_H 1 | #define HAVE_SYS_PARAM_H 1 | #define HAVE_GETPAGESIZE 1 | #define HAVE_MMAP 1 | #define HAVE_GMTIME_R 1 | #define HAVE_FSYNC 1 | #define HAVE_DRAND48 1 | #define HAVE_FDATASYNC 1 | /* end confdefs.h. */ | | /* Override any GCC internal prototype to avoid an error. | Use char because int might match the return type of a GCC | builtin and then its argument prototype would still apply. */ | #ifdef __cplusplus | extern "C" | #endif | char log (); | int | main () | { | return log (); | ; | return 0; | } configure:4920: gcc -o conftest -Wall -g -O2 -fvisibility=hidden -fvisibility=hidden conftest.c -lm >&5 conftest.c:40:6: warning: conflicting types for built-in function 'log' [enabled by default] char log (); ^ configure:4920: $? = 0 configure:4937: result: -lm configure:4957: checking for zlib.h configure:4957: gcc -c -Wall -g -O2 -fvisibility=hidden conftest.c >&5 configure:4957: $? = 0 configure:4957: result: yes configure:4966: checking for inflate in -lz configure:4991: gcc -o conftest -Wall -g -O2 -fvisibility=hidden -fvisibility=hidden conftest.c -lz -lm >&5 configure:4991: $? = 0 configure:5000: result: yes configure:5031: checking for library containing recv configure:5062: gcc -o conftest -Wall -g -O2 -fvisibility=hidden -fvisibility=hidden conftest.c -lz -lm >&5 configure:5062: $? = 0 configure:5079: result: none required configure:5125: checking for bzlib.h configure:5125: gcc -c -Wall -g -O2 -fvisibility=hidden conftest.c >&5 configure:5125: $? = 0 configure:5125: result: yes configure:5134: checking for BZ2_bzBuffToBuffCompress in -lbz2 configure:5159: gcc -o conftest -Wall -g -O2 -fvisibility=hidden -fvisibility=hidden conftest.c -lbz2 -lz -lm >&5 configure:5159: $? = 0 configure:5168: result: yes configure:5212: checking for lzma.h configure:5212: gcc -c -Wall -g -O2 -fvisibility=hidden conftest.c >&5 configure:5212: $? = 0 configure:5212: result: yes configure:5225: checking for lzma_easy_buffer_encode in -llzma configure:5250: gcc -o conftest -Wall -g -O2 -fvisibility=hidden -fvisibility=hidden conftest.c -llzma -lbz2 -lz -lm >&5 configure:5250: $? = 0 configure:5259: result: yes configure:5372: checking whether htscodecs files are present configure:5375: result: yes configure:5413: checking for libdeflate.h configure:5413: gcc -c -Wall -g -O2 -fvisibility=hidden conftest.c >&5 conftest.c:39:24: fatal error: libdeflate.h: No such file or directory #include ^ compilation terminated. configure:5413: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "HTSlib" | #define PACKAGE_TARNAME "htslib" | #define PACKAGE_VERSION "1.17" | #define PACKAGE_STRING "HTSlib 1.17" | #define PACKAGE_BUGREPORT "samtools-help@lists.sourceforge.net" | #define PACKAGE_URL "http://www.htslib.org/" | #define HAVE_SSSE3 1 | #define HAVE_POPCNT 1 | #define HAVE_SSE4_1 1 | #define UBSAN 1 | #define HAVE_AVX2 1 | #define STDC_HEADERS 1 | #define HAVE_SYS_TYPES_H 1 | #define HAVE_SYS_STAT_H 1 | #define HAVE_STDLIB_H 1 | #define HAVE_STRING_H 1 | #define HAVE_MEMORY_H 1 | #define HAVE_STRINGS_H 1 | #define HAVE_INTTYPES_H 1 | #define HAVE_STDINT_H 1 | #define HAVE_UNISTD_H 1 | #define HAVE_STDLIB_H 1 | #define HAVE_UNISTD_H 1 | #define HAVE_SYS_PARAM_H 1 | #define HAVE_GETPAGESIZE 1 | #define HAVE_MMAP 1 | #define HAVE_GMTIME_R 1 | #define HAVE_FSYNC 1 | #define HAVE_DRAND48 1 | #define HAVE_FDATASYNC 1 | #define HAVE_LIBZ 1 | #define HAVE_LIBBZ2 1 | #define HAVE_LZMA_H 1 | #define HAVE_LIBLZMA 1 | /* end confdefs.h. */ | ; | | #include configure:5413: result: no configure:5422: checking for libdeflate_deflate_compress in -ldeflate configure:5447: gcc -o conftest -Wall -g -O2 -fvisibility=hidden -fvisibility=hidden conftest.c -ldeflate -llzma -lbz2 -lz -lm >&5 /usr/bin/ld: cannot find -ldeflate collect2: error: ld returned 1 exit status configure:5447: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "HTSlib" | #define PACKAGE_TARNAME "htslib" | #define PACKAGE_VERSION "1.17" | #define PACKAGE_STRING "HTSlib 1.17" | #define PACKAGE_BUGREPORT "samtools-help@lists.sourceforge.net" | #define PACKAGE_URL "http://www.htslib.org/" | #define HAVE_SSSE3 1 | #define HAVE_POPCNT 1 | #define HAVE_SSE4_1 1 | #define UBSAN 1 | #define HAVE_AVX2 1 | #define STDC_HEADERS 1 | #define HAVE_SYS_TYPES_H 1 | #define HAVE_SYS_STAT_H 1 | #define HAVE_STDLIB_H 1 | #define HAVE_STRING_H 1 | #define HAVE_MEMORY_H 1 | #define HAVE_STRINGS_H 1 | #define HAVE_INTTYPES_H 1 | #define HAVE_STDINT_H 1 | #define HAVE_UNISTD_H 1 | #define HAVE_STDLIB_H 1 | #define HAVE_UNISTD_H 1 | #define HAVE_SYS_PARAM_H 1 | #define HAVE_GETPAGESIZE 1 | #define HAVE_MMAP 1 | #define HAVE_GMTIME_R 1 | #define HAVE_FSYNC 1 | #define HAVE_DRAND48 1 | #define HAVE_FDATASYNC 1 | #define HAVE_LIBZ 1 | #define HAVE_LIBBZ2 1 | #define HAVE_LZMA_H 1 | #define HAVE_LIBLZMA 1 | /* end confdefs.h. */ | | /* Override any GCC internal prototype to avoid an error. | Use char because int might match the return type of a GCC | builtin and then its argument prototype would still apply. */ | #ifdef __cplusplus | extern "C" | #endif | char libdeflate_deflate_compress (); | int | main () | { | return libdeflate_deflate_compress (); | ; | return 0; | } configure:5456: result: no configure:5495: checking for curl/curl.h configure:5495: gcc -c -Wall -g -O2 -fvisibility=hidden conftest.c >&5 configure:5495: $? = 0 configure:5495: result: yes configure:5504: checking for curl_easy_pause in -lcurl configure:5529: gcc -o conftest -Wall -g -O2 -fvisibility=hidden -fvisibility=hidden conftest.c -lcurl -llzma -lbz2 -lz -lm >&5 configure:5529: $? = 0 configure:5538: result: yes configure:5673: checking for CCHmac configure:5673: gcc -o conftest -Wall -g -O2 -fvisibility=hidden -fvisibility=hidden conftest.c -llzma -lbz2 -lz -lm >&5 /tmp/cc3O3j9g.o: In function `main': /home/psgendb/BIRCHDEV/install/samtools-1.17/htslib-1.17/conftest.c:73: undefined reference to `CCHmac' collect2: error: ld returned 1 exit status configure:5673: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "HTSlib" | #define PACKAGE_TARNAME "htslib" | #define PACKAGE_VERSION "1.17" | #define PACKAGE_STRING "HTSlib 1.17" | #define PACKAGE_BUGREPORT "samtools-help@lists.sourceforge.net" | #define PACKAGE_URL "http://www.htslib.org/" | #define HAVE_SSSE3 1 | #define HAVE_POPCNT 1 | #define HAVE_SSE4_1 1 | #define UBSAN 1 | #define HAVE_AVX2 1 | #define STDC_HEADERS 1 | #define HAVE_SYS_TYPES_H 1 | #define HAVE_SYS_STAT_H 1 | #define HAVE_STDLIB_H 1 | #define HAVE_STRING_H 1 | #define HAVE_MEMORY_H 1 | #define HAVE_STRINGS_H 1 | #define HAVE_INTTYPES_H 1 | #define HAVE_STDINT_H 1 | #define HAVE_UNISTD_H 1 | #define HAVE_STDLIB_H 1 | #define HAVE_UNISTD_H 1 | #define HAVE_SYS_PARAM_H 1 | #define HAVE_GETPAGESIZE 1 | #define HAVE_MMAP 1 | #define HAVE_GMTIME_R 1 | #define HAVE_FSYNC 1 | #define HAVE_DRAND48 1 | #define HAVE_FDATASYNC 1 | #define HAVE_LIBZ 1 | #define HAVE_LIBBZ2 1 | #define HAVE_LZMA_H 1 | #define HAVE_LIBLZMA 1 | #define HAVE_LIBCURL 1 | #define ENABLE_GCS 1 | /* end confdefs.h. */ | /* Define CCHmac to an innocuous variant, in case declares CCHmac. | For example, HP-UX 11i declares gettimeofday. */ | #define CCHmac innocuous_CCHmac | | /* System header to define __stub macros and hopefully few prototypes, | which can conflict with char CCHmac (); below. | Prefer to if __STDC__ is defined, since | exists even on freestanding compilers. */ | | #ifdef __STDC__ | # include | #else | # include | #endif | | #undef CCHmac | | /* 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 CCHmac (); | /* 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_CCHmac || defined __stub___CCHmac | choke me | #endif | | int | main () | { | return CCHmac (); | ; | return 0; | } configure:5673: result: no configure:5680: checking for library containing HMAC configure:5711: gcc -o conftest -Wall -g -O2 -fvisibility=hidden -fvisibility=hidden conftest.c -llzma -lbz2 -lz -lm >&5 /tmp/cceYlw9g.o: In function `main': /home/psgendb/BIRCHDEV/install/samtools-1.17/htslib-1.17/conftest.c:50: undefined reference to `HMAC' collect2: error: ld returned 1 exit status configure:5711: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "HTSlib" | #define PACKAGE_TARNAME "htslib" | #define PACKAGE_VERSION "1.17" | #define PACKAGE_STRING "HTSlib 1.17" | #define PACKAGE_BUGREPORT "samtools-help@lists.sourceforge.net" | #define PACKAGE_URL "http://www.htslib.org/" | #define HAVE_SSSE3 1 | #define HAVE_POPCNT 1 | #define HAVE_SSE4_1 1 | #define UBSAN 1 | #define HAVE_AVX2 1 | #define STDC_HEADERS 1 | #define HAVE_SYS_TYPES_H 1 | #define HAVE_SYS_STAT_H 1 | #define HAVE_STDLIB_H 1 | #define HAVE_STRING_H 1 | #define HAVE_MEMORY_H 1 | #define HAVE_STRINGS_H 1 | #define HAVE_INTTYPES_H 1 | #define HAVE_STDINT_H 1 | #define HAVE_UNISTD_H 1 | #define HAVE_STDLIB_H 1 | #define HAVE_UNISTD_H 1 | #define HAVE_SYS_PARAM_H 1 | #define HAVE_GETPAGESIZE 1 | #define HAVE_MMAP 1 | #define HAVE_GMTIME_R 1 | #define HAVE_FSYNC 1 | #define HAVE_DRAND48 1 | #define HAVE_FDATASYNC 1 | #define HAVE_LIBZ 1 | #define HAVE_LIBBZ2 1 | #define HAVE_LZMA_H 1 | #define HAVE_LIBLZMA 1 | #define HAVE_LIBCURL 1 | #define ENABLE_GCS 1 | /* end confdefs.h. */ | | /* Override any GCC internal prototype to avoid an error. | Use char because int might match the return type of a GCC | builtin and then its argument prototype would still apply. */ | #ifdef __cplusplus | extern "C" | #endif | char HMAC (); | int | main () | { | return HMAC (); | ; | return 0; | } configure:5711: gcc -o conftest -Wall -g -O2 -fvisibility=hidden -fvisibility=hidden conftest.c -lcrypto -llzma -lbz2 -lz -lm >&5 configure:5711: $? = 0 configure:5728: result: -lcrypto configure:5770: checking for library containing regcomp configure:5801: gcc -o conftest -Wall -g -O2 -fvisibility=hidden -fvisibility=hidden conftest.c -llzma -lbz2 -lz -lm >&5 configure:5801: $? = 0 configure:5818: result: none required configure:5827: checking whether PTHREAD_MUTEX_RECURSIVE is declared configure:5827: gcc -c -Wall -g -O2 -fvisibility=hidden conftest.c >&5 configure:5827: $? = 0 configure:5827: result: yes configure:5993: creating ./config.status ## ---------------------- ## ## Running config.status. ## ## ---------------------- ## This file was extended by HTSlib config.status 1.17, which was generated by GNU Autoconf 2.69. Invocation command line was CONFIG_FILES = CONFIG_HEADERS = CONFIG_LINKS = CONFIG_COMMANDS = $ ./config.status on venus.cc.umanitoba.ca config.status:861: creating config.mk config.status:861: creating htslib.pc.tmp config.status:861: creating config.h config.status:1057: linking htscodecs_bundled.mk to htscodecs.mk ## ---------------- ## ## Cache variables. ## ## ---------------- ## ac_cv_c_compiler_gnu=yes 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_LDFLAGS_set= ac_cv_env_LDFLAGS_value= ac_cv_env_LIBS_set= ac_cv_env_LIBS_value= ac_cv_env_PKG_CONFIG_LIBDIR_set= ac_cv_env_PKG_CONFIG_LIBDIR_value= ac_cv_env_PKG_CONFIG_PATH_set= ac_cv_env_PKG_CONFIG_PATH_value= ac_cv_env_PKG_CONFIG_set= ac_cv_env_PKG_CONFIG_value= ac_cv_env_build_alias_set= ac_cv_env_build_alias_value= ac_cv_env_host_alias_set= ac_cv_env_host_alias_value= ac_cv_env_target_alias_set= ac_cv_env_target_alias_value= ac_cv_func_CCHmac=no ac_cv_func_drand48=yes ac_cv_func_fdatasync=yes ac_cv_func_fsync=yes ac_cv_func_getpagesize=yes ac_cv_func_gmtime_r=yes ac_cv_func_mmap_fixed_mapped=yes ac_cv_func_srand48_deterministic=no ac_cv_have_decl_PTHREAD_MUTEX_RECURSIVE=yes ac_cv_have_decl_fdatasync_int_=yes ac_cv_header_bzlib_h=yes ac_cv_header_curl_curl_h=yes ac_cv_header_inttypes_h=yes ac_cv_header_libdeflate_h=no ac_cv_header_lzma_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_param_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_zlib_h=yes ac_cv_lib_bz2_BZ2_bzBuffToBuffCompress=yes ac_cv_lib_curl_curl_easy_pause=yes ac_cv_lib_deflate_libdeflate_deflate_compress=no ac_cv_lib_lzma_lzma_easy_buffer_encode=yes ac_cv_lib_z_inflate=yes ac_cv_objext=o ac_cv_path_EGREP='/usr/bin/grep -E' ac_cv_path_GREP=/usr/bin/grep ac_cv_path_ac_pt_PKG_CONFIG=/usr/bin/pkg-config ac_cv_prog_CPP='gcc -E' ac_cv_prog_ac_ct_CC=gcc ac_cv_prog_ac_ct_RANLIB=ranlib ac_cv_prog_cc_c89= ac_cv_prog_cc_g=yes ac_cv_search_HMAC=-lcrypto ac_cv_search_log=-lm ac_cv_search_recv='none required' ac_cv_search_regcomp='none required' ac_cv_sys_file_offset_bits=no ac_cv_sys_largefile_CC=no ax_cv_check_cflags___mavx2=yes ax_cv_check_cflags___mavx512f=no ax_cv_check_cflags___mssse3__mpopcnt__msse4_1=yes hts_cv_check__fvisibility_hidden=yes hts_cv_have_neon=no hts_cv_have_versioned_symbols=yes hts_cv_prog_cc_warnings=-Wall ## ----------------- ## ## Output variables. ## ## ----------------- ## CC='gcc' CFLAGS=' -Wall -g -O2 -fvisibility=hidden' CPP='gcc -E' CPPFLAGS='' CRYPTO_LIBS='-lcrypto' DEFS='-DHAVE_CONFIG_H' ECHO_C='' ECHO_N='-n' ECHO_T='' EGREP='/usr/bin/grep -E' EXEEXT='' GREP='/usr/bin/grep' HTSDIRslash_if_relsrcdir='$(HTSDIR)/' LDFLAGS=' -fvisibility=hidden' LIBOBJS='' LIBS='-llzma -lbz2 -lz -lm ' LTLIBOBJS='' OBJEXT='o' PACKAGE_BUGREPORT='samtools-help@lists.sourceforge.net' PACKAGE_NAME='HTSlib' PACKAGE_STRING='HTSlib 1.17' PACKAGE_TARNAME='htslib' PACKAGE_URL='http://www.htslib.org/' PACKAGE_VERSION='1.17' PATH_SEPARATOR=':' PKG_CONFIG='/usr/bin/pkg-config' PKG_CONFIG_LIBDIR='' PKG_CONFIG_PATH='' PLATFORM='default' PLUGIN_EXT='.so' RANLIB='ranlib' SHELL='/bin/sh' VERSION_SCRIPT_LDFLAGS='-Wl,-version-script,$(srcprefix)htslib.map' ac_ct_CC='gcc' bindir='${exec_prefix}/bin' build_alias='' datadir='${datarootdir}' datarootdir='${prefix}/share' docdir='${datarootdir}/doc/${PACKAGE_TARNAME}' dvidir='${docdir}' enable_plugins='no' exec_prefix='${prefix}' gcs='enabled' host_alias='' htmldir='${docdir}' hts_cflags_avx2='-mavx2' hts_cflags_avx512='' hts_cflags_sse4='-mssse3 -mpopcnt -msse4.1' hts_have_neon='' includedir='${prefix}/include' infodir='${datarootdir}/info' libcurl='enabled' libdir='${exec_prefix}/lib' libexecdir='${exec_prefix}/libexec' localedir='${datarootdir}/locale' localstatedir='${prefix}/var' mandir='${datarootdir}/man' oldincludedir='/usr/include' pc_requires=' liblzma' pdfdir='${docdir}' plugindir='$(libexecdir)/htslib' pluginpath='$(libexecdir)/htslib' prefix='/usr/local' private_LIBS=' -lbz2' program_transform_name='s,x,x,' psdir='${docdir}' runstatedir='${localstatedir}/run' s3='enabled' sbindir='${exec_prefix}/sbin' sharedstatedir='${prefix}/com' static_LDFLAGS='' static_LIBS='-lpthread -lz -lm -lbz2 -llzma -lcurl -lcrypto' sysconfdir='${prefix}/etc' target_alias='' with_external_htscodecs='no' ## ----------- ## ## confdefs.h. ## ## ----------- ## /* confdefs.h */ #define PACKAGE_NAME "HTSlib" #define PACKAGE_TARNAME "htslib" #define PACKAGE_VERSION "1.17" #define PACKAGE_STRING "HTSlib 1.17" #define PACKAGE_BUGREPORT "samtools-help@lists.sourceforge.net" #define PACKAGE_URL "http://www.htslib.org/" #define HAVE_SSSE3 1 #define HAVE_POPCNT 1 #define HAVE_SSE4_1 1 #define UBSAN 1 #define HAVE_AVX2 1 #define STDC_HEADERS 1 #define HAVE_SYS_TYPES_H 1 #define HAVE_SYS_STAT_H 1 #define HAVE_STDLIB_H 1 #define HAVE_STRING_H 1 #define HAVE_MEMORY_H 1 #define HAVE_STRINGS_H 1 #define HAVE_INTTYPES_H 1 #define HAVE_STDINT_H 1 #define HAVE_UNISTD_H 1 #define HAVE_STDLIB_H 1 #define HAVE_UNISTD_H 1 #define HAVE_SYS_PARAM_H 1 #define HAVE_GETPAGESIZE 1 #define HAVE_MMAP 1 #define HAVE_GMTIME_R 1 #define HAVE_FSYNC 1 #define HAVE_DRAND48 1 #define HAVE_FDATASYNC 1 #define HAVE_LIBZ 1 #define HAVE_LIBBZ2 1 #define HAVE_LZMA_H 1 #define HAVE_LIBLZMA 1 #define HAVE_LIBCURL 1 #define ENABLE_GCS 1 #define HAVE_HMAC 1 #define ENABLE_S3 1 configure: exit 0