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 1.10.2, which was generated by GNU Autoconf 2.69. Invocation command line was $ ./configure --prefix=/home/psgendb/BIRCHDEV/install/trinityrnaseq-v2.14.0/trinity-plugins/bamsifter/htslib/build/ ## --------- ## ## Platform. ## ## --------- ## hostname = mars.cc.umanitoba.ca uname -m = x86_64 uname -r = 3.10.0-1160.53.1.el7.x86_64 uname -s = Linux uname -v = #1 SMP Thu Dec 16 10:19:28 UTC 2021 /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:2195: checking for gcc configure:2211: found /usr/bin/gcc configure:2222: result: gcc configure:2451: checking for C compiler version configure:2460: 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:2471: $? = 0 configure:2460: 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:2471: $? = 0 configure:2460: gcc -V >&5 gcc: error: unrecognized command line option '-V' gcc: fatal error: no input files compilation terminated. configure:2471: $? = 4 configure:2460: gcc -qversion >&5 gcc: error: unrecognized command line option '-qversion' gcc: fatal error: no input files compilation terminated. configure:2471: $? = 4 configure:2491: checking whether the C compiler works configure:2513: gcc conftest.c >&5 configure:2517: $? = 0 configure:2565: result: yes configure:2568: checking for C compiler default output file name configure:2570: result: a.out configure:2576: checking for suffix of executables configure:2583: gcc -o conftest conftest.c >&5 configure:2587: $? = 0 configure:2609: result: configure:2631: checking whether we are cross compiling configure:2639: gcc -o conftest conftest.c >&5 configure:2643: $? = 0 configure:2650: ./conftest configure:2654: $? = 0 configure:2669: result: no configure:2674: checking for suffix of object files configure:2696: gcc -c conftest.c >&5 configure:2700: $? = 0 configure:2721: result: o configure:2725: checking whether we are using the GNU C compiler configure:2744: gcc -c conftest.c >&5 configure:2744: $? = 0 configure:2753: result: yes configure:2762: checking whether gcc accepts -g configure:2782: gcc -c -g conftest.c >&5 configure:2782: $? = 0 configure:2823: result: yes configure:2840: checking for gcc option to accept ISO C89 configure:2903: gcc -c -g -O2 conftest.c >&5 configure:2903: $? = 0 configure:2916: result: none needed configure:2979: checking for ranlib configure:2995: found /usr/bin/ranlib configure:3006: result: ranlib configure:3029: checking for grep that handles long lines and -e configure:3087: result: /usr/bin/grep configure:3112: checking for C compiler warning flags configure:3225: result: -Wall configure:3366: checking for pkg-config configure:3384: found /usr/bin/pkg-config configure:3396: result: /usr/bin/pkg-config configure:3421: checking pkg-config is at least version 0.9.0 configure:3424: result: yes configure:3463: checking for special C compiler options needed for large files configure:3508: result: no configure:3514: checking for _FILE_OFFSET_BITS value needed for large files configure:3539: gcc -c -Wall -g -O2 conftest.c >&5 configure:3539: $? = 0 configure:3571: result: no configure:3737: checking shared library type for unknown-Linux configure:3765: result: plain .so configure:3775: checking whether the compiler accepts -fvisibility=hidden configure:3795: gcc -o conftest -Wall -g -O2 -fvisibility=hidden -fvisibility=hidden conftest.c >&5 configure:3795: $? = 0 configure:3808: result: yes configure:3862: checking how to run the C preprocessor configure:3893: gcc -E conftest.c configure:3893: $? = 0 configure:3907: gcc -E conftest.c conftest.c:9:28: fatal error: ac_nonexistent.h: No such file or directory #include ^ compilation terminated. configure:3907: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "HTSlib" | #define PACKAGE_TARNAME "htslib" | #define PACKAGE_VERSION "1.10.2" | #define PACKAGE_STRING "HTSlib 1.10.2" | #define PACKAGE_BUGREPORT "samtools-help@lists.sourceforge.net" | #define PACKAGE_URL "http://www.htslib.org/" | /* end confdefs.h. */ | #include configure:3932: result: gcc -E configure:3952: gcc -E conftest.c configure:3952: $? = 0 configure:3966: gcc -E conftest.c conftest.c:9:28: fatal error: ac_nonexistent.h: No such file or directory #include ^ compilation terminated. configure:3966: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "HTSlib" | #define PACKAGE_TARNAME "htslib" | #define PACKAGE_VERSION "1.10.2" | #define PACKAGE_STRING "HTSlib 1.10.2" | #define PACKAGE_BUGREPORT "samtools-help@lists.sourceforge.net" | #define PACKAGE_URL "http://www.htslib.org/" | /* end confdefs.h. */ | #include configure:3995: checking for egrep configure:4057: result: /usr/bin/grep -E configure:4062: checking for ANSI C header files configure:4082: gcc -c -Wall -g -O2 -fvisibility=hidden conftest.c >&5 configure:4082: $? = 0 configure:4155: gcc -o conftest -Wall -g -O2 -fvisibility=hidden -fvisibility=hidden conftest.c >&5 configure:4155: $? = 0 configure:4155: ./conftest configure:4155: $? = 0 configure:4166: result: yes configure:4179: checking for sys/types.h configure:4179: gcc -c -Wall -g -O2 -fvisibility=hidden conftest.c >&5 configure:4179: $? = 0 configure:4179: result: yes configure:4179: checking for sys/stat.h configure:4179: gcc -c -Wall -g -O2 -fvisibility=hidden conftest.c >&5 configure:4179: $? = 0 configure:4179: result: yes configure:4179: checking for stdlib.h configure:4179: gcc -c -Wall -g -O2 -fvisibility=hidden conftest.c >&5 configure:4179: $? = 0 configure:4179: result: yes configure:4179: checking for string.h configure:4179: gcc -c -Wall -g -O2 -fvisibility=hidden conftest.c >&5 configure:4179: $? = 0 configure:4179: result: yes configure:4179: checking for memory.h configure:4179: gcc -c -Wall -g -O2 -fvisibility=hidden conftest.c >&5 configure:4179: $? = 0 configure:4179: result: yes configure:4179: checking for strings.h configure:4179: gcc -c -Wall -g -O2 -fvisibility=hidden conftest.c >&5 configure:4179: $? = 0 configure:4179: result: yes configure:4179: checking for inttypes.h configure:4179: gcc -c -Wall -g -O2 -fvisibility=hidden conftest.c >&5 configure:4179: $? = 0 configure:4179: result: yes configure:4179: checking for stdint.h configure:4179: gcc -c -Wall -g -O2 -fvisibility=hidden conftest.c >&5 configure:4179: $? = 0 configure:4179: result: yes configure:4179: checking for unistd.h configure:4179: gcc -c -Wall -g -O2 -fvisibility=hidden conftest.c >&5 configure:4179: $? = 0 configure:4179: result: yes configure:4197: checking for stdlib.h configure:4197: result: yes configure:4197: checking for unistd.h configure:4197: result: yes configure:4197: checking for sys/param.h configure:4197: gcc -c -Wall -g -O2 -fvisibility=hidden conftest.c >&5 configure:4197: $? = 0 configure:4197: result: yes configure:4217: checking for getpagesize configure:4217: gcc -o conftest -Wall -g -O2 -fvisibility=hidden -fvisibility=hidden conftest.c >&5 configure:4217: $? = 0 configure:4217: result: yes configure:4226: checking for working mmap configure:4373: gcc -o conftest -Wall -g -O2 -fvisibility=hidden -fvisibility=hidden conftest.c >&5 configure:4373: $? = 0 configure:4373: ./conftest configure:4373: $? = 0 configure:4383: result: yes configure:4395: checking for gmtime_r configure:4395: gcc -o conftest -Wall -g -O2 -fvisibility=hidden -fvisibility=hidden conftest.c >&5 configure:4395: $? = 0 configure:4395: result: yes configure:4395: checking for fsync configure:4395: gcc -o conftest -Wall -g -O2 -fvisibility=hidden -fvisibility=hidden conftest.c >&5 configure:4395: $? = 0 configure:4395: result: yes configure:4395: checking for drand48 configure:4395: gcc -o conftest -Wall -g -O2 -fvisibility=hidden -fvisibility=hidden conftest.c >&5 configure:4395: $? = 0 configure:4395: result: yes configure:4407: checking whether fdatasync is declared configure:4407: gcc -c -Wall -g -O2 -fvisibility=hidden conftest.c >&5 configure:4407: $? = 0 configure:4407: result: yes configure:4411: checking for fdatasync configure:4411: gcc -o conftest -Wall -g -O2 -fvisibility=hidden -fvisibility=hidden conftest.c >&5 configure:4411: $? = 0 configure:4411: result: yes configure:4546: checking for library containing log configure:4577: gcc -o conftest -Wall -g -O2 -fvisibility=hidden -fvisibility=hidden conftest.c >&5 conftest.c:35:6: warning: conflicting types for built-in function 'log' [enabled by default] char log (); ^ /tmp/cc0c5DWZ.o: In function `main': /home/psgendb/BIRCHDEV/install/trinityrnaseq-v2.14.0/trinity-plugins/bamsifter/htslib/conftest.c:39: undefined reference to `log' collect2: error: ld returned 1 exit status configure:4577: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "HTSlib" | #define PACKAGE_TARNAME "htslib" | #define PACKAGE_VERSION "1.10.2" | #define PACKAGE_STRING "HTSlib 1.10.2" | #define PACKAGE_BUGREPORT "samtools-help@lists.sourceforge.net" | #define PACKAGE_URL "http://www.htslib.org/" | #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:4577: gcc -o conftest -Wall -g -O2 -fvisibility=hidden -fvisibility=hidden conftest.c -lm >&5 conftest.c:35:6: warning: conflicting types for built-in function 'log' [enabled by default] char log (); ^ configure:4577: $? = 0 configure:4594: result: -lm configure:4614: checking for zlib.h configure:4614: gcc -c -Wall -g -O2 -fvisibility=hidden conftest.c >&5 configure:4614: $? = 0 configure:4614: result: yes configure:4623: checking for inflate in -lz configure:4648: gcc -o conftest -Wall -g -O2 -fvisibility=hidden -fvisibility=hidden conftest.c -lz -lm >&5 configure:4648: $? = 0 configure:4657: result: yes configure:4688: checking for library containing recv configure:4719: gcc -o conftest -Wall -g -O2 -fvisibility=hidden -fvisibility=hidden conftest.c -lz -lm >&5 configure:4719: $? = 0 configure:4736: result: none required configure:4758: checking for bzlib.h configure:4758: gcc -c -Wall -g -O2 -fvisibility=hidden conftest.c >&5 configure:4758: $? = 0 configure:4758: result: yes configure:4767: checking for BZ2_bzBuffToBuffCompress in -lbz2 configure:4792: gcc -o conftest -Wall -g -O2 -fvisibility=hidden -fvisibility=hidden conftest.c -lbz2 -lz -lm >&5 configure:4792: $? = 0 configure:4801: result: yes configure:4845: checking for lzma.h configure:4845: gcc -c -Wall -g -O2 -fvisibility=hidden conftest.c >&5 configure:4845: $? = 0 configure:4845: result: yes configure:4858: checking for lzma_easy_buffer_encode in -llzma configure:4883: gcc -o conftest -Wall -g -O2 -fvisibility=hidden -fvisibility=hidden conftest.c -llzma -lbz2 -lz -lm >&5 configure:4883: $? = 0 configure:4892: result: yes configure:4930: checking for libdeflate.h configure:4930: gcc -c -Wall -g -O2 -fvisibility=hidden conftest.c >&5 conftest.c:34:24: fatal error: libdeflate.h: No such file or directory #include ^ compilation terminated. configure:4930: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "HTSlib" | #define PACKAGE_TARNAME "htslib" | #define PACKAGE_VERSION "1.10.2" | #define PACKAGE_STRING "HTSlib 1.10.2" | #define PACKAGE_BUGREPORT "samtools-help@lists.sourceforge.net" | #define PACKAGE_URL "http://www.htslib.org/" | #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:4930: result: no configure:4939: checking for libdeflate_deflate_compress in -ldeflate configure:4964: 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:4964: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "HTSlib" | #define PACKAGE_TARNAME "htslib" | #define PACKAGE_VERSION "1.10.2" | #define PACKAGE_STRING "HTSlib 1.10.2" | #define PACKAGE_BUGREPORT "samtools-help@lists.sourceforge.net" | #define PACKAGE_URL "http://www.htslib.org/" | #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:4973: result: no configure:5011: checking for curl_easy_pause in -lcurl configure:5036: gcc -o conftest -Wall -g -O2 -fvisibility=hidden -fvisibility=hidden conftest.c -lcurl -llzma -lbz2 -lz -lm >&5 configure:5036: $? = 0 configure:5045: result: yes configure:5176: checking for CCHmac configure:5176: gcc -o conftest -Wall -g -O2 -fvisibility=hidden -fvisibility=hidden conftest.c -llzma -lbz2 -lz -lm >&5 /tmp/ccVDVD1n.o: In function `main': /home/psgendb/BIRCHDEV/install/trinityrnaseq-v2.14.0/trinity-plugins/bamsifter/htslib/conftest.c:68: undefined reference to `CCHmac' collect2: error: ld returned 1 exit status configure:5176: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "HTSlib" | #define PACKAGE_TARNAME "htslib" | #define PACKAGE_VERSION "1.10.2" | #define PACKAGE_STRING "HTSlib 1.10.2" | #define PACKAGE_BUGREPORT "samtools-help@lists.sourceforge.net" | #define PACKAGE_URL "http://www.htslib.org/" | #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:5176: result: no configure:5183: checking for library containing HMAC configure:5214: gcc -o conftest -Wall -g -O2 -fvisibility=hidden -fvisibility=hidden conftest.c -llzma -lbz2 -lz -lm >&5 /tmp/ccp7omMy.o: In function `main': /home/psgendb/BIRCHDEV/install/trinityrnaseq-v2.14.0/trinity-plugins/bamsifter/htslib/conftest.c:45: undefined reference to `HMAC' collect2: error: ld returned 1 exit status configure:5214: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "HTSlib" | #define PACKAGE_TARNAME "htslib" | #define PACKAGE_VERSION "1.10.2" | #define PACKAGE_STRING "HTSlib 1.10.2" | #define PACKAGE_BUGREPORT "samtools-help@lists.sourceforge.net" | #define PACKAGE_URL "http://www.htslib.org/" | #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:5214: gcc -o conftest -Wall -g -O2 -fvisibility=hidden -fvisibility=hidden conftest.c -lcrypto -llzma -lbz2 -lz -lm >&5 configure:5214: $? = 0 configure:5231: result: -lcrypto configure:5273: checking whether PTHREAD_MUTEX_RECURSIVE is declared configure:5273: gcc -c -Wall -g -O2 -fvisibility=hidden conftest.c >&5 configure:5273: $? = 0 configure:5273: result: yes configure:5418: creating ./config.status ## ---------------------- ## ## Running config.status. ## ## ---------------------- ## This file was extended by HTSlib config.status 1.10.2, which was generated by GNU Autoconf 2.69. Invocation command line was CONFIG_FILES = CONFIG_HEADERS = CONFIG_LINKS = CONFIG_COMMANDS = $ ./config.status on mars.cc.umanitoba.ca config.status:833: creating config.mk config.status:833: creating htslib.pc.tmp config.status:833: creating config.h ## ---------------- ## ## 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_have_decl_PTHREAD_MUTEX_RECURSIVE=yes ac_cv_have_decl_fdatasync_int_=yes ac_cv_header_bzlib_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_sys_file_offset_bits=no ac_cv_sys_largefile_CC=no hts_cv_check__fvisibility_hidden=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' 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 1.10.2' PACKAGE_TARNAME='htslib' PACKAGE_URL='http://www.htslib.org/' PACKAGE_VERSION='1.10.2' PATH_SEPARATOR=':' PKG_CONFIG='/usr/bin/pkg-config' PKG_CONFIG_LIBDIR='' PKG_CONFIG_PATH='' PLATFORM='default' PLUGIN_EXT='.so' RANLIB='ranlib' SHELL='/bin/sh' 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='${prefix}' gcs='enabled' host_alias='unknown-Linux' htmldir='${docdir}' 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='/home/psgendb/BIRCHDEV/install/trinityrnaseq-v2.14.0/trinity-plugins/bamsifter/htslib/build' private_LIBS=' -lbz2' program_transform_name='s,x,x,' psdir='${docdir}' s3='enabled' sbindir='${exec_prefix}/sbin' sharedstatedir='${prefix}/com' static_LDFLAGS='' static_LIBS='-lpthread -lz -lm -lbz2 -llzma -lcurl -lcrypto' sysconfdir='${prefix}/etc' target_alias='' ## ----------- ## ## confdefs.h. ## ## ----------- ## /* confdefs.h */ #define PACKAGE_NAME "HTSlib" #define PACKAGE_TARNAME "htslib" #define PACKAGE_VERSION "1.10.2" #define PACKAGE_STRING "HTSlib 1.10.2" #define PACKAGE_BUGREPORT "samtools-help@lists.sourceforge.net" #define PACKAGE_URL "http://www.htslib.org/" #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