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 1.16, which was generated by GNU Autoconf 2.69. Invocation command line was $ ./configure --prefix=/broad/hptmp/bhaas/trinityrnaseq-v2.15.1/trinity-plugins/bamsifter/htslib/build/ ## --------- ## ## Platform. ## ## --------- ## hostname = methods01.broadinstitute.org uname -m = x86_64 uname -r = 3.10.0-1160.15.2.el7.x86_64 uname -s = Linux uname -v = #1 SMP Thu Jan 21 16:15:07 EST 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: /broad/software/free/Linux/redhat_7_x86_64/pkgs/cmake_3.18.3/bin PATH: /broad/software/free/Linux/redhat_7_x86_64/pkgs/autoconf_2.69/bin PATH: /broad/software/free/Linux/redhat_7_x86_64/pkgs/perl_5.28.0/bin PATH: /broad/software/free/Linux/redhat_7_x86_64/pkgs/mysql_5.6.20/bin PATH: /broad/software/nonfree/Linux/redhat_7_x86_64/pkgs/oracle_instantclient-11.2.0.4.0/instantclient_11_2 PATH: /broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_5.2.0/bin PATH: /broad/software/free/Linux/redhat_7_x86_64/pkgs/google-cloud-sdk/bin PATH: /home/unix/bhaas/miniconda2/envs/py3/bin PATH: /home/unix/bhaas/miniconda2/condabin PATH: /home/unix/bhaas/utilities/emboss PATH: . PATH: /broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/bin PATH: /broad/software/free/Linux/redhat_7_x86_64/pkgs/hmmer_3.1/bin PATH: /broad/software/free/Linux/redhat_7_x86_64/pkgs/git_2.12.0/bin PATH: /broad/software/free/Linux/redhat_7_x86_64/pkgs/jdk1.8.0_345/bin PATH: /broad/software/free/Linux/redhat_7_x86_64/pkgs/ncbi-blast_2.2.30+-x86_64/bin PATH: /broad/uge/8.5.5/bin/lx-amd64 PATH: /home/unix/bhaas/utilities PATH: /home/unix/bhaas/GITHUB/pasapipeline/misc_utilities/ PATH: /home/unix/bhaas/bin PATH: /seq/regev_genome_portal/SOFTWARE/SRA_TOOLKIT/sratoolkit.2.5.1-centos_linux64/bin PATH: /usr/local/bin PATH: /usr/bin PATH: /usr/local/sbin PATH: /usr/sbin PATH: /opt/puppetlabs/bin PATH: /opt/dell/srvadmin/bin PATH: /home/unix/bhaas/.local/bin PATH: /seq/RNASEQ/TOOLS/SPADES/SPAdes-3.14.1-Linux/bin PATH: /seq/regev_genome_portal/SOFTWARE/OpenMPI/openmpi-1.6.5/bin PATH: /home/unix/bhaas/GITHUB/Trinity_CTAT/fusion PATH: /home/unix/bhaas/GITHUB/trinityrnaseq PATH: /home/unix/bhaas/.firecloud-cli/ubin ## ----------- ## ## Core tests. ## ## ----------- ## configure:2275: checking for gcc configure:2302: result: gcc configure:2531: checking for C compiler version configure:2540: gcc --version >&5 gcc (GCC) 5.2.0 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:2551: $? = 0 configure:2540: gcc -v >&5 Using built-in specs. COLLECT_GCC=gcc COLLECT_LTO_WRAPPER=/broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_5.2.0/libexec/gcc/x86_64-redhat-linux/5.2.0/lto-wrapper Target: x86_64-redhat-linux Configured with: /tmp/redhat_7_x86_64/build/tmp/gcc-5.2.0/configure --prefix=/broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_5.2.0 --enable-lto --with-cloog --enable-plugins --enable-languages=c,c++,objc,obj-c++,fortran --build=x86_64-redhat-linux --disable-multilib --with-gmp=/broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_5.2.0 --with-mpfr=/broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_5.2.0 Thread model: posix gcc version 5.2.0 (GCC) configure:2551: $? = 0 configure:2540: gcc -V >&5 gcc: error: unrecognized command line option '-V' gcc: fatal error: no input files compilation terminated. configure:2551: $? = 1 configure:2540: gcc -qversion >&5 gcc: error: unrecognized command line option '-qversion' gcc: fatal error: no input files compilation terminated. configure:2551: $? = 1 configure:2571: checking whether the C compiler works configure:2593: gcc conftest.c >&5 configure:2597: $? = 0 configure:2645: result: yes configure:2648: checking for C compiler default output file name configure:2650: result: a.out configure:2656: checking for suffix of executables configure:2663: gcc -o conftest conftest.c >&5 configure:2667: $? = 0 configure:2689: result: configure:2711: checking whether we are cross compiling configure:2719: gcc -o conftest conftest.c >&5 configure:2723: $? = 0 configure:2730: ./conftest configure:2734: $? = 0 configure:2749: result: no configure:2754: checking for suffix of object files configure:2776: gcc -c conftest.c >&5 configure:2780: $? = 0 configure:2801: result: o configure:2805: checking whether we are using the GNU C compiler configure:2824: gcc -c conftest.c >&5 configure:2824: $? = 0 configure:2833: result: yes configure:2842: checking whether gcc accepts -g configure:2862: gcc -c -g conftest.c >&5 configure:2862: $? = 0 configure:2903: result: yes configure:2920: checking for gcc option to accept ISO C89 configure:2983: gcc -c -g -O2 conftest.c >&5 configure:2983: $? = 0 configure:2996: result: none needed configure:3059: checking for ranlib configure:3075: found /broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_5.2.0/bin/ranlib configure:3086: result: ranlib configure:3109: checking for grep that handles long lines and -e configure:3167: result: /usr/bin/grep configure:3192: checking for C compiler warning flags configure:3305: result: -Wall configure:3393: checking whether C compiler accepts -mssse3 -mpopcnt -msse4.1 configure:3420: gcc -o conftest -Wall -g -O2 -mssse3 -mpopcnt -msse4.1 conftest.c >&5 configure:3420: $? = 0 configure:3429: result: yes configure:3453: checking whether C compiler accepts -mavx2 configure:3479: gcc -o conftest -Wall -g -O2 -mavx2 conftest.c >&5 configure:3479: $? = 0 configure:3488: result: yes configure:3503: checking whether C compiler accepts -mavx512f configure:3528: gcc -o conftest -Wall -g -O2 -mavx512f conftest.c >&5 configure:3528: $? = 0 configure:3537: result: yes configure:3552: checking whether C compiler supports ARM Neon configure:3576: gcc -c -Wall -g -O2 conftest.c >&5 conftest.c:17:28: fatal error: arm_neon.h: No such file or directory compilation terminated. configure:3576: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "HTSlib" | #define PACKAGE_TARNAME "htslib" | #define PACKAGE_VERSION "1.16" | #define PACKAGE_STRING "HTSlib 1.16" | #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 HAVE_AVX512 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:3583: result: no configure:3645: checking for pkg-config configure:3663: found /usr/bin/pkg-config configure:3675: result: /usr/bin/pkg-config configure:3700: checking pkg-config is at least version 0.9.0 configure:3703: result: yes configure:3741: checking for special C compiler options needed for large files configure:3786: result: no configure:3792: checking for _FILE_OFFSET_BITS value needed for large files configure:3817: gcc -c -Wall -g -O2 conftest.c >&5 configure:3817: $? = 0 configure:3849: result: no configure:4025: checking shared library type for unknown-Linux configure:4053: result: plain .so configure:4063: checking whether the compiler accepts -fvisibility=hidden configure:4083: gcc -o conftest -Wall -g -O2 -fvisibility=hidden -fvisibility=hidden conftest.c >&5 configure:4083: $? = 0 configure:4096: result: yes configure:4150: checking how to run the C preprocessor configure:4181: gcc -E conftest.c configure:4181: $? = 0 configure:4195: gcc -E conftest.c conftest.c:15:28: fatal error: ac_nonexistent.h: No such file or directory compilation terminated. configure:4195: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "HTSlib" | #define PACKAGE_TARNAME "htslib" | #define PACKAGE_VERSION "1.16" | #define PACKAGE_STRING "HTSlib 1.16" | #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 HAVE_AVX512 1 | /* end confdefs.h. */ | #include configure:4220: result: gcc -E configure:4240: gcc -E conftest.c configure:4240: $? = 0 configure:4254: gcc -E conftest.c conftest.c:15:28: fatal error: ac_nonexistent.h: No such file or directory compilation terminated. configure:4254: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "HTSlib" | #define PACKAGE_TARNAME "htslib" | #define PACKAGE_VERSION "1.16" | #define PACKAGE_STRING "HTSlib 1.16" | #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 HAVE_AVX512 1 | /* end confdefs.h. */ | #include configure:4283: checking for egrep configure:4345: result: /usr/bin/grep -E configure:4350: checking for ANSI C header files configure:4370: gcc -c -Wall -g -O2 -fvisibility=hidden conftest.c >&5 configure:4370: $? = 0 configure:4443: gcc -o conftest -Wall -g -O2 -fvisibility=hidden -fvisibility=hidden conftest.c >&5 configure:4443: $? = 0 configure:4443: ./conftest configure:4443: $? = 0 configure:4454: result: yes configure:4467: checking for sys/types.h configure:4467: gcc -c -Wall -g -O2 -fvisibility=hidden conftest.c >&5 configure:4467: $? = 0 configure:4467: result: yes configure:4467: checking for sys/stat.h configure:4467: gcc -c -Wall -g -O2 -fvisibility=hidden conftest.c >&5 configure:4467: $? = 0 configure:4467: result: yes configure:4467: checking for stdlib.h configure:4467: gcc -c -Wall -g -O2 -fvisibility=hidden conftest.c >&5 configure:4467: $? = 0 configure:4467: result: yes configure:4467: checking for string.h configure:4467: gcc -c -Wall -g -O2 -fvisibility=hidden conftest.c >&5 configure:4467: $? = 0 configure:4467: result: yes configure:4467: checking for memory.h configure:4467: gcc -c -Wall -g -O2 -fvisibility=hidden conftest.c >&5 configure:4467: $? = 0 configure:4467: result: yes configure:4467: checking for strings.h configure:4467: gcc -c -Wall -g -O2 -fvisibility=hidden conftest.c >&5 configure:4467: $? = 0 configure:4467: result: yes configure:4467: checking for inttypes.h configure:4467: gcc -c -Wall -g -O2 -fvisibility=hidden conftest.c >&5 configure:4467: $? = 0 configure:4467: result: yes configure:4467: checking for stdint.h configure:4467: gcc -c -Wall -g -O2 -fvisibility=hidden conftest.c >&5 configure:4467: $? = 0 configure:4467: result: yes configure:4467: checking for unistd.h configure:4467: gcc -c -Wall -g -O2 -fvisibility=hidden conftest.c >&5 configure:4467: $? = 0 configure:4467: result: yes configure:4485: checking for stdlib.h configure:4485: result: yes configure:4485: checking for unistd.h configure:4485: result: yes configure:4485: checking for sys/param.h configure:4485: gcc -c -Wall -g -O2 -fvisibility=hidden conftest.c >&5 configure:4485: $? = 0 configure:4485: result: yes configure:4505: checking for getpagesize configure:4505: gcc -o conftest -Wall -g -O2 -fvisibility=hidden -fvisibility=hidden conftest.c >&5 configure:4505: $? = 0 configure:4505: result: yes configure:4514: checking for working mmap configure:4663: gcc -o conftest -Wall -g -O2 -fvisibility=hidden -fvisibility=hidden conftest.c >&5 configure:4663: $? = 0 configure:4663: ./conftest configure:4663: $? = 0 configure:4673: result: yes configure:4685: checking for gmtime_r configure:4685: gcc -o conftest -Wall -g -O2 -fvisibility=hidden -fvisibility=hidden conftest.c >&5 configure:4685: $? = 0 configure:4685: result: yes configure:4685: checking for fsync configure:4685: gcc -o conftest -Wall -g -O2 -fvisibility=hidden -fvisibility=hidden conftest.c >&5 configure:4685: $? = 0 configure:4685: result: yes configure:4685: checking for drand48 configure:4685: gcc -o conftest -Wall -g -O2 -fvisibility=hidden -fvisibility=hidden conftest.c >&5 configure:4685: $? = 0 configure:4685: result: yes configure:4685: checking for srand48_deterministic configure:4685: gcc -o conftest -Wall -g -O2 -fvisibility=hidden -fvisibility=hidden conftest.c >&5 /local/tmp/cckHHVR7.o: In function `main': /broad/hptmp/bhaas/trinityrnaseq-v2.15.1/trinity-plugins/bamsifter/htslib/conftest.c:67: undefined reference to `srand48_deterministic' collect2: error: ld returned 1 exit status configure:4685: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "HTSlib" | #define PACKAGE_TARNAME "htslib" | #define PACKAGE_VERSION "1.16" | #define PACKAGE_STRING "HTSlib 1.16" | #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 HAVE_AVX512 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:4685: result: no configure:4697: checking whether fdatasync is declared configure:4697: gcc -c -Wall -g -O2 -fvisibility=hidden conftest.c >&5 configure:4697: $? = 0 configure:4697: result: yes configure:4701: checking for fdatasync configure:4701: gcc -o conftest -Wall -g -O2 -fvisibility=hidden -fvisibility=hidden conftest.c >&5 configure:4701: $? = 0 configure:4701: result: yes configure:4836: checking for library containing log configure:4867: gcc -o conftest -Wall -g -O2 -fvisibility=hidden -fvisibility=hidden conftest.c >&5 conftest.c:41:6: warning: conflicting types for built-in function 'log' char log (); ^ /local/tmp/ccQa3Vno.o: In function `main': /broad/hptmp/bhaas/trinityrnaseq-v2.15.1/trinity-plugins/bamsifter/htslib/conftest.c:45: undefined reference to `log' collect2: error: ld returned 1 exit status configure:4867: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "HTSlib" | #define PACKAGE_TARNAME "htslib" | #define PACKAGE_VERSION "1.16" | #define PACKAGE_STRING "HTSlib 1.16" | #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 HAVE_AVX512 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:4867: gcc -o conftest -Wall -g -O2 -fvisibility=hidden -fvisibility=hidden conftest.c -lm >&5 conftest.c:41:6: warning: conflicting types for built-in function 'log' char log (); ^ configure:4867: $? = 0 configure:4884: result: -lm configure:4904: checking for zlib.h configure:4904: gcc -c -Wall -g -O2 -fvisibility=hidden conftest.c >&5 configure:4904: $? = 0 configure:4904: result: yes configure:4913: checking for inflate in -lz configure:4938: gcc -o conftest -Wall -g -O2 -fvisibility=hidden -fvisibility=hidden conftest.c -lz -lm >&5 configure:4938: $? = 0 configure:4947: result: yes configure:4978: checking for library containing recv configure:5009: gcc -o conftest -Wall -g -O2 -fvisibility=hidden -fvisibility=hidden conftest.c -lz -lm >&5 configure:5009: $? = 0 configure:5026: result: none required configure:5072: checking for bzlib.h configure:5072: gcc -c -Wall -g -O2 -fvisibility=hidden conftest.c >&5 configure:5072: $? = 0 configure:5072: result: yes configure:5081: checking for BZ2_bzBuffToBuffCompress in -lbz2 configure:5106: gcc -o conftest -Wall -g -O2 -fvisibility=hidden -fvisibility=hidden conftest.c -lbz2 -lz -lm >&5 configure:5106: $? = 0 configure:5115: result: yes configure:5159: checking for lzma.h configure:5159: gcc -c -Wall -g -O2 -fvisibility=hidden conftest.c >&5 configure:5159: $? = 0 configure:5159: result: yes configure:5172: checking for lzma_easy_buffer_encode in -llzma configure:5197: gcc -o conftest -Wall -g -O2 -fvisibility=hidden -fvisibility=hidden conftest.c -llzma -lbz2 -lz -lm >&5 configure:5197: $? = 0 configure:5206: result: yes configure:5319: checking whether htscodecs files are present configure:5322: result: yes configure:5360: checking for libdeflate.h configure:5360: gcc -c -Wall -g -O2 -fvisibility=hidden conftest.c >&5 conftest.c:40:24: fatal error: libdeflate.h: No such file or directory compilation terminated. configure:5360: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "HTSlib" | #define PACKAGE_TARNAME "htslib" | #define PACKAGE_VERSION "1.16" | #define PACKAGE_STRING "HTSlib 1.16" | #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 HAVE_AVX512 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:5360: result: no configure:5369: checking for libdeflate_deflate_compress in -ldeflate configure:5394: gcc -o conftest -Wall -g -O2 -fvisibility=hidden -fvisibility=hidden conftest.c -ldeflate -llzma -lbz2 -lz -lm >&5 /broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_5.2.0/bin/ld: cannot find -ldeflate collect2: error: ld returned 1 exit status configure:5394: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "HTSlib" | #define PACKAGE_TARNAME "htslib" | #define PACKAGE_VERSION "1.16" | #define PACKAGE_STRING "HTSlib 1.16" | #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 HAVE_AVX512 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:5403: result: no configure:5442: checking for curl/curl.h configure:5442: gcc -c -Wall -g -O2 -fvisibility=hidden conftest.c >&5 configure:5442: $? = 0 configure:5442: result: yes configure:5451: checking for curl_easy_pause in -lcurl configure:5476: gcc -o conftest -Wall -g -O2 -fvisibility=hidden -fvisibility=hidden conftest.c -lcurl -llzma -lbz2 -lz -lm >&5 configure:5476: $? = 0 configure:5485: result: yes configure:5620: checking for CCHmac configure:5620: gcc -o conftest -Wall -g -O2 -fvisibility=hidden -fvisibility=hidden conftest.c -llzma -lbz2 -lz -lm >&5 /local/tmp/ccFo1Bjj.o: In function `main': /broad/hptmp/bhaas/trinityrnaseq-v2.15.1/trinity-plugins/bamsifter/htslib/conftest.c:74: undefined reference to `CCHmac' collect2: error: ld returned 1 exit status configure:5620: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "HTSlib" | #define PACKAGE_TARNAME "htslib" | #define PACKAGE_VERSION "1.16" | #define PACKAGE_STRING "HTSlib 1.16" | #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 HAVE_AVX512 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:5620: result: no configure:5627: checking for library containing HMAC configure:5658: gcc -o conftest -Wall -g -O2 -fvisibility=hidden -fvisibility=hidden conftest.c -llzma -lbz2 -lz -lm >&5 /local/tmp/ccdkEvrs.o: In function `main': /broad/hptmp/bhaas/trinityrnaseq-v2.15.1/trinity-plugins/bamsifter/htslib/conftest.c:51: undefined reference to `HMAC' collect2: error: ld returned 1 exit status configure:5658: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "HTSlib" | #define PACKAGE_TARNAME "htslib" | #define PACKAGE_VERSION "1.16" | #define PACKAGE_STRING "HTSlib 1.16" | #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 HAVE_AVX512 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:5658: gcc -o conftest -Wall -g -O2 -fvisibility=hidden -fvisibility=hidden conftest.c -lcrypto -llzma -lbz2 -lz -lm >&5 /broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_5.2.0/bin/ld: cannot find -lcrypto collect2: error: ld returned 1 exit status configure:5658: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "HTSlib" | #define PACKAGE_TARNAME "htslib" | #define PACKAGE_VERSION "1.16" | #define PACKAGE_STRING "HTSlib 1.16" | #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 HAVE_AVX512 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:5675: result: no configure:5688: WARNING: S3 support not enabled: requires SSL development files configure:5717: checking for library containing regcomp configure:5748: gcc -o conftest -Wall -g -O2 -fvisibility=hidden -fvisibility=hidden conftest.c -llzma -lbz2 -lz -lm >&5 configure:5748: $? = 0 configure:5765: result: none required configure:5774: checking whether PTHREAD_MUTEX_RECURSIVE is declared configure:5774: gcc -c -Wall -g -O2 -fvisibility=hidden conftest.c >&5 configure:5774: $? = 0 configure:5774: result: yes configure:5940: creating ./config.status ## ---------------------- ## ## Running config.status. ## ## ---------------------- ## This file was extended by HTSlib config.status 1.16, which was generated by GNU Autoconf 2.69. Invocation command line was CONFIG_FILES = CONFIG_HEADERS = CONFIG_LINKS = CONFIG_COMMANDS = $ ./config.status on methods01.broadinstitute.org config.status:859: creating config.mk config.status:859: creating htslib.pc.tmp config.status:859: creating config.h config.status:1055: linking htscodecs_bundled.mk to htscodecs.mk ## ---------------- ## ## Cache variables. ## ## ---------------- ## ac_cv_c_compiler_gnu=yes ac_cv_env_CC_set=set ac_cv_env_CC_value=gcc 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=no 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=yes ax_cv_check_cflags___mssse3__mpopcnt__msse4_1=yes hts_cv_check__fvisibility_hidden=yes hts_cv_have_neon=no hts_cv_prog_cc_warnings=-Wall ## ----------------- ## ## Output variables. ## ## ----------------- ## CC='gcc' CFLAGS=' -Wall -g -O2 -fvisibility=hidden' CPP='gcc -E' CPPFLAGS='' CRYPTO_LIBS='' DEFS='-DHAVE_CONFIG_H' ECHO_C='' ECHO_N='-n' ECHO_T='' EGREP='/usr/bin/grep -E' EXEEXT='' GREP='/usr/bin/grep' HTSDIRslash_if_relsrcdir='$(HTSDIR)/' LDFLAGS=' -fvisibility=hidden' LIBOBJS='' LIBS='-llzma -lbz2 -lz -lm ' LTLIBOBJS='' OBJEXT='o' PACKAGE_BUGREPORT='samtools-help@lists.sourceforge.net' PACKAGE_NAME='HTSlib' PACKAGE_STRING='HTSlib 1.16' PACKAGE_TARNAME='htslib' PACKAGE_URL='http://www.htslib.org/' PACKAGE_VERSION='1.16' PATH_SEPARATOR=':' PKG_CONFIG='/usr/bin/pkg-config' PKG_CONFIG_LIBDIR='' PKG_CONFIG_PATH='' PLATFORM='default' PLUGIN_EXT='.so' RANLIB='ranlib' SHELL='/bin/sh' ac_ct_CC='gcc' bindir='${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='' htmldir='${docdir}' hts_cflags_avx2='-mavx2' hts_cflags_avx512='-mavx512f' hts_cflags_sse4='-mssse3 -mpopcnt -msse4.1' hts_have_neon='' includedir='${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='$(libexecdir)/htslib' prefix='/broad/hptmp/bhaas/trinityrnaseq-v2.15.1/trinity-plugins/bamsifter/htslib/build' private_LIBS=' -lbz2' program_transform_name='s,x,x,' psdir='${docdir}' runstatedir='${localstatedir}/run' s3='disabled' sbindir='${exec_prefix}/sbin' sharedstatedir='${prefix}/com' static_LDFLAGS='' static_LIBS='-lpthread -lz -lm -lbz2 -llzma -lcurl ' sysconfdir='${prefix}/etc' target_alias='' with_external_htscodecs='no' ## ----------- ## ## confdefs.h. ## ## ----------- ## /* confdefs.h */ #define PACKAGE_NAME "HTSlib" #define PACKAGE_TARNAME "htslib" #define PACKAGE_VERSION "1.16" #define PACKAGE_STRING "HTSlib 1.16" #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 HAVE_AVX512 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 configure: exit 0