7df6e18265341f87a69fba808aa1f92f8ebca841 markd Wed Apr 15 13:39:42 2026 -0700 move copy of htslib diff --git src/htslib/config.log src/htslib/config.log deleted file mode 100644 index ebd670d1cc1..00000000000 --- src/htslib/config.log +++ /dev/null @@ -1,418 +0,0 @@ -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 1.3, which was -generated by GNU Autoconf 2.69. Invocation command line was - - $ ./configure - -## --------- ## -## Platform. ## -## --------- ## - -hostname = hgwdev -uname -m = x86_64 -uname -r = 2.6.32-504.3.3.el6.x86_64 -uname -s = Linux -uname -v = #1 SMP Wed Dec 17 01:55:02 UTC 2014 - -/usr/bin/uname -p = unknown -/bin/uname -X = unknown - -/bin/arch = x86_64 -/usr/bin/arch -k = unknown -/usr/convex/getsysinfo = unknown -/usr/bin/hostinfo = unknown -/bin/machine = unknown -/usr/bin/oslevel = unknown -/bin/universe = unknown - -PATH: /parasol/bin -PATH: /parasol/bin -PATH: /cluster/bin/x86_64 -PATH: /cluster/software/bin -PATH: /parasol/bin -PATH: /parasol/bin -PATH: /cluster/bin/x86_64 -PATH: /cluster/software/bin -PATH: /usr/lib64/qt-3.3/bin -PATH: /usr/NX/bin -PATH: /parasol/bin -PATH: /parasol/bin -PATH: /cluster/bin/x86_64 -PATH: /cluster/software/bin -PATH: /usr/local/bin -PATH: /bin -PATH: /usr/bin -PATH: /projects/linux/matlab/bin -PATH: /cluster/bin/scripts -PATH: /cluster/home/braney/bin/scripts -PATH: /cluster/bin/scripts -PATH: /cluster/home/braney/bin -PATH: /cluster/bin/x86_64 -PATH: /cluster/home/braney/bin/x86_64 -PATH: /projects/compbio/bin -PATH: /projects/compbio/bin/i686 -PATH: /hive/groups/recon/local/bin -PATH: /usr/local/sbin -PATH: /usr/sbin -PATH: /sbin -PATH: /usr/lpp/mmfs/bin/ -PATH: /opt/dell/srvadmin/bin -PATH: /projects/linux/matlab/bin -PATH: /cluster/bin/scripts -PATH: /cluster/home/braney/bin/scripts -PATH: /cluster/bin/scripts -PATH: /cluster/home/braney/bin -PATH: /cluster/bin/x86_64 -PATH: /cluster/home/braney/bin/x86_64 -PATH: /projects/compbio/bin -PATH: /projects/compbio/bin/i686 -PATH: /hive/groups/recon/local/bin -PATH: /cluster/home/braney/bin -PATH: /projects/linux/matlab/bin -PATH: /cluster/bin/scripts -PATH: /cluster/home/braney/bin/scripts -PATH: /cluster/bin/scripts -PATH: /cluster/home/braney/bin -PATH: /cluster/bin/x86_64 -PATH: /cluster/home/braney/bin/x86_64 -PATH: /projects/compbio/bin -PATH: /projects/compbio/bin/i686 -PATH: /hive/groups/recon/local/bin - - -## ----------- ## -## Core tests. ## -## ----------- ## - -configure:2091: checking for gcc -configure:2118: result: gcc34 -configure:2347: checking for C compiler version -configure:2356: gcc34 --version >&5 -gcc34 (GCC) 3.4.6 20060404 (Red Hat 3.4.6-19.el6) -Copyright (C) 2006 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:2367: $? = 0 -configure:2356: gcc34 -v >&5 -Reading specs from /usr/lib/gcc/x86_64-redhat-linux/3.4.6/specs -Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --enable-shared --enable-threads=posix --disable-checking --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-languages=c,c++,f77 --disable-libgcj --host=x86_64-redhat-linux -Thread model: posix -gcc version 3.4.6 20060404 (Red Hat 3.4.6-19.el6) -configure:2367: $? = 0 -configure:2356: gcc34 -V >&5 -gcc34: `-V' option must have argument -configure:2367: $? = 1 -configure:2356: gcc34 -qversion >&5 -gcc34: unrecognized option `-qversion' -gcc34: no input files -configure:2367: $? = 1 -configure:2387: checking whether the C compiler works -configure:2409: gcc34 conftest.c >&5 -configure:2413: $? = 0 -configure:2461: result: yes -configure:2464: checking for C compiler default output file name -configure:2466: result: a.out -configure:2472: checking for suffix of executables -configure:2479: gcc34 -o conftest conftest.c >&5 -configure:2483: $? = 0 -configure:2505: result: -configure:2527: checking whether we are cross compiling -configure:2535: gcc34 -o conftest conftest.c >&5 -configure:2539: $? = 0 -configure:2546: ./conftest -configure:2550: $? = 0 -configure:2565: result: no -configure:2570: checking for suffix of object files -configure:2592: gcc34 -c conftest.c >&5 -configure:2596: $? = 0 -configure:2617: result: o -configure:2621: checking whether we are using the GNU C compiler -configure:2640: gcc34 -c conftest.c >&5 -configure:2640: $? = 0 -configure:2649: result: yes -configure:2658: checking whether gcc34 accepts -g -configure:2678: gcc34 -c -g conftest.c >&5 -configure:2678: $? = 0 -configure:2719: result: yes -configure:2736: checking for gcc34 option to accept ISO C89 -configure:2799: gcc34 -c -g -O2 conftest.c >&5 -configure:2799: $? = 0 -configure:2812: result: none needed -configure:2875: checking for ranlib -configure:2891: found /usr/bin/ranlib -configure:2902: result: ranlib -configure:2990: checking how to run the C preprocessor -configure:3021: gcc34 -E conftest.c -configure:3021: $? = 0 -configure:3035: gcc34 -E conftest.c -conftest.c:9:28: ac_nonexistent.h: No such file or directory -configure:3035: $? = 1 -configure: failed program was: -| /* confdefs.h */ -| #define PACKAGE_NAME "HTSlib" -| #define PACKAGE_TARNAME "htslib" -| #define PACKAGE_VERSION "1.3" -| #define PACKAGE_STRING "HTSlib 1.3" -| #define PACKAGE_BUGREPORT "samtools-help@lists.sourceforge.net" -| #define PACKAGE_URL "http://www.htslib.org/" -| /* end confdefs.h. */ -| #include <ac_nonexistent.h> -configure:3060: result: gcc34 -E -configure:3080: gcc34 -E conftest.c -configure:3080: $? = 0 -configure:3094: gcc34 -E conftest.c -conftest.c:9:28: ac_nonexistent.h: No such file or directory -configure:3094: $? = 1 -configure: failed program was: -| /* confdefs.h */ -| #define PACKAGE_NAME "HTSlib" -| #define PACKAGE_TARNAME "htslib" -| #define PACKAGE_VERSION "1.3" -| #define PACKAGE_STRING "HTSlib 1.3" -| #define PACKAGE_BUGREPORT "samtools-help@lists.sourceforge.net" -| #define PACKAGE_URL "http://www.htslib.org/" -| /* end confdefs.h. */ -| #include <ac_nonexistent.h> -configure:3123: checking for grep that handles long lines and -e -configure:3181: result: /bin/grep -configure:3186: checking for egrep -configure:3248: result: /bin/grep -E -configure:3253: checking for ANSI C header files -configure:3273: gcc34 -c -g -O2 conftest.c >&5 -configure:3273: $? = 0 -configure:3346: gcc34 -o conftest -g -O2 conftest.c >&5 -configure:3346: $? = 0 -configure:3346: ./conftest -configure:3346: $? = 0 -configure:3357: result: yes -configure:3370: checking for sys/types.h -configure:3370: gcc34 -c -g -O2 conftest.c >&5 -configure:3370: $? = 0 -configure:3370: result: yes -configure:3370: checking for sys/stat.h -configure:3370: gcc34 -c -g -O2 conftest.c >&5 -configure:3370: $? = 0 -configure:3370: result: yes -configure:3370: checking for stdlib.h -configure:3370: gcc34 -c -g -O2 conftest.c >&5 -configure:3370: $? = 0 -configure:3370: result: yes -configure:3370: checking for string.h -configure:3370: gcc34 -c -g -O2 conftest.c >&5 -configure:3370: $? = 0 -configure:3370: result: yes -configure:3370: checking for memory.h -configure:3370: gcc34 -c -g -O2 conftest.c >&5 -configure:3370: $? = 0 -configure:3370: result: yes -configure:3370: checking for strings.h -configure:3370: gcc34 -c -g -O2 conftest.c >&5 -configure:3370: $? = 0 -configure:3370: result: yes -configure:3370: checking for inttypes.h -configure:3370: gcc34 -c -g -O2 conftest.c >&5 -configure:3370: $? = 0 -configure:3370: result: yes -configure:3370: checking for stdint.h -configure:3370: gcc34 -c -g -O2 conftest.c >&5 -configure:3370: $? = 0 -configure:3370: result: yes -configure:3370: checking for unistd.h -configure:3370: gcc34 -c -g -O2 conftest.c >&5 -configure:3370: $? = 0 -configure:3370: result: yes -configure:3388: checking for stdlib.h -configure:3388: result: yes -configure:3388: checking for unistd.h -configure:3388: result: yes -configure:3388: checking for sys/param.h -configure:3388: gcc34 -c -g -O2 conftest.c >&5 -configure:3388: $? = 0 -configure:3388: result: yes -configure:3408: checking for getpagesize -configure:3408: gcc34 -o conftest -g -O2 conftest.c >&5 -configure:3408: $? = 0 -configure:3408: result: yes -configure:3417: checking for working mmap -configure:3564: gcc34 -o conftest -g -O2 conftest.c >&5 -configure:3564: $? = 0 -configure:3564: ./conftest -configure:3564: $? = 0 -configure:3574: result: yes -configure:3585: checking for gmtime_r -configure:3585: gcc34 -o conftest -g -O2 conftest.c >&5 -configure:3585: $? = 0 -configure:3585: result: yes -configure:3666: checking for zlib.h -configure:3666: gcc34 -c -g -O2 conftest.c >&5 -configure:3666: $? = 0 -configure:3666: result: yes -configure:3675: checking for inflate in -lz -configure:3700: gcc34 -o conftest -g -O2 conftest.c -lz >&5 -configure:3700: $? = 0 -configure:3709: result: yes -configure:4109: creating ./config.status - -## ---------------------- ## -## Running config.status. ## -## ---------------------- ## - -This file was extended by HTSlib config.status 1.3, which was -generated by GNU Autoconf 2.69. Invocation command line was - - CONFIG_FILES = - CONFIG_HEADERS = - CONFIG_LINKS = - CONFIG_COMMANDS = - $ ./config.status - -on hgwdev - -config.status:813: creating config.mk -config.status:813: creating config.h -config.status:983: config.h is unchanged - -## ---------------- ## -## Cache variables. ## -## ---------------- ## - -ac_cv_c_compiler_gnu=yes -ac_cv_env_CC_set=set -ac_cv_env_CC_value=gcc34 -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_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_getpagesize=yes -ac_cv_func_gmtime_r=yes -ac_cv_func_mmap_fixed_mapped=yes -ac_cv_header_inttypes_h=yes -ac_cv_header_memory_h=yes -ac_cv_header_stdc=yes -ac_cv_header_stdint_h=yes -ac_cv_header_stdlib_h=yes -ac_cv_header_string_h=yes -ac_cv_header_strings_h=yes -ac_cv_header_sys_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_z_inflate=yes -ac_cv_objext=o -ac_cv_path_EGREP='/bin/grep -E' -ac_cv_path_GREP=/bin/grep -ac_cv_prog_CPP='gcc34 -E' -ac_cv_prog_ac_ct_CC=gcc34 -ac_cv_prog_ac_ct_RANLIB=ranlib -ac_cv_prog_cc_c89= -ac_cv_prog_cc_g=yes - -## ----------------- ## -## Output variables. ## -## ----------------- ## - -CC='gcc34' -CFLAGS='-g -O2' -CPP='gcc34 -E' -CPPFLAGS='' -CRYPTO_LIBS='' -DEFS='-DHAVE_CONFIG_H' -ECHO_C='' -ECHO_N='-n' -ECHO_T='' -EGREP='/bin/grep -E' -EXEEXT='' -GREP='/bin/grep' -LDFLAGS='' -LIBOBJS='' -LIBS='' -LTLIBOBJS='' -OBJEXT='o' -PACKAGE_BUGREPORT='samtools-help@lists.sourceforge.net' -PACKAGE_NAME='HTSlib' -PACKAGE_STRING='HTSlib 1.3' -PACKAGE_TARNAME='htslib' -PACKAGE_URL='http://www.htslib.org/' -PACKAGE_VERSION='1.3' -PATH_SEPARATOR=':' -RANLIB='ranlib' -SHELL='/bin/sh' -ac_ct_CC='gcc34' -bindir='${exec_prefix}/bin' -build_alias='' -datadir='${datarootdir}' -datarootdir='${prefix}/share' -define_IRODS_HOME='IRODS_HOME ?= /disabled' -docdir='${datarootdir}/doc/${PACKAGE_TARNAME}' -dvidir='${docdir}' -enable_plugins='no' -exec_prefix='${prefix}' -host_alias='' -htmldir='${docdir}' -includedir='${prefix}/include' -infodir='${datarootdir}/info' -irods='disabled' -libcurl='disabled' -libdir='${exec_prefix}/lib' -libexecdir='${exec_prefix}/libexec' -localedir='${datarootdir}/locale' -localstatedir='${prefix}/var' -mandir='${datarootdir}/man' -oldincludedir='/usr/include' -pdfdir='${docdir}' -plugindir='$(libexecdir)/htslib' -pluginpath='$(libexecdir)/htslib' -prefix='/usr/local' -program_transform_name='s,x,x,' -psdir='${docdir}' -sbindir='${exec_prefix}/sbin' -sharedstatedir='${prefix}/com' -sysconfdir='${prefix}/etc' -target_alias='' - -## ----------- ## -## confdefs.h. ## -## ----------- ## - -/* confdefs.h */ -#define PACKAGE_NAME "HTSlib" -#define PACKAGE_TARNAME "htslib" -#define PACKAGE_VERSION "1.3" -#define PACKAGE_STRING "HTSlib 1.3" -#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_LIBZ 1 - -configure: exit 0