11e45667d4e291b3038ccda729a1cdf5bcaf004a braney Mon Jul 11 15:46:54 2016 -0700 incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX defines, modify a bunch of makefiles to include kentSrc variable pointing to top of the tree. diff --git src/htslib/config.log src/htslib/config.log new file mode 100644 index 0000000..ebd670d --- /dev/null +++ src/htslib/config.log @@ -0,0 +1,418 @@ +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