This file contains any messages produced by compilers while
running configure, to aid debugging if configure makes a mistake.

It was created by Samtools configure 1.17, which was
generated by GNU Autoconf 2.69.  Invocation command line was

  $ ./configure 

## --------- ##
## 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:2164: checking for gawk
configure:2180: found /usr/bin/gawk
configure:2191: result: gawk
configure:2250: checking for gcc
configure:2266: found /usr/bin/gcc
configure:2277: result: gcc
configure:2506: checking for C compiler version
configure:2515: 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:2526: $? = 0
configure:2515: 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:2526: $? = 0
configure:2515: gcc -V >&5
gcc: error: unrecognized command line option '-V'
gcc: fatal error: no input files
compilation terminated.
configure:2526: $? = 4
configure:2515: gcc -qversion >&5
gcc: error: unrecognized command line option '-qversion'
gcc: fatal error: no input files
compilation terminated.
configure:2526: $? = 4
configure:2546: checking whether the C compiler works
configure:2568: gcc    conftest.c  >&5
configure:2572: $? = 0
configure:2620: result: yes
configure:2623: checking for C compiler default output file name
configure:2625: result: a.out
configure:2631: checking for suffix of executables
configure:2638: gcc -o conftest    conftest.c  >&5
configure:2642: $? = 0
configure:2664: result: 
configure:2686: checking whether we are cross compiling
configure:2694: gcc -o conftest    conftest.c  >&5
configure:2698: $? = 0
configure:2705: ./conftest
configure:2709: $? = 0
configure:2724: result: no
configure:2729: checking for suffix of object files
configure:2751: gcc -c   conftest.c >&5
configure:2755: $? = 0
configure:2776: result: o
configure:2780: checking whether we are using the GNU C compiler
configure:2799: gcc -c   conftest.c >&5
configure:2799: $? = 0
configure:2808: result: yes
configure:2817: checking whether gcc accepts -g
configure:2837: gcc -c -g  conftest.c >&5
configure:2837: $? = 0
configure:2878: result: yes
configure:2895: checking for gcc option to accept ISO C89
configure:2958: gcc  -c -g -O2  conftest.c >&5
configure:2958: $? = 0
configure:2971: result: none needed
configure:2992: checking for grep that handles long lines and -e
configure:3050: result: /usr/bin/grep
configure:3075: checking for C compiler warning flags
configure:3187: result: -Wall
configure:3281: checking for special C compiler options needed for large files
configure:3326: result: no
configure:3332: checking for _FILE_OFFSET_BITS value needed for large files
configure:3357: gcc -c  -Wall -g -O2  conftest.c >&5
configure:3357: $? = 0
configure:3389: result: no
configure:3524: checking location of HTSlib source tree
configure:3545: result: htslib-1.17
configure:3782: checking for NcursesW wide-character library
configure:3806: gcc -o conftest  -Wall -g -O2   conftest.c  -lncursesw >&5
configure:3806: $? = 0
configure:3815: result: yes
configure:3828: checking for working ncursesw/curses.h
configure:3861: gcc -o conftest  -Wall -g -O2   conftest.c  -lncursesw >&5
conftest.c: In function 'main':
conftest.c:24:21: warning: unused variable 'h' [-Wunused-variable]
                 int h = getcurx(stdscr) + getmaxx(stdscr);
                     ^
conftest.c:23:21: warning: unused variable 'g' [-Wunused-variable]
                 int g = getattrs(stdscr);
                     ^
conftest.c:21:25: warning: unused variable 'e' [-Wunused-variable]
                 cchar_t e;
                         ^
conftest.c:19:24: warning: unused variable 'c' [-Wunused-variable]
                 chtype c = COLOR_PAIR(1) & A_COLOR;
                        ^
conftest.c:18:21: warning: unused variable 'b' [-Wunused-variable]
                 int b = KEY_LEFT;
                     ^
conftest.c:17:24: warning: unused variable 'a' [-Wunused-variable]
                 chtype a = A_BOLD;
                        ^
configure:3861: $? = 0
configure:3870: result: yes
configure:4570: checking for library containing cbreak
configure:4601: gcc -o conftest  -Wall -g -O2   conftest.c  -lncursesw >&5
configure:4601: $? = 0
configure:4618: result: none required
configure:4670: checking for zlib.h
configure:4670: gcc -c  -Wall -g -O2  conftest.c >&5
configure:4670: $? = 0
configure:4670: result: yes
configure:4679: checking for inflate in -lz
configure:4704: gcc -o conftest  -Wall -g -O2   conftest.c -lz   >&5
configure:4704: $? = 0
configure:4713: result: yes
configure:4739: checking for library containing regcomp
configure:4770: gcc -o conftest  -Wall -g -O2   conftest.c  >&5
configure:4770: $? = 0
configure:4787: result: none required
configure:4929: creating ./config.status

## ---------------------- ##
## Running config.status. ##
## ---------------------- ##

This file was extended by Samtools 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:803: creating config.mk
config.status:803: creating config.h
configure:6155: === configuring in htslib-1.17 (/home/psgendb/BIRCHDEV/install/samtools-1.17/htslib-1.17)
configure:6218: running /bin/sh ./configure --disable-option-checking '--prefix=/usr/local'  --cache-file=/dev/null --srcdir=.

## ---------------- ##
## 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_CURSES_LIB_set=
ac_cv_env_CURSES_LIB_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_header_zlib_h=yes
ac_cv_lib_z_inflate=yes
ac_cv_objext=o
ac_cv_path_GREP=/usr/bin/grep
ac_cv_prog_AWK=gawk
ac_cv_prog_ac_ct_CC=gcc
ac_cv_prog_cc_c89=
ac_cv_prog_cc_g=yes
ac_cv_search_cbreak='none required'
ac_cv_search_regcomp='none required'
ac_cv_sys_file_offset_bits=no
ac_cv_sys_largefile_CC=no
ax_cv_curses=yes
ax_cv_curses_color=yes
ax_cv_curses_enhanced=yes
ax_cv_curses_obsolete=yes
ax_cv_curses_which=ncursesw
ax_cv_header_ncursesw_curses_h=yes
ax_cv_htslib=yes
ax_cv_htslib_which=source
ax_cv_ncursesw=yes
hts_cv_prog_cc_warnings=-Wall

## ----------------- ##
## Output variables. ##
## ----------------- ##

AWK='gawk'
CC='gcc'
CFLAGS=' -Wall -g -O2'
CPPFLAGS=''
CURSES_LIB='-lncursesw'
DEFS='-DHAVE_CONFIG_H'
ECHO_C=''
ECHO_N='-n'
ECHO_T=''
EXEEXT=''
GREP='/usr/bin/grep'
HTSDIR='htslib-1.17'
HTSLIB_CPPFLAGS='-Ihtslib-1.17'
HTSLIB_LDFLAGS='-Lhtslib-1.17'
Hinstall='#'
Hsource=''
LDFLAGS=''
LIBOBJS=''
LIBS=''
LTLIBOBJS=''
OBJEXT='o'
PACKAGE_BUGREPORT='samtools-help@lists.sourceforge.net'
PACKAGE_NAME='Samtools'
PACKAGE_STRING='Samtools 1.17'
PACKAGE_TARNAME='samtools'
PACKAGE_URL='http://www.htslib.org/'
PACKAGE_VERSION='1.17'
PATH_SEPARATOR=':'
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}'
exec_prefix='${prefix}'
host_alias='unknown-Linux'
htmldir='${docdir}'
includedir='${prefix}/include'
infodir='${datarootdir}/info'
libdir='${exec_prefix}/lib'
libexecdir='${exec_prefix}/libexec'
localedir='${datarootdir}/locale'
localstatedir='${prefix}/var'
mandir='${datarootdir}/man'
oldincludedir='/usr/include'
pdfdir='${docdir}'
prefix='/usr/local'
program_transform_name='s,x,x,'
psdir='${docdir}'
runstatedir='${localstatedir}/run'
sbindir='${exec_prefix}/sbin'
sharedstatedir='${prefix}/com'
subdirs=' htslib-1.17'
sysconfdir='${prefix}/etc'
target_alias=''

## ----------- ##
## confdefs.h. ##
## ----------- ##

/* confdefs.h */
#define PACKAGE_NAME "Samtools"
#define PACKAGE_TARNAME "samtools"
#define PACKAGE_VERSION "1.17"
#define PACKAGE_STRING "Samtools 1.17"
#define PACKAGE_BUGREPORT "samtools-help@lists.sourceforge.net"
#define PACKAGE_URL "http://www.htslib.org/"
#define HAVE_NCURSESW_CURSES_H 1
#define HAVE_NCURSESW 1
#define HAVE_CURSES 1
#define HAVE_CURSES_ENHANCED 1
#define HAVE_CURSES_COLOR 1
#define HAVE_CURSES_OBSOLETE 1
#define HAVE_LIBZ 1

configure: exit 0