This file contains any messages produced by compilers while running configure, to aid debugging if configure makes a mistake. It was created by cluster configure 1.59, which was generated by GNU Autoconf 2.69. Invocation command line was $ ./configure --without-x ## --------- ## ## Platform. ## ## --------- ## hostname = sh02-10n11.int uname -m = x86_64 uname -r = 3.10.0-1160.76.1.el7.x86_64 uname -s = Linux uname -v = #1 SMP Wed Aug 10 16:21:17 UTC 2022 /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: /share/software/user/srcc/bin PATH: /share/software/user/open/java/1.8.0_131/bin PATH: /share/software/user/open/R/3.6.1/bin PATH: /share/software/user/open/gsl/2.3/bin PATH: /share/software/user/open/texinfo/6.6/bin PATH: /share/software/user/open/texlive/2019/bin/x86_64-linux PATH: /share/software/user/open/perl/5.26.0/bin PATH: /share/software/user/open/libtiff/4.0.8/bin PATH: /share/software/user/open/pango/1.40.10/bin PATH: /share/software/user/open/harfbuzz/1.4.8/bin PATH: /share/software/user/open/icu/59.1/bin PATH: /share/software/user/open/curl/7.54.0/bin PATH: /share/software/user/open/xz/5.2.3/bin PATH: /share/software/user/open/pcre/8.40/bin PATH: /share/software/user/open/libjpeg-turbo/1.5.1/bin PATH: /share/software/user/open/py-numpy/1.14.3_py27/bin PATH: /oak/stanford/groups/akundaje/marinovg/programs/Anaconda2/bin PATH: /oak/stanford/groups/akundaje/marinovg/programs/Anaconda2/condabin PATH: /home/users/marinovg/perl5/bin PATH: /share/software/user/open/cairo/1.14.10/bin PATH: /share/software/user/open/gobject-introspection/1.52.1/bin PATH: /share/software/user/open/glib/2.52.3/bin PATH: /share/software/user/open/fontconfig/2.12.4/bin PATH: /share/software/user/open/x11/7.7/bin PATH: /share/software/user/open/llvm/4.0.0/bin PATH: /share/software/user/open/libxml2/2.9.4/bin PATH: /share/software/user/open/freetype/2.8/bin PATH: /share/software/user/open/libpng/1.2.57/bin PATH: /share/software/user/open/python/2.7.13/bin PATH: /share/software/user/open/sqlite/3.18.0/bin PATH: /share/software/user/open/tcltk/8.6.6/bin PATH: /share/software/user/open/libressl/2.5.3/bin PATH: /share/software/user/srcc/bin PATH: /usr/local/bin PATH: /usr/bin PATH: /usr/local/sbin PATH: /usr/sbin PATH: /opt/dell/srvadmin/bin PATH: /home/users/marinovg/anaconda2-V2 PATH: /oak/stanford/groups/akundaje/marinovg/programs/htslib-1.10.2 PATH: /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19 PATH: /opt/dell/srvadmin/iSM/bin PATH: /home/users/marinovg/bin PATH: /oak/stanford/groups/akundaje/marinovg/programs/parallel-20190722-0/bin ## ----------- ## ## Core tests. ## ## ----------- ## configure:2256: checking for a BSD-compatible install configure:2324: result: /usr/bin/install -c configure:2335: checking whether build environment is sane configure:2390: result: yes configure:2541: checking for a thread-safe mkdir -p configure:2580: result: /usr/bin/mkdir -p configure:2587: checking for gawk configure:2603: found /usr/bin/gawk configure:2614: result: gawk configure:2625: checking whether make sets $(MAKE) configure:2647: result: yes configure:2676: checking whether make supports nested variables configure:2693: result: yes configure:2871: checking for gcc configure:2887: found /usr/bin/gcc configure:2898: result: gcc configure:3127: checking for C compiler version configure:3136: 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:3147: $? = 0 configure:3136: 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:3147: $? = 0 configure:3136: gcc -V >&5 gcc: error: unrecognized command line option '-V' gcc: fatal error: no input files compilation terminated. configure:3147: $? = 4 configure:3136: gcc -qversion >&5 gcc: error: unrecognized command line option '-qversion' gcc: fatal error: no input files compilation terminated. configure:3147: $? = 4 configure:3167: checking whether the C compiler works configure:3189: gcc conftest.c >&5 configure:3193: $? = 0 configure:3241: result: yes configure:3244: checking for C compiler default output file name configure:3246: result: a.out configure:3252: checking for suffix of executables configure:3259: gcc -o conftest conftest.c >&5 configure:3263: $? = 0 configure:3285: result: configure:3307: checking whether we are cross compiling configure:3315: gcc -o conftest conftest.c >&5 configure:3319: $? = 0 configure:3326: ./conftest configure:3330: $? = 0 configure:3345: result: no configure:3350: checking for suffix of object files configure:3372: gcc -c conftest.c >&5 configure:3376: $? = 0 configure:3397: result: o configure:3401: checking whether we are using the GNU C compiler configure:3420: gcc -c conftest.c >&5 configure:3420: $? = 0 configure:3429: result: yes configure:3438: checking whether gcc accepts -g configure:3458: gcc -c -g conftest.c >&5 configure:3458: $? = 0 configure:3499: result: yes configure:3516: checking for gcc option to accept ISO C89 configure:3579: gcc -c -g -O2 conftest.c >&5 configure:3579: $? = 0 configure:3592: result: none needed configure:3617: checking whether gcc understands -c and -o together configure:3639: gcc -c conftest.c -o conftest2.o configure:3642: $? = 0 configure:3639: gcc -c conftest.c -o conftest2.o configure:3642: $? = 0 configure:3654: result: yes configure:3674: checking whether make supports the include directive configure:3689: make -f confmf.GNU && cat confinc.out this is the am__doit target configure:3692: $? = 0 configure:3711: result: yes (GNU style) configure:3736: checking dependency style of gcc configure:3847: result: gcc3 configure:3870: checking how to run the C preprocessor configure:3901: gcc -E conftest.c configure:3901: $? = 0 configure:3915: gcc -E conftest.c conftest.c:11:28: fatal error: ac_nonexistent.h: No such file or directory #include ^ compilation terminated. configure:3915: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "cluster" | #define PACKAGE_TARNAME "cluster" | #define PACKAGE_VERSION "1.59" | #define PACKAGE_STRING "cluster 1.59" | #define PACKAGE_BUGREPORT "" | #define PACKAGE_URL "" | #define PACKAGE "cluster" | #define VERSION "1.59" | /* end confdefs.h. */ | #include configure:3940: result: gcc -E configure:3960: gcc -E conftest.c configure:3960: $? = 0 configure:3974: gcc -E conftest.c conftest.c:11:28: fatal error: ac_nonexistent.h: No such file or directory #include ^ compilation terminated. configure:3974: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "cluster" | #define PACKAGE_TARNAME "cluster" | #define PACKAGE_VERSION "1.59" | #define PACKAGE_STRING "cluster 1.59" | #define PACKAGE_BUGREPORT "" | #define PACKAGE_URL "" | #define PACKAGE "cluster" | #define VERSION "1.59" | /* end confdefs.h. */ | #include configure:4003: checking for grep that handles long lines and -e configure:4061: result: /usr/bin/grep configure:4066: checking for egrep configure:4128: result: /usr/bin/grep -E configure:4133: checking for ANSI C header files configure:4153: gcc -c -g -O2 conftest.c >&5 configure:4153: $? = 0 configure:4226: gcc -o conftest -g -O2 conftest.c >&5 configure:4226: $? = 0 configure:4226: ./conftest configure:4226: $? = 0 configure:4237: result: yes configure:4250: checking for sys/types.h configure:4250: gcc -c -g -O2 conftest.c >&5 configure:4250: $? = 0 configure:4250: result: yes configure:4250: checking for sys/stat.h configure:4250: gcc -c -g -O2 conftest.c >&5 configure:4250: $? = 0 configure:4250: result: yes configure:4250: checking for stdlib.h configure:4250: gcc -c -g -O2 conftest.c >&5 configure:4250: $? = 0 configure:4250: result: yes configure:4250: checking for string.h configure:4250: gcc -c -g -O2 conftest.c >&5 configure:4250: $? = 0 configure:4250: result: yes configure:4250: checking for memory.h configure:4250: gcc -c -g -O2 conftest.c >&5 configure:4250: $? = 0 configure:4250: result: yes configure:4250: checking for strings.h configure:4250: gcc -c -g -O2 conftest.c >&5 configure:4250: $? = 0 configure:4250: result: yes configure:4250: checking for inttypes.h configure:4250: gcc -c -g -O2 conftest.c >&5 configure:4250: $? = 0 configure:4250: result: yes configure:4250: checking for stdint.h configure:4250: gcc -c -g -O2 conftest.c >&5 configure:4250: $? = 0 configure:4250: result: yes configure:4250: checking for unistd.h configure:4250: gcc -c -g -O2 conftest.c >&5 configure:4250: $? = 0 configure:4250: result: yes configure:4262: checking float.h usability configure:4262: gcc -c -g -O2 conftest.c >&5 configure:4262: $? = 0 configure:4262: result: yes configure:4262: checking float.h presence configure:4262: gcc -E conftest.c configure:4262: $? = 0 configure:4262: result: yes configure:4262: checking for float.h configure:4262: result: yes configure:4268: checking math.h usability configure:4268: gcc -c -g -O2 conftest.c >&5 configure:4268: $? = 0 configure:4268: result: yes configure:4268: checking math.h presence configure:4268: gcc -E conftest.c configure:4268: $? = 0 configure:4268: result: yes configure:4268: checking for math.h configure:4268: result: yes configure:4274: checking stdio.h usability configure:4274: gcc -c -g -O2 conftest.c >&5 configure:4274: $? = 0 configure:4274: result: yes configure:4274: checking stdio.h presence configure:4274: gcc -E conftest.c configure:4274: $? = 0 configure:4274: result: yes configure:4274: checking for stdio.h configure:4274: result: yes configure:4280: checking for stdlib.h configure:4280: result: yes configure:4286: checking for string.h configure:4286: result: yes configure:4292: checking time.h usability configure:4292: gcc -c -g -O2 conftest.c >&5 configure:4292: $? = 0 configure:4292: result: yes configure:4292: checking time.h presence configure:4292: gcc -E conftest.c configure:4292: $? = 0 configure:4292: result: yes configure:4292: checking for time.h configure:4292: result: yes configure:4300: checking for an ANSI C-conforming const configure:4366: gcc -c -g -O2 conftest.c >&5 configure:4366: $? = 0 configure:4373: result: yes configure:4381: checking for size_t configure:4381: gcc -c -g -O2 conftest.c >&5 configure:4381: $? = 0 configure:4381: gcc -c -g -O2 conftest.c >&5 conftest.c: In function 'main': conftest.c:57:21: error: expected expression before ')' token if (sizeof ((size_t))) ^ configure:4381: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "cluster" | #define PACKAGE_TARNAME "cluster" | #define PACKAGE_VERSION "1.59" | #define PACKAGE_STRING "cluster 1.59" | #define PACKAGE_BUGREPORT "" | #define PACKAGE_URL "" | #define PACKAGE "cluster" | #define VERSION "1.59" | #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 | /* end confdefs.h. */ | #include | #ifdef HAVE_SYS_TYPES_H | # include | #endif | #ifdef HAVE_SYS_STAT_H | # include | #endif | #ifdef STDC_HEADERS | # include | # include | #else | # ifdef HAVE_STDLIB_H | # include | # endif | #endif | #ifdef HAVE_STRING_H | # if !defined STDC_HEADERS && defined HAVE_MEMORY_H | # include | # endif | # include | #endif | #ifdef HAVE_STRINGS_H | # include | #endif | #ifdef HAVE_INTTYPES_H | # include | #endif | #ifdef HAVE_STDINT_H | # include | #endif | #ifdef HAVE_UNISTD_H | # include | #endif | int | main () | { | if (sizeof ((size_t))) | return 0; | ; | return 0; | } configure:4381: result: yes configure:4396: checking for stdlib.h configure:4396: result: yes configure:4406: checking for GNU libc compatible malloc configure:4430: gcc -o conftest -g -O2 conftest.c >&5 configure:4430: $? = 0 configure:4430: ./conftest configure:4430: $? = 0 configure:4440: result: yes configure:4461: checking for sqrt,exp,log in -lm configure:4486: gcc -o conftest -g -O2 conftest.c -lm >&5 conftest.c:30:6: warning: built-in function 'sqrt' declared as non-function [enabled by default] char sqrt,exp,log (); ^ conftest.c:30:11: warning: built-in function 'exp' declared as non-function [enabled by default] char sqrt,exp,log (); ^ conftest.c:30:15: warning: conflicting types for built-in function 'log' [enabled by default] char sqrt,exp,log (); ^ configure:4486: $? = 0 configure:4495: result: yes configure:4511: Building command-line version of Cluster 3.0 configure:5583: checking that generated files are newer than configure configure:5589: result: done configure:5620: creating ./config.status ## ---------------------- ## ## Running config.status. ## ## ---------------------- ## This file was extended by cluster config.status 1.59, which was generated by GNU Autoconf 2.69. Invocation command line was CONFIG_FILES = CONFIG_HEADERS = CONFIG_LINKS = CONFIG_COMMANDS = $ ./config.status on sh02-10n11.int config.status:865: creating Makefile config.status:865: creating src/Makefile config.status:865: creating config.h config.status:1094: executing depfiles commands config.status:1171: cd src && sed -e '/# am--include-marker/d' Makefile | make -f - am--depfiles config.status:1176: $? = 0 ## ---------------- ## ## Cache variables. ## ## ---------------- ## ac_cv_c_compiler_gnu=yes ac_cv_c_const=yes ac_cv_env_CC_set= ac_cv_env_CC_value= ac_cv_env_CFLAGS_set= ac_cv_env_CFLAGS_value= ac_cv_env_CPPFLAGS_set= ac_cv_env_CPPFLAGS_value= ac_cv_env_CPP_set= ac_cv_env_CPP_value= ac_cv_env_LDFLAGS_set= ac_cv_env_LDFLAGS_value= ac_cv_env_LIBS_set= ac_cv_env_LIBS_value= ac_cv_env_XMKMF_set= ac_cv_env_XMKMF_value= ac_cv_env_build_alias_set= ac_cv_env_build_alias_value= ac_cv_env_host_alias_set= ac_cv_env_host_alias_value= ac_cv_env_target_alias_set= ac_cv_env_target_alias_value= ac_cv_func_malloc_0_nonnull=yes ac_cv_header_float_h=yes ac_cv_header_inttypes_h=yes ac_cv_header_math_h=yes ac_cv_header_memory_h=yes ac_cv_header_stdc=yes ac_cv_header_stdint_h=yes ac_cv_header_stdio_h=yes ac_cv_header_stdlib_h=yes ac_cv_header_string_h=yes ac_cv_header_strings_h=yes ac_cv_header_sys_stat_h=yes ac_cv_header_sys_types_h=yes ac_cv_header_time_h=yes ac_cv_header_unistd_h=yes ac_cv_lib_m_sqrt_exp_log=yes ac_cv_objext=o ac_cv_path_EGREP='/usr/bin/grep -E' ac_cv_path_GREP=/usr/bin/grep ac_cv_path_install='/usr/bin/install -c' ac_cv_path_mkdir=/usr/bin/mkdir ac_cv_prog_AWK=gawk ac_cv_prog_CPP='gcc -E' ac_cv_prog_ac_ct_CC=gcc ac_cv_prog_cc_c89= ac_cv_prog_cc_g=yes ac_cv_prog_make_make_set=yes ac_cv_type_size_t=yes am_cv_CC_dependencies_compiler_type=gcc3 am_cv_make_support_nested_variables=yes am_cv_prog_cc_c_o=yes ## ----------------- ## ## Output variables. ## ## ----------------- ## ACLOCAL='${SHELL} /home/users/marinovg/programs/cluster-1.59/missing aclocal-1.16' AMDEPBACKSLASH='\' AMDEP_FALSE='#' AMDEP_TRUE='' AMTAR='$${TAR-tar}' AM_BACKSLASH='\' AM_DEFAULT_V='$(AM_DEFAULT_VERBOSITY)' AM_DEFAULT_VERBOSITY='1' AM_V='$(V)' AUTOCONF='${SHELL} /home/users/marinovg/programs/cluster-1.59/missing autoconf' AUTOHEADER='${SHELL} /home/users/marinovg/programs/cluster-1.59/missing autoheader' AUTOMAKE='${SHELL} /home/users/marinovg/programs/cluster-1.59/missing automake-1.16' AWK='gawk' CC='gcc' CCDEPMODE='depmode=gcc3' CFLAGS='-g -O2' CPP='gcc -E' CPPFLAGS='' CYGPATH_W='echo' DEFS='-DHAVE_CONFIG_H' DEPDIR='.deps' ECHO_C='' ECHO_N='-n' ECHO_T='' EGREP='/usr/bin/grep -E' EXEEXT='' GREP='/usr/bin/grep' INSTALL_DATA='${INSTALL} -m 644' INSTALL_PROGRAM='${INSTALL}' INSTALL_SCRIPT='${INSTALL}' INSTALL_STRIP_PROGRAM='$(install_sh) -c -s' LDFLAGS='' LIBOBJS='' LIBS='-lm ' LTLIBOBJS='' MAKEINFO='${SHELL} /home/users/marinovg/programs/cluster-1.59/missing makeinfo' MKDIR_P='/usr/bin/mkdir -p' MOTIF_FALSE='' MOTIF_TRUE='#' OBJEXT='o' PACKAGE='cluster' PACKAGE_BUGREPORT='' PACKAGE_NAME='cluster' PACKAGE_STRING='cluster 1.59' PACKAGE_TARNAME='cluster' PACKAGE_URL='' PACKAGE_VERSION='1.59' PATH_SEPARATOR=':' RANLIB='' SET_MAKE='' SHELL='/bin/sh' STRIP='' VERSION='1.59' XMKMF='' X_CFLAGS='' X_EXTRA_LIBS='' X_LIBS='' X_PRE_LIBS='' ac_ct_CC='gcc' am__EXEEXT_FALSE='' am__EXEEXT_TRUE='#' am__fastdepCC_FALSE='#' am__fastdepCC_TRUE='' am__include='include' am__isrc='' am__leading_dot='.' am__nodep='_no' am__quote='' am__tar='$${TAR-tar} chof - "$$tardir"' am__untar='$${TAR-tar} xf -' bindir='${exec_prefix}/bin' build_alias='' datadir='${datarootdir}' datarootdir='${prefix}/share' docdir='${datarootdir}/doc/${PACKAGE_TARNAME}' dvidir='${docdir}' exec_prefix='${prefix}' host_alias='' htmldir='${docdir}' includedir='${prefix}/include' infodir='${datarootdir}/info' install_sh='${SHELL} /home/users/marinovg/programs/cluster-1.59/install-sh' libdir='${exec_prefix}/lib' libexecdir='${exec_prefix}/libexec' localedir='${datarootdir}/locale' localstatedir='${prefix}/var' mandir='${datarootdir}/man' mkdir_p='$(MKDIR_P)' oldincludedir='/usr/include' pdfdir='${docdir}' 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 "cluster" #define PACKAGE_TARNAME "cluster" #define PACKAGE_VERSION "1.59" #define PACKAGE_STRING "cluster 1.59" #define PACKAGE_BUGREPORT "" #define PACKAGE_URL "" #define PACKAGE "cluster" #define VERSION "1.59" #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_MALLOC 1 #define HAVE_LIBM 1 configure: exit 0