Error in installation
Iman Nazari
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a race-free mkdir -p... ./config/install-sh -c -d
checking for gawk... no
checking for mawk... no
checking for nawk... no
checking for awk... awk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking whether make supports nested variables... (cached) yes
checking for gcc... x86_64-apple-darwin13.4.0-clang
checking whether the C compiler works... no
configure: error: in `/Users/MEME_database/meme-5.5.3':
configure: error: C compiler cannot create executables
See `config.log' for more details
AND config.log:
This file contains any messages produced by compilers while
running configure, to aid debugging if configure makes a mistake.
It was created by meme configure 5.5.3, which was
generated by GNU Autoconf 2.71. Invocation command line was
$ ./configure --prefix=/opt/meme-5.5.3 --enable-web --with-url=http://host/meme-5.5.3
## --------- ##
## Platform. ##
## --------- ##
hostname = macprospare02.local
uname -m = x86_64
uname -r = 21.3.0
uname -s = Darwin
uname -v = Darwin Kernel Version 21.3.0: Wed Jan 5 21:37:58 PST 2022; root:xnu-8019.80.24~20/RELEASE_X86_64
/usr/bin/uname -p = i386
/bin/uname -X = unknown
/bin/arch = unknown
/usr/bin/arch -k = unknown
/usr/convex/getsysinfo = unknown
/usr/bin/hostinfo = Mach kernel version:
Darwin Kernel Version 21.3.0: Wed Jan 5 21:37:58 PST 2022; root:xnu-8019.80.24~20/RELEASE_X86_64
Kernel configured for up to 8 processors.
4 processors are physically available.
8 processors are logically available.
Processor type: x86_64h (Intel x86-64h Haswell)
Processors active: 0 1 2 3 4 5 6 7
Primary memory available: 16.00 gigabytes
Default processor set: 612 tasks, 3147 threads, 8 processors
Load average: 3.23, Mach factor: 4.75
/bin/machine = unknown
/usr/bin/oslevel = unknown
/bin/universe = unknown
PATH: /opt/anaconda3/bin/
PATH: /opt/anaconda3/condabin/
PATH: /Library/Frameworks/Python.framework/Versions/3.8/bin/
PATH: /usr/local/bin/
PATH: /usr/bin/
PATH: /bin/
PATH: /usr/sbin/
PATH: /sbin/
PATH: /opt/X11/bin/
## ----------- ##
## Core tests. ##
## ----------- ##
configure:2684: looking for aux files: config.guess config.sub ltmain.sh compile missing install-sh
configure:2697: trying ./config/
configure:2726: ./config/config.guess found
configure:2726: ./config/config.sub found
configure:2726: ./config/ltmain.sh found
configure:2726: ./config/compile found
configure:2726: ./config/missing found
configure:2708: ./config/install-sh found
configure:2862: checking for a BSD-compatible install
configure:2935: result: /usr/bin/install -c
configure:2946: checking whether build environment is sane
configure:3001: result: yes
configure:3160: checking for a race-free mkdir -p
configure:3204: result: ./config/install-sh -c -d
configure:3211: checking for gawk
configure:3246: result: no
configure:3211: checking for mawk
configure:3246: result: no
configure:3211: checking for nawk
configure:3246: result: no
configure:3211: checking for awk
configure:3232: found /usr/bin/awk
configure:3243: result: awk
configure:3254: checking whether make sets $(MAKE)
configure:3277: result: yes
configure:3307: checking whether make supports nested variables
configure:3325: result: yes
configure:3473: checking whether make supports nested variables
configure:3491: result: yes
configure:3575: checking for gcc
configure:3607: result: x86_64-apple-darwin13.4.0-clang
configure:3960: checking for C compiler version
configure:3969: x86_64-apple-darwin13.4.0-clang --version >&5
clang version 4.0.1 (tags/RELEASE_401/final)
Target: x86_64-apple-darwin13.4.0
Thread model: posix
InstalledDir: /opt/anaconda3/bin
configure:3980: $? = 0
configure:3969: x86_64-apple-darwin13.4.0-clang -v >&5
clang version 4.0.1 (tags/RELEASE_401/final)
Target: x86_64-apple-darwin13.4.0
Thread model: posix
InstalledDir: /opt/anaconda3/bin
configure:3980: $? = 0
configure:3969: x86_64-apple-darwin13.4.0-clang -V >&5
clang-4.0: error: argument to '-V' is missing (expected 1 value)
clang-4.0: error: no input files
configure:3980: $? = 1
configure:3969: x86_64-apple-darwin13.4.0-clang -qversion >&5
clang-4.0: error: unknown argument: '-qversion'
clang-4.0: error: no input files
configure:3980: $? = 1
configure:3969: x86_64-apple-darwin13.4.0-clang -version >&5
clang-4.0: error: unknown argument: '-version'
clang-4.0: error: no input files
configure:3980: $? = 1
configure:4000: checking whether the C compiler works
configure:4022: x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs conftest.c >&5
clang-4.0: error: unable to execute command: Segmentation fault: 11
clang-4.0: error: linker command failed due to signal (use -v to see invocation)
configure:4026: $? = 254
configure:4066: result: no
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "meme"
| #define PACKAGE_TARNAME "meme"
| #define PACKAGE_VERSION "5.5.3"
| #define PACKAGE_STRING "meme 5.5.3"
| #define PACKAGE_BUGREPORT ""
| #define PACKAGE_URL ""
| #define PACKAGE "meme"
| #define VERSION "5.5.3"
| /* end confdefs.h. */
|
| int
| main (void)
| {
|
| ;
| return 0;
| }
configure:4071: error: in `/Users/ieo5268/Documents/Thesis_Iman/cluster/MEME_database/meme-5.5.3':
configure:4073: error: C compiler cannot create executables
See `config.log' for more details
## ---------------- ##
## Cache variables. ##
## ---------------- ##
ac_cv_env_CC_set=set
ac_cv_env_CC_value=x86_64-apple-darwin13.4.0-clang
ac_cv_env_CFLAGS_set=set
ac_cv_env_CFLAGS_value='-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe'
ac_cv_env_CPPFLAGS_set=set
ac_cv_env_CPPFLAGS_value='-D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9'
ac_cv_env_LDFLAGS_set=set
ac_cv_env_LDFLAGS_value='-Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs'
ac_cv_env_LIBS_set=
ac_cv_env_LIBS_value=
ac_cv_env_LT_SYS_LIBRARY_PATH_set=
ac_cv_env_LT_SYS_LIBRARY_PATH_value=
ac_cv_env_PYTHON_set=
ac_cv_env_PYTHON_value=
ac_cv_env_build_alias_set=
ac_cv_env_build_alias_value=
ac_cv_env_host_alias_set=
ac_cv_env_host_alias_value=
ac_cv_env_target_alias_set=
ac_cv_env_target_alias_value=
ac_cv_path_install='/usr/bin/install -c'
ac_cv_prog_AWK=awk
ac_cv_prog_ac_ct_CC=x86_64-apple-darwin13.4.0-clang
ac_cv_prog_make_make_set=yes
am_cv_make_support_nested_variables=yes
## ----------------- ##
## Output variables. ##
## ----------------- ##
ACLOCAL='${SHELL} '\''/Users/ieo5268/Documents/Thesis_Iman/cluster/MEME_database/meme-5.5.3/config/missing'\'' aclocal-1.16'
ALT_URL=''
AMDEPBACKSLASH=''
AMDEP_FALSE=''
AMDEP_TRUE=''
AMTAR='$${TAR-tar}'
AM_BACKSLASH='\'
AM_DEFAULT_V='$(AM_DEFAULT_VERBOSITY)'
AM_DEFAULT_VERBOSITY='1'
AM_V='$(V)'
ANT=''
AR='/opt/anaconda3/bin/x86_64-apple-darwin13.4.0-ar'
AUTOCONF='${SHELL} '\''/Users/ieo5268/Documents/Thesis_Iman/cluster/MEME_database/meme-5.5.3/config/missing'\'' autoconf'
AUTOHEADER='${SHELL} '\''/Users/ieo5268/Documents/Thesis_Iman/cluster/MEME_database/meme-5.5.3/config/missing'\'' autoheader'
AUTOMAKE='${SHELL} '\''/Users/ieo5268/Documents/Thesis_Iman/cluster/MEME_database/meme-5.5.3/config/missing'\'' automake-1.16'
AWK='awk'
BUILD_LIBXML2_FALSE=''
BUILD_LIBXML2_TRUE=''
BUILD_LIBXSLT_FALSE=''
BUILD_LIBXSLT_TRUE=''
CATALINA_BASE=''
CATALINA_HOME=''
CC='x86_64-apple-darwin13.4.0-clang'
CCDEPMODE=''
CFLAGS='-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe'
CONTACT=''
CONVERT=''
CPPFLAGS='-D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9'
CSCOPE='cscope'
CTAGS='ctags'
CYGPATH_W='echo'
DEBUG_FLAGS=''
DEFS=''
DEPDIR=''
DEV_CONTACT=''
DLLTOOL=''
DRMAA_QUEUE=''
DRMAA_QUEUE_SHORT=''
DSYMUTIL=''
DUMPBIN=''
ECHO_C='\c'
ECHO_N=''
ECHO_T=''
EGREP=''
ETAGS='etags'
EXEEXT=''
EXPIRY=''
FGREP=''
FILECMD=''
GHOSTSCRIPT=''
GOSERVER_URL=''
GREP=''
HAVE_PYTHON_3_FALSE=''
HAVE_PYTHON_3_TRUE=''
HAVE_PYTHON_FALSE=''
HAVE_PYTHON_TRUE=''
HOSTNAME='macprospare02.local'
INSTALL_DATA='${INSTALL} -m 644'
INSTALL_PROGRAM='${INSTALL}'
INSTALL_SCRIPT='${INSTALL}'
INSTALL_STRIP_PROGRAM='$(install_sh) -c -s'
LAMBIN=''
LD='/opt/anaconda3/bin/x86_64-apple-darwin13.4.0-ld'
LDFLAGS='-Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs'
LIBEXSLT_CFLAGS=''
LIBEXSLT_LIBS=''
LIBOBJS=''
LIBS=''
LIBTOOL='/opt/anaconda3/bin/x86_64-apple-darwin13.4.0-libtool'
LIBXML2_CFLAGS=''
LIBXML2_LIBS=''
LIBXSLT_CFLAGS=''
LIBXSLT_LIBS=''
LIPO='/opt/anaconda3/bin/x86_64-apple-darwin13.4.0-lipo'
LN_S=''
LTLIBOBJS=''
LT_SYS_LIBRARY_PATH=''
MACHID=''
MAKEINFO='${SHELL} '\''/Users/ieo5268/Documents/Thesis_Iman/cluster/MEME_database/meme-5.5.3/config/missing'\'' makeinfo'
MANIFEST_TOOL=''
MAST_PORT=''
MAXMEMORY=''
MAXMEMORY_SHORT=''
MAXTIME=''
MAXTIME_SHORT=''
MEME_DB=''
MEME_DIRECTORY=''
MEME_LOGS=''
MEME_PORT=''
MEME_TEMP=''
METAMEME_EXTERNAL_FALSE=''
METAMEME_EXTERNAL_TRUE=''
MKDIR_P='./config/install-sh -c -d'
MPICC=''
MPIFLAGS=''
MPIINC=''
MPILIBDIR=''
MPIRUN=''
MPITYPE=''
MPI_CMD=''
MPI_NPROCS=''
NEWS_URL=''
NM='/opt/anaconda3/bin/x86_64-apple-darwin13.4.0-nm'
NMEDIT='/opt/anaconda3/bin/x86_64-apple-darwin13.4.0-nmedit'
NOTICES_URL=''
OBJDUMP=''
OBJEXT=''
OPAL_DEPLOY=''
OPAL_URL=''
OPT_FLAGS=''
OTOOL64=''
OTOOL='/opt/anaconda3/bin/x86_64-apple-darwin13.4.0-otool'
PACKAGE='meme'
PACKAGE_BUGREPORT=''
PACKAGE_NAME='meme'
PACKAGE_STRING='meme 5.5.3'
PACKAGE_TARNAME='meme'
PACKAGE_URL=''
PACKAGE_VERSION='5.5.3'
PARALLEL_FALSE=''
PARALLEL_IS_LAM_FALSE=''
PARALLEL_IS_LAM_TRUE=''
PARALLEL_TRUE=''
PATH_SEPARATOR=':'
PERL=''
PREV_URL=''
PREV_VER=''
PYTHON=''
PYTHON_EXEC_PREFIX=''
PYTHON_PLATFORM=''
PYTHON_PREFIX=''
PYTHON_VERSION=''
QUOTA=''
RANLIB='/opt/anaconda3/bin/x86_64-apple-darwin13.4.0-ranlib'
SED=''
SENDMAIL=''
SET_MAKE=''
SHELL='/bin/sh'
SOURCE_URL=''
STREME_LENGTH_FACTOR=''
STRIP='/opt/anaconda3/bin/x86_64-apple-darwin13.4.0-strip'
URL=''
VERSION='5.5.3'
WANT_STRLCPY_FALSE=''
WANT_STRLCPY_TRUE=''
WEBSERVICE=''
WEBSERVICE_FALSE=''
WEBSERVICE_TRUE=''
WEBSITE_FALSE=''
WEBSITE_TRUE=''
WEB_FALSE=''
WEB_TRUE=''
XML2_CONFIG=''
XSLT_CONFIG=''
ac_ct_AR=''
ac_ct_CC='x86_64-apple-darwin13.4.0-clang'
ac_ct_DUMPBIN=''
am__EXEEXT_FALSE=''
am__EXEEXT_TRUE=''
am__fastdepCC_FALSE=''
am__fastdepCC_TRUE=''
am__include=''
am__isrc=''
am__leading_dot='.'
am__nodep=''
am__quote=''
am__tar='$${TAR-tar} chof - "$$tardir"'
am__untar='$${TAR-tar} xf -'
bindir='${exec_prefix}/bin'
build=''
build_alias=''
build_cpu=''
build_os=''
build_vendor=''
datadir='${datarootdir}'
datarootdir='${prefix}/share'
docdir='${datarootdir}/doc/${PACKAGE_TARNAME}'
dvidir='${docdir}'
exec_prefix='NONE'
host=''
host_alias=''
host_cpu=''
host_os=''
host_vendor=''
htmldir='${docdir}'
includedir='${prefix}/include'
infodir='${datarootdir}/info'
install_sh='${SHELL} /Users/ieo5268/Documents/Thesis_Iman/cluster/MEME_database/meme-5.5.3/config/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='${docdir}'
pkgpyexecdir=''
pkgpythondir=''
prefix='/opt/meme-5.5.3'
program_transform_name='s,x,x,'
psdir='${docdir}'
pyexecdir=''
pythondir=''
runstatedir='${localstatedir}/run'
sbindir='${exec_prefix}/sbin'
sharedstatedir='${prefix}/com'
sysconfdir='${prefix}/etc'
target_alias=''
## ----------- ##
## confdefs.h. ##
## ----------- ##
/* confdefs.h */
#define PACKAGE_NAME "meme"
#define PACKAGE_TARNAME "meme"
#define PACKAGE_VERSION "5.5.3"
#define PACKAGE_STRING "meme 5.5.3"
#define PACKAGE_BUGREPORT ""
#define PACKAGE_URL ""
#define PACKAGE "meme"
#define VERSION "5.5.3"
configure: exit 77
appreciate any help in advance.
thanks
cegrant
PATH: /opt/anaconda3/bin/
PATH: /opt/anaconda3/condabin/