eriqande
commented
6 years ago Hi Giuliano,
Thanks for the detailed message. I am sorry that is happening. I have not updated to High Sierra yet so can't diagnose it. My guess is that it is an autoconf issue. I've never been super comfy with autoconf.
I would recommend trying to using the binaries in bin/OSX. Let me know if that does not work on High Sierra.
If you figure out how to fix the compilation for High Sierra, send me a pull request.
Cheers,
eric
GiulianoColosimo
Hello everyone, I am experiencing problems with the installation of NewHybrids. My OS is High Sierra 10.13.1 I have installed the Xcode tools, but when I try to follow the installation instruction my ./configure command gets the following error in the 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 newhybrids configure 2.0beta, which was generated by GNU Autoconf 2.69. Invocation command line was
$ ./configure --without-x
---------
Platform.
---------
hostname = Giulianos-MacBook-Pro.local uname -m = x86_64 uname -r = 17.2.0 uname -s = Darwin uname -v = Darwin Kernel Version 17.2.0: Fri Sep 29 18:27:05 PDT 2017; root:xnu-4570.20.62~3/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 17.2.0: Fri Sep 29 18:27:05 PDT 2017; root:xnu-4570.20.62~3/RELEASE_X86_64 Kernel configured for up to 4 processors. 2 processors are physically available. 4 processors are logically available. Processor type: x86_64h (Intel x86-64h Haswell) Processors active: 0 1 2 3 Primary memory available: 16.00 gigabytes Default processor set: 408 tasks, 1626 threads, 4 processors Load average: 1.35, Mach factor: 2.64 /bin/machine = unknown /usr/bin/oslevel = unknown /bin/universe = unknown
PATH: /opt/local/bin PATH: /opt/local/sbin PATH: /sw/bin PATH: /sw/sbin PATH: /Applications/PhyML-3.1 PATH: /Applications/colony2-mac_0 PATH: /Applications/Genepop PATH: /Applications/sratoolkit.2.5.4-mac64/bin PATH: /Applications/SamTools/bin PATH: /Applications/bowtie2-2.2.6 PATH: /Users/Cinghio/bin/x86_64 PATH: /Applications/transabyss-1.5.3 PATH: /Applications/quast-3.1 PATH: /Applications/abyss-1.5.2 PATH: /Applications/kmergenie-1.6982 PATH: /Applications/seqtk-master PATH: /Applications/FastQC PATH: /Applications/arlecore_macosx PATH: /usr/local/mysql-5.7.19-macos10.12-x86_64/bin PATH: /usr/local/pgsql/bin PATH: /usr/local/bin PATH: /usr/bin PATH: /bin PATH: /usr/sbin PATH: /sbin PATH: /Library/TeX/texbin PATH: /opt/X11/bin
-----------
Core tests.
-----------
configure:2268: checking for a BSD-compatible install configure:2336: result: /usr/bin/install -c configure:2347: checking whether build environment is sane configure:2402: result: yes configure:2553: checking for a thread-safe mkdir -p configure:2592: result: ./install-sh -c -d configure:2599: checking for gawk configure:2629: result: no configure:2599: checking for mawk configure:2629: result: no configure:2599: checking for nawk configure:2629: result: no configure:2599: checking for awk configure:2615: found /usr/bin/awk configure:2626: result: awk configure:2637: checking whether make sets $(MAKE) configure:2659: result: yes configure:2688: checking whether make supports nested variables configure:2705: result: yes configure:2834: checking build system type configure:2848: result: x86_64-apple-darwin17.2.0 configure:2868: checking host system type configure:2881: result: x86_64-apple-darwin17.2.0 configure:2913: checking for style of include used by make configure:2941: result: GNU configure:3012: checking for gcc configure:3028: found /usr/local/bin/gcc configure:3039: result: gcc configure:3268: checking for C compiler version configure:3277: gcc --version >&5 gcc (GCC) 5.3.0 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:3288: $? = 0 configure:3277: gcc -v >&5 Using built-in specs. COLLECT_GCC=gcc COLLECT_LTO_WRAPPER=/usr/local/libexec/gcc/x86_64-apple-darwin15.0.0/5.3.0/lto-wrapper Target: x86_64-apple-darwin15.0.0 Configured with: ../gcc-5.3.0/configure --enable-languages=fortran,c,c++ Thread model: posix gcc version 5.3.0 (GCC) configure:3288: $? = 0 configure:3277: gcc -V >&5 gcc: error: unrecognized command line option '-V' gcc: fatal error: no input files compilation terminated. configure:3288: $? = 1 configure:3277: gcc -qversion >&5 gcc: error: unrecognized command line option '-qversion' gcc: fatal error: no input files compilation terminated. configure:3288: $? = 1 configure:3307: checking whether the C compiler works configure:3329: gcc conftest.c >&5 conftest.c:12:2: error: invalid preprocessing directive #int
int
^ conftest.c:13:2: error: invalid preprocessing directive #main
main ()
^ conftest.c:14:2: error: invalid preprocessing directive #{
{
^ conftest.c:16:4: error: invalid preprocessing directive #;
;
conftest.c:17:4: error: invalid preprocessing directive #return
return 0;
conftest.c:18:2: error: invalid preprocessing directive #}
}
configure:3376: error: in
/Users/Cinghio/Documents/newhybrids': configure:3378: error: C compiler cannot create executables Seeconfig.log' for more details----------------
Cache variables.
----------------
ac_cv_build=x86_64-apple-darwin17.2.0 ac_cv_env_CCC_set= ac_cv_env_CCC_value= ac_cv_env_CC_set= ac_cv_env_CC_value= ac_cv_env_CFLAGS_set= ac_cv_env_CFLAGS_value= ac_cv_env_CPPFLAGS_set= ac_cv_env_CPPFLAGS_value= ac_cv_env_CPP_set= ac_cv_env_CPP_value= ac_cv_env_CXXFLAGS_set= ac_cv_env_CXXFLAGS_value= ac_cv_env_CXX_set= ac_cv_env_CXX_value= ac_cv_env_LDFLAGS_set= ac_cv_env_LDFLAGS_value= ac_cv_env_LIBS_set= ac_cv_env_LIBS_value= ac_cv_env_XMKMF_set= ac_cv_env_XMKMF_value= ac_cv_env_build_alias_set= ac_cv_env_build_alias_value= ac_cv_env_host_alias_set= ac_cv_env_host_alias_value= ac_cv_env_target_alias_set= ac_cv_env_target_alias_value= ac_cv_host=x86_64-apple-darwin17.2.0 ac_cv_path_install='/usr/bin/install -c' ac_cv_prog_AWK=awk ac_cv_prog_ac_ct_CC=gcc ac_cv_prog_make_make_set=yes am_cv_make_support_nested_variables=yes
-----------------
Output variables.
-----------------
ACLOCAL='${SHELL} /Users/Cinghio/Documents/newhybrids/missing aclocal-1.14' AMDEPBACKSLASH='\' AMDEP_FALSE='#' AMDEP_TRUE='' AMTAR='$${TAR-tar}' AM_BACKSLASH='\' AM_DEFAULT_V='$(AM_DEFAULT_VERBOSITY)' AM_DEFAULT_VERBOSITY='1' AM_V='$(V)' AUTOCONF='${SHELL} /Users/Cinghio/Documents/newhybrids/missing autoconf' AUTOHEADER='${SHELL} /Users/Cinghio/Documents/newhybrids/missing autoheader' AUTOMAKE='${SHELL} /Users/Cinghio/Documents/newhybrids/missing automake-1.14' AWK='awk' CC='gcc' CCDEPMODE='' CFLAGS='' CPP='' CPPFLAGS='' CXX='' CXXDEPMODE='' CXXFLAGS='' CYGPATH_W='echo' DEFS='' DEPDIR='.deps' ECHO_C='\c' ECHO_N='' ECHO_T='' EGREP='' EXEEXT='' GLUT_CFLAGS='' GLUT_LIBS='' GLU_CFLAGS='' GLU_LIBS='' GL_CFLAGS='' GL_LIBS='' GREP='' INSTALL_DATA='${INSTALL} -m 644' INSTALL_PROGRAM='${INSTALL}' INSTALL_SCRIPT='${INSTALL}' INSTALL_STRIP_PROGRAM='$(install_sh) -c -s' LDFLAGS='' LIBOBJS='' LIBS='' LTLIBOBJS='' MAKEINFO='${SHELL} /Users/Cinghio/Documents/newhybrids/missing makeinfo' MKDIR_P='./install-sh -c -d' OBJEXT='' PACKAGE='newhybrids' PACKAGE_BUGREPORT='' PACKAGE_NAME='newhybrids' PACKAGE_STRING='newhybrids 2.0beta' PACKAGE_TARNAME='newhybrids' PACKAGE_URL='' PACKAGE_VERSION='2.0beta' PATH_SEPARATOR=':' RANLIB='' SED='' SET_MAKE='' SHELL='/bin/sh' STRIP='' VERSION='2.0beta' XMKMF='' X_CFLAGS='' X_EXTRA_LIBS='' X_LIBS='' X_PRE_LIBS='' ac_ct_CC='gcc' ac_ct_CXX='' amEXEEXT_FALSE='' am__EXEEXT_TRUE='' amfastdepCC_FALSE='' amfastdepCC_TRUE='' am__fastdepCXX_FALSE='' amfastdepCXX_TRUE='' aminclude='include' amisrc='' amleading_dot='.' am__nodep='_no' amquote='' amtar='$${TAR-tar} chof - "$$tardir"' amuntar='$${TAR-tar} xf -' bindir='${exec_prefix}/bin' build='x86_64-apple-darwin17.2.0' build_alias='' build_cpu='x86_64' build_os='darwin17.2.0' build_vendor='apple' datadir='${datarootdir}' datarootdir='${prefix}/share' docdir='${datarootdir}/doc/${PACKAGE_TARNAME}' dvidir='${docdir}' exec_prefix='NONE' host='x86_64-apple-darwin17.2.0' host_alias='' host_cpu='x86_64' host_os='darwin17.2.0' host_vendor='apple' htmldir='${docdir}' includedir='${prefix}/include' infodir='${datarootdir}/info' install_sh='${SHELL} /Users/Cinghio/Documents/newhybrids/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='${docdir}' prefix='NONE' program_transform_name='s,x,x,' psdir='${docdir}' sbindir='${exec_prefix}/sbin' sharedstatedir='${prefix}/com' subdirs='' sysconfdir='${prefix}/etc' target_alias=''
-----------
confdefs.h.
-----------
/ confdefs.h /
define PACKAGE_NAME "newhybrids"
define PACKAGE_TARNAME "newhybrids"
define PACKAGE_VERSION "2.0beta"
define PACKAGE_STRING "newhybrids 2.0beta"
define PACKAGE_BUGREPORT ""
define PACKAGE_URL ""
define PACKAGE "newhybrids"
define VERSION "2.0beta"
configure: exit 77
I have tried to play around with the error and changing a few things in the configure file but I am running out of options. Anybody know how to fix the issue?