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cmbi / hssp

Create DSSP and HSSP files
GNU General Public License v3.0
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Could not link against boost_date_time #113

Closed albumns closed 5 years ago

albumns commented 5 years ago

Hello,

I am trying to complie XSSP 3.0.8 for my Linux X64 OS. but it always failed with the following messages:

checking for perl... perl checking for cppcheck... no checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking for boostlib >= 1.48... yes checking whether the Boost::Date_Time library is available... yes checking for exit in -lboost_date_time... yes checking whether the Boost::Filesystem library is available... yes configure: error: Could not link against boost_date_time !

cbaakman commented 5 years ago

This means that the boost library can be included as a header, but not linked as a library. Could be that your boost installation is incomplete. You should look for "libboost_date_time.so" on your system. if it is missing, then re-installing boost would help.

albumns commented 5 years ago

Hi, I found this file in my directory:

/usr/lib64/libboost_date_time.so

but still failed.

thanks a lot.

cbaakman commented 5 years ago

Can the xssp configuration file find this library?

albumns commented 5 years ago

probably not. Here is the full log file:

Downloads/xssp-3.0.8> ./configure --prefix=/home/alpha/install/xssp configure: loading site script /usr/share/site/x86_64-unknown-linux-gnu checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /usr/bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking for g++... g++ checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking whether make supports the include directive... yes (GNU style) checking dependency style of g++... gcc3 checking for gcc... gcc checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking whether gcc understands -c and -o together... yes checking dependency style of gcc... gcc3 checking for perl... perl checking for cppcheck... no checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking for boostlib >= 1.48... yes checking whether the Boost::Date_Time library is available... yes checking for exit in -lboost_date_time... yes checking whether the Boost::Filesystem library is available... yes configure: error: Could not link against boost_date_time !

cbaakman commented 5 years ago

Try using the '--with-boost-date-time' or '--with_boost' arguments. Type ./configure --help for more information.

albumns commented 5 years ago

still failed with similar errors:

./configure --with-boost-date-time=/usr/lib64/libboost_date_time.so

checking for main in -lboost_date_time-/usr/lib64/libboost_date_time.so... no
configure: error: Could not link against boost_date_time-/usr/lib64/libboost_date_time.so !
cbaakman commented 5 years ago

Could you give me the output of:

ls -l /usr/lib64/libboost_date_time.so

and of 

uname -p
albumns commented 5 years ago

alpha/Desktop> ls -l /usr/lib64/libboost_date_time.so lrwxrwxrwx 1 root root 28 Apr 22 13:13 /usr/lib64/libboost_date_time.so -> libboost_date_time.so.1.69.0 alpha/Desktop> uname -p x86_64

cbaakman commented 5 years ago

I've made a test source file:

#include <iostream>
#include <string>
#include <boost/date_time/gregorian/gregorian.hpp>
#include <boost/date_time/date_formatting.hpp>
#include <boost/date_time/gregorian/greg_month.hpp>

using namespace boost::gregorian;

int main()
{
    time_t rawtime;
    struct tm *timeinfo;

    time (&rawtime);
    timeinfo = localtime (&rawtime);

    date cdate(timeinfo->tm_year+1900, timeinfo->tm_mon+1, timeinfo->tm_mday);
    cdate += date_duration(-7);

    std::string date = to_iso_string(cdate);

    std::cout << date << std::endl;

    return 0;
}

Could you try to compile this with:

g++ test.cpp -o test -lboost_date_time

and then tell me what happens?

albumns commented 5 years ago

it goes well. No any errors. I also obtained a "test" binary file.

cbaakman commented 5 years ago

So the boost library is alright. Could you tell me if there's a file named "conftest.err" in your xssp directory? If so, what are its contents?

YuhaoTan2 commented 4 years ago

I encountered the same problem when installing hssp-3.1.5. I have run with ./configure --prefix=/gpfs/user/tanyh/miniconda3/envs/mutabind --with-boost=/gpfs/user/tanyh/miniconda3/envs/mutabind --with-boost-date-time=/gpfs/user/tanyh/miniconda3/envs/mutabind/lib/libboost_date_time.so and it tells me configure: error: Could not link against boost_date_time-/gpfs/user/tanyh/miniconda3/envs/mutabind/lib/libboost_date_time.so !. The output of ls -l /gpfs/user/tanyh/miniconda3/envs/mutabind/lib/libboost_date_time.so is /gpfs/user/tanyh/miniconda3/envs/mutabind/lib/libboost_date_time.so -> libboost_date_time.so.1.67.0 I have tried the test source file mentioned above and got no errors.

There is a file named "config.log" in my hssp directory as below.

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

It was created by hssp configure 3.1.0, which was generated by GNU Autoconf 2.69. Invocation command line was

$ ./configure --prefix=/gpfs/user/tanyh/miniconda3/envs/mutabind --with-boost=/gpfs/user/tanyh/miniconda3/envs/mutabind --with-boost-date-time=/gpfs/user/tanyh/miniconda3/envs/mutabind/lib/libboost_date_time.so

---------

Platform.

---------

hostname = GPU uname -m = x86_64 uname -r = 3.10.0-327.el7.x86_64 uname -s = Linux uname -v = #1 SMP Thu Nov 19 22:10:57 UTC 2015

/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: /gpfs/user/tanyh/miniconda3/envs/mutabind/bin PATH: /gpfs/user/tanyh/miniconda3/condabin PATH: /usr/lib64/qt-3.3/bin PATH: /home/tanyh/perl5/bin PATH: /usr/local/bin PATH: /usr/bin PATH: /usr/local/sbin PATH: /usr/sbin PATH: /opt/ibutils/bin PATH: /usr/local/cuda/bin PATH: /gpfs/user/tanyh/ensembl-vep PATH: /home/tanyh/.local/bin PATH: /home/tanyh/bin

-----------

Core tests.

-----------

configure:2530: checking for a BSD-compatible install configure:2598: result: /usr/bin/install -c configure:2609: checking whether build environment is sane configure:2664: result: yes configure:2815: checking for a thread-safe mkdir -p configure:2854: result: /usr/bin/mkdir -p configure:2861: checking for gawk configure:2877: found /usr/bin/gawk configure:2888: result: gawk configure:2899: checking whether make sets $(MAKE) configure:2921: result: yes configure:2950: checking whether make supports nested variables configure:2967: result: yes configure:3115: checking for g++ configure:3131: found /usr/bin/g++ configure:3142: result: g++ configure:3169: checking for C++ compiler version configure:3178: g++ --version >&5 g++ (GCC) 4.8.5 20150623 (Red Hat 4.8.5-16) 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:3189: $? = 0 configure:3178: g++ -v >&5 Using built-in specs. COLLECT_GCC=g++ 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 4.8.5-16) (GCC) configure:3189: $? = 0 configure:3178: g++ -V >&5 g++: error: unrecognized command line option '-V' g++: fatal error: no input files compilation terminated. configure:3189: $? = 4 configure:3178: g++ -qversion >&5 g++: error: unrecognized command line option '-qversion' g++: fatal error: no input files compilation terminated. configure:3189: $? = 4 configure:3209: checking whether the C++ compiler works configure:3231: g++ conftest.cpp >&5 configure:3235: $? = 0 configure:3283: result: yes configure:3286: checking for C++ compiler default output file name configure:3288: result: a.out configure:3294: checking for suffix of executables configure:3301: g++ -o conftest conftest.cpp >&5 configure:3305: $? = 0 configure:3327: result: configure:3349: checking whether we are cross compiling configure:3357: g++ -o conftest conftest.cpp >&5 configure:3361: $? = 0 configure:3368: ./conftest configure:3372: $? = 0 configure:3387: result: no configure:3392: checking for suffix of object files configure:3414: g++ -c conftest.cpp >&5 configure:3418: $? = 0 configure:3439: result: o configure:3443: checking whether we are using the GNU C++ compiler configure:3462: g++ -c conftest.cpp >&5 configure:3462: $? = 0 configure:3471: result: yes configure:3480: checking whether g++ accepts -g configure:3500: g++ -c -g conftest.cpp >&5 configure:3500: $? = 0 configure:3541: result: yes configure:3575: checking for style of include used by make configure:3603: result: GNU configure:3629: checking dependency style of g++ configure:3740: result: gcc3 configure:3803: checking for gcc configure:3819: found /usr/bin/gcc configure:3830: result: gcc configure:4059: checking for C compiler version configure:4068: gcc --version >&5 gcc (GCC) 4.8.5 20150623 (Red Hat 4.8.5-16) 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:4079: $? = 0 configure:4068: 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 4.8.5-16) (GCC) configure:4079: $? = 0 configure:4068: gcc -V >&5 gcc: error: unrecognized command line option '-V' gcc: fatal error: no input files compilation terminated. configure:4079: $? = 4 configure:4068: gcc -qversion >&5 gcc: error: unrecognized command line option '-qversion' gcc: fatal error: no input files compilation terminated. configure:4079: $? = 4 configure:4083: checking whether we are using the GNU C compiler configure:4102: gcc -c conftest.c >&5 configure:4102: $? = 0 configure:4111: result: yes configure:4120: checking whether gcc accepts -g configure:4140: gcc -c -g conftest.c >&5 configure:4140: $? = 0 configure:4181: result: yes configure:4198: checking for gcc option to accept ISO C89 configure:4261: gcc -c -g -O2 conftest.c >&5 configure:4261: $? = 0 configure:4274: result: none needed configure:4296: checking dependency style of gcc configure:4407: result: gcc3 configure:4427: checking for perl configure:4443: found /usr/bin/perl configure:4454: result: perl configure:4474: checking for cppcheck configure:4504: result: no configure:4523: checking build system type configure:4537: result: x86_64-unknown-linux-gnu configure:4557: checking host system type configure:4570: result: x86_64-unknown-linux-gnu configure:4639: checking for boostlib >= 1.54 configure:4719: g++ -c -g -O2 -I/gpfs/user/tanyh/miniconda3/envs/mutabind/include conftest.cpp >&5 configure:4719: $? = 0 configure:4721: result: yes configure:4899: checking whether the Boost::Date_Time library is available configure:4923: g++ -c -g -O2 -I/gpfs/user/tanyh/miniconda3/envs/mutabind/include conftest.cpp >&5 configure:4923: $? = 0 configure:4937: result: yes configure:5045: checking for main in -l/gpfs/user/tanyh/miniconda3/envs/mutabind/lib/libboost_date_time.so configure:5064: gcc -o conftest -g -O2 -I/gpfs/user/tanyh/miniconda3/envs/mutabind/include -L/gpfs/user/tanyh/miniconda3/envs/mutabind/lib conftest.c -l/gpfs/user/tanyh/miniconda3/envs/mutabind/lib/libboost_date_time.so >&5 /usr/bin/ld: cannot find -l/gpfs/user/tanyh/miniconda3/envs/mutabind/lib/libboost_date_time.so collect2: error: ld returned 1 exit status configure:5064: $? = 1 configure: failed program was: / confdefs.h / #define PACKAGE_NAME "hssp" #define PACKAGE_TARNAME "hssp" #define PACKAGE_VERSION "3.1.0" #define PACKAGE_STRING "hssp 3.1.0" #define PACKAGE_BUGREPORT "Coos.Baakman@radboudumc.nl" #define PACKAGE_URL "" #define PACKAGE "hssp" #define VERSION "3.1.0" #define HAVE_BOOST /**/ #define HAVE_BOOST_DATE_TIME /**/ / end confdefs.h. /
int
main ()
{
return main ();
;
return 0;
}
configure:5074: result: no configure:5045: checking for main in -lboost_date_time-/gpfs/user/tanyh/miniconda3/envs/mutabind/lib/libboost_date_time.so configure:5064: gcc -o conftest -g -O2 -I/gpfs/user/tanyh/miniconda3/envs/mutabind/include -L/gpfs/user/tanyh/miniconda3/envs/mutabind/lib conftest.c -lboost_date_time-/gpfs/user/tanyh/miniconda3/envs/mutabind/lib/libboost_date_time.so >&5 /usr/bin/ld: cannot find -lboost_date_time-/gpfs/user/tanyh/miniconda3/envs/mutabind/lib/libboost_date_time.so collect2: error: ld returned 1 exit status configure:5064: $? = 1 configure: failed program was: / confdefs.h / #define PACKAGE_NAME "hssp" #define PACKAGE_TARNAME "hssp" #define PACKAGE_VERSION "3.1.0" #define PACKAGE_STRING "hssp 3.1.0" #define PACKAGE_BUGREPORT "Coos.Baakman@radboudumc.nl" #define PACKAGE_URL "" #define PACKAGE "hssp" #define VERSION "3.1.0" #define HAVE_BOOST /**/ #define HAVE_BOOST_DATE_TIME /**/ / end confdefs.h. /
int
main ()
{
return main ();
;
return 0;
}

configure:5074: result: no configure:5089: error: Could not link against boost_date_time-/gpfs/user/tanyh/miniconda3/envs/mutabind/lib/libboost_date_time.so !

----------------

Cache variables.

----------------

ac_cv_build=x86_64-unknown-linux-gnu ac_cv_c_compiler_gnu=yes ac_cv_cxx_compiler_gnu=yes 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_LIBBZ2_CPPFLAGS_set= ac_cv_env_LIBBZ2_CPPFLAGS_value= ac_cv_env_LIBBZ2_LDFLAGS_set= ac_cv_env_LIBBZ2_LDFLAGS_value= ac_cv_env_LIBS_set= ac_cv_env_LIBS_value= ac_cv_env_LIBZ_CPPFLAGS_set= ac_cv_env_LIBZ_CPPFLAGS_value= ac_cv_env_LIBZ_LDFLAGS_set= ac_cv_env_LIBZ_LDFLAGS_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-unknown-linux-gnu ac_cv_libgpfs_user_tanyh_miniconda3_envs_mutabind_lib_libboost_date_time_so___main=no ac_cv_lib_boost_date_timegpfs_user_tanyh_miniconda3_envs_mutabind_lib_libboost_date_time_so___main=no ac_cv_objext=o ac_cv_path_install='/usr/bin/install -c' ac_cv_path_mkdir=/usr/bin/mkdir ac_cv_prog_AWK=gawk ac_cv_prog_PERL=perl ac_cv_prog_ac_ct_CC=gcc ac_cv_prog_ac_ct_CXX=g++ ac_cv_prog_cc_c89= ac_cv_prog_cc_g=yes ac_cv_prog_cxx_g=yes ac_cv_prog_make_make_set=yes am_cv_CC_dependencies_compiler_type=gcc3 am_cv_CXX_dependencies_compiler_type=gcc3 am_cv_make_support_nested_variables=yes ax_cv_boost_date_time=yes

-----------------

Output variables.

-----------------

ACLOCAL='${SHELL} /gpfs/user/tanyh/mutabindm/hssp-3.1.5/missing aclocal-1.13' AMDEPBACKSLASH='\' AMDEP_FALSE='#' AMDEP_TRUE='' AMTAR='$${TAR-tar}' AM_BACKSLASH='\' AM_DEFAULT_V='$(AM_DEFAULT_VERBOSITY)' AM_DEFAULT_VERBOSITY='1' AM_V='$(V)' AUTOCONF='${SHELL} /gpfs/user/tanyh/mutabindm/hssp-3.1.5/missing autoconf' AUTOHEADER='${SHELL} /gpfs/user/tanyh/mutabindm/hssp-3.1.5/missing autoheader' AUTOMAKE='${SHELL} /gpfs/user/tanyh/mutabindm/hssp-3.1.5/missing automake-1.13' AWK='gawk' BOOST_CPPFLAGS='-I/gpfs/user/tanyh/miniconda3/envs/mutabind/include' BOOST_DATE_TIME_LIB='' BOOST_FILESYSTEM_LIB='' BOOST_IOSTREAMS_LIB='' BOOST_LDFLAGS='-L/gpfs/user/tanyh/miniconda3/envs/mutabind/lib' BOOST_PROGRAM_OPTIONS_LIB='' BOOST_REGEX_LIB='' BOOST_SYSTEM_LIB='' BOOST_THREAD_LIB='' BOOST_TIMER_LIB='' BOOST_UNIT_TEST_FRAMEWORK_LIB='' CC='gcc' CCDEPMODE='depmode=gcc3' CFLAGS='-g -O2' CPP='' CPPCHECK='yes' CPPFLAGS=' -I/gpfs/user/tanyh/miniconda3/envs/mutabind/include' CXX='g++' CXXDEPMODE='depmode=gcc3' CXXFLAGS='-g -O2' CYGPATH_W='echo' DEFS='' DEPDIR='.deps' ECHO_C='' ECHO_N='-n' ECHO_T='' EGREP='' EXEEXT='' GREP='' HAVE_CPPCHECK_FALSE='' HAVE_CPPCHECK_TRUE='' INSTALL_DATA='${INSTALL} -m 644' INSTALL_PROGRAM='${INSTALL}' INSTALL_SCRIPT='${INSTALL}' INSTALL_STRIP_PROGRAM='$(install_sh) -c -s' LDFLAGS=' -L/gpfs/user/tanyh/miniconda3/envs/mutabind/lib' LIBBZ2_CPPFLAGS='' LIBBZ2_LDFLAGS='' LIBOBJS='' LIBS='' LIBZ_CPPFLAGS='' LIBZ_LDFLAGS='' LTLIBOBJS='' MAKEINFO='${SHELL} /gpfs/user/tanyh/mutabindm/hssp-3.1.5/missing makeinfo' MKDIR_P='/usr/bin/mkdir -p' OBJEXT='o' PACKAGE='hssp' PACKAGE_BUGREPORT='Coos.Baakman@radboudumc.nl' PACKAGE_NAME='hssp' PACKAGE_STRING='hssp 3.1.0' PACKAGE_TARNAME='hssp' PACKAGE_URL='' PACKAGE_VERSION='3.1.0' PATH_SEPARATOR=':' PERL='perl' SET_MAKE='' SHELL='/bin/sh' STRIP='' USE_FETCH_DBREFS_FALSE='' USE_FETCH_DBREFS_TRUE='' VERSION='3.1.0' ac_ct_CC='gcc' ac_ct_CXX='g++' amEXEEXT_FALSE='' am__EXEEXT_TRUE='' amfastdepCC_FALSE='#' amfastdepCC_TRUE='' am__fastdepCXX_FALSE='#' amfastdepCXX_TRUE='' aminclude='include' amisrc='' amleading_dot='.' am__nodep='_no' amquote='' amtar='$${TAR-tar} chof - "$$tardir"' amuntar='$${TAR-tar} xf -' bindir='${exec_prefix}/bin' build='x86_64-unknown-linux-gnu' build_alias='' build_cpu='x86_64' build_os='linux-gnu' build_vendor='unknown' datadir='${datarootdir}' datarootdir='${prefix}/share' docdir='${datarootdir}/doc/${PACKAGE_TARNAME}' dvidir='${docdir}' exec_prefix='NONE' host='x86_64-unknown-linux-gnu' host_alias='' host_cpu='x86_64' host_os='linux-gnu' host_vendor='unknown' htmldir='${docdir}' includedir='${prefix}/include' infodir='${datarootdir}/info' install_sh='${SHELL} /gpfs/user/tanyh/mutabindm/hssp-3.1.5/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='${docdir}' prefix='/gpfs/user/tanyh/miniconda3/envs/mutabind' program_transform_name='s,x,x,' psdir='${docdir}' sbindir='${exec_prefix}/sbin' sharedstatedir='${prefix}/com' sysconfdir='${prefix}/etc' target_alias=''

-----------

confdefs.h.

-----------

/ confdefs.h /

define PACKAGE_NAME "hssp"

define PACKAGE_TARNAME "hssp"

define PACKAGE_VERSION "3.1.0"

define PACKAGE_STRING "hssp 3.1.0"

define PACKAGE_BUGREPORT "Coos.Baakman@radboudumc.nl"

define PACKAGE_URL ""

define PACKAGE "hssp"

define VERSION "3.1.0"

define HAVE_BOOST /**/

define HAVE_BOOST_DATE_TIME /**/

configure: exit 1

cbaakman commented 4 years ago

The --with-boost-date-time configure option is not supposed to be given a full library path. It should just contain the name of the library, without the 'lib' prefix and the '.so' suffix. Example:

./configure --with-boost-date-time=boost_date_time-gcc-mt-d-1_33_1

I don't think you need to use that option here, since your library file has the default name.

Check ./configure --help for further details.

YuhaoTan2 commented 4 years ago

Thanks for your help. I try it without with-boost-date-time and get the same error, but the content in "config.log" is different this time.

configure:4948: checking for exit in -lboost_date_time configure:4973: gcc -o conftest -g -O2 -I/gpfs/user/tanyh/miniconda3/envs/mutabind/include -L/gpfs/user/tanyh/miniconda3/envs/mutabind/lib conftest.c -lboost_date_time >&5 conftest.c:20:6: warning: conflicting types for built-in function 'exit' [enabled by default] char exit (); ^ /gpfs/user/tanyh/miniconda3/envs/mutabind/lib/libboost_date_time.so: undefined reference to std::out_of_range::out_of_range(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)@GLIBCXX_3.4.21' /gpfs/user/tanyh/miniconda3/envs/mutabind/lib/libboost_date_time.so: undefined reference tooperator delete(void*, unsigned long)@CXXABI_1.3.9' /gpfs/user/tanyh/miniconda3/envs/mutabind/lib/libboost_date_time.so: undefined reference to `std::logic_error::logic_error(std::logic_error const&)@GLIBCXX_3.4.21' collect2: error: ld returned 1 exit status configure:4973: $? = 1 configure: failed program was: / confdefs.h / #define PACKAGE_NAME "hssp" #define PACKAGE_TARNAME "hssp" #define PACKAGE_VERSION "3.1.0" #define PACKAGE_STRING "hssp 3.1.0" #define PACKAGE_BUGREPORT "Coos.Baakman@radboudumc.nl" #define PACKAGE_URL "" #define PACKAGE "hssp" #define VERSION "3.1.0" #define HAVE_BOOST /**/ #define HAVE_BOOST_DATE_TIME /**/ / end confdefs.h. /
/* Override any GCC internal prototype to avoid an error.
Use char because int might match the return type of a GCC
builtin and then its argument prototype would still apply. */
#ifdef __cplusplus
extern "C"
#endif
char exit ();
int
main ()
{
return exit ();
;
return 0;
}

configure:4983: result: no configure:4948: checking for exit in -lboost_date_time configure:4983: result: no configure:4948: checking for exit in -lboost_date_time configure:4983: result: no configure:5089: error: Could not link against boost_date_time !

I guess there is something wrong with boost. I install boost with conda and I am trying to figure out the problem.