Build error with make [Makefile:661: src/hssp-convert-3to1.o] Error 1

[nschiraldi]

I am trying to build xssp-3.0.7 but keep running into a make error. Any help is greatly appreciated!

./configure output

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 for style of include used by make... GNU
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 dependency style of gcc... gcc3
checking for perl... perl
checking for cppcheck... no
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-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-mt... yes
checking whether the Boost::Filesystem library is available... yes
checking for exit in -lboost_filesystem... yes
checking whether the Boost::IOStreams library is available... yes
checking for exit in -lboost_iostreams-mt... yes
checking whether the Boost::Program_Options library is available... yes
checking for exit in -lboost_program_options-mt... yes
checking whether the Boost::Regex library is available... yes
checking for exit in -lboost_regex-mt... yes
checking whether the Boost::System library is available... yes
checking for exit in -lboost_system... yes
checking whether the Boost::Thread library is available... yes
checking for exit in -lboost_thread... yes
checking whether the Boost::Unit_Test_Framework library is available... yes
checking for main in -lzeep... no
configure: WARNING: libzeep not found - fetch-dbrefs is disabled in mkhssp
./configure: line 6755: test: : integer expression expected
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking bzlib.h usability... yes
checking bzlib.h presence... yes
checking for bzlib.h... yes
checking for main in -lbz2... yes
checking zlib.h usability... yes
checking zlib.h presence... yes
checking for zlib.h... yes
checking for main in -lz... yes
checking sys/ioctl.h usability... yes
checking sys/ioctl.h presence... yes
checking for sys/ioctl.h... yes
checking termios.h usability... yes
checking termios.h presence... yes
checking for termios.h... yes
checking for stdbool.h that conforms to C99... yes
checking for _Bool... yes
checking for inline... inline
checking for int16_t... yes
checking for int32_t... yes
checking for int64_t... yes
checking for int8_t... yes
checking for size_t... yes
checking for uint16_t... yes
checking for uint32_t... yes
checking for uint64_t... yes
checking for uint8_t... yes
checking for error_at_line... yes
checking for pid_t... yes
checking vfork.h usability... no
checking vfork.h presence... no
checking for vfork.h... no
checking for fork... yes
checking for vfork... yes
checking for working fork... yes
checking for working vfork... (cached) yes
checking for dup2... yes
checking for floor... no
checking for pow... no
checking for socket... yes
checking for sqrt... no
checking for strchr... yes
checking for strerror... yes
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating config.h
config.status: executing depfiles commands

make version

make --v
GNU Make 4.2.1

make output

make
perl mtrx/mkmat_h.pl mtrx/
make  all-am
make[1]: Entering directory '/network/rit/lab/pandelab/xssp-3.0.7'
depbase=`echo src/dssp.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
g++ -DHAVE_CONFIG_H -I.  -std=c++11 -pedantic -Wall -Werror -Wno-reorder -pthread -I/usr/include -I./src/   -g -O2 -MT src/dssp.o -MD -MP -MF $depbase.Tpo -c -o src/dssp.o src/dssp.cpp &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/iocif.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
g++ -DHAVE_CONFIG_H -I.  -std=c++11 -pedantic -Wall -Werror -Wno-reorder -pthread -I/usr/include -I./src/   -g -O2 -MT src/iocif.o -MD -MP -MF $depbase.Tpo -c -o src/iocif.o src/iocif.cpp &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/mas.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
g++ -DHAVE_CONFIG_H -I.  -std=c++11 -pedantic -Wall -Werror -Wno-reorder -pthread -I/usr/include -I./src/   -g -O2 -MT src/mas.o -MD -MP -MF $depbase.Tpo -c -o src/mas.o src/mas.cpp &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/mkdssp.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
g++ -DHAVE_CONFIG_H -I.  -std=c++11 -pedantic -Wall -Werror -Wno-reorder -pthread -I/usr/include -I./src/   -g -O2 -MT src/mkdssp.o -MD -MP -MF $depbase.Tpo -c -o src/mkdssp.o src/mkdssp.cpp &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/primitives-3d.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
g++ -DHAVE_CONFIG_H -I.  -std=c++11 -pedantic -Wall -Werror -Wno-reorder -pthread -I/usr/include -I./src/   -g -O2 -MT src/primitives-3d.o -MD -MP -MF $depbase.Tpo -c -o src/primitives-3d.o src/primitives-3d.cpp &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/structure.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
g++ -DHAVE_CONFIG_H -I.  -std=c++11 -pedantic -Wall -Werror -Wno-reorder -pthread -I/usr/include -I./src/   -g -O2 -MT src/structure.o -MD -MP -MF $depbase.Tpo -c -o src/structure.o src/structure.cpp &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/utils.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
g++ -DHAVE_CONFIG_H -I.  -std=c++11 -pedantic -Wall -Werror -Wno-reorder -pthread -I/usr/include -I./src/   -g -O2 -MT src/utils.o -MD -MP -MF $depbase.Tpo -c -o src/utils.o src/utils.cpp &&\
mv -f $depbase.Tpo $depbase.Po
g++  -g -O2   -o mkdssp src/dssp.o src/iocif.o src/mas.o src/mkdssp.o src/primitives-3d.o src/structure.o src/utils.o -lboost_date_time-mt -lboost_filesystem -lboost_iostreams-mt -lboost_program_options-mt -lboost_regex-mt -lboost_system -lboost_thread -lpthread
depbase=`echo src/blast.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
g++ -DHAVE_CONFIG_H -I.  -std=c++11 -pedantic -Wall -Werror -Wno-reorder -pthread -I/usr/include -I./src/   -g -O2 -MT src/blast.o -MD -MP -MF $depbase.Tpo -c -o src/blast.o src/blast.cpp &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/fasta.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
g++ -DHAVE_CONFIG_H -I.  -std=c++11 -pedantic -Wall -Werror -Wno-reorder -pthread -I/usr/include -I./src/   -g -O2 -MT src/fasta.o -MD -MP -MF $depbase.Tpo -c -o src/fasta.o src/fasta.cpp &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/hssp-nt.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
g++ -DHAVE_CONFIG_H -I.  -std=c++11 -pedantic -Wall -Werror -Wno-reorder -pthread -I/usr/include -I./src/   -g -O2 -MT src/hssp-nt.o -MD -MP -MF $depbase.Tpo -c -o src/hssp-nt.o src/hssp-nt.cpp &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/matrix.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
g++ -DHAVE_CONFIG_H -I.  -std=c++11 -pedantic -Wall -Werror -Wno-reorder -pthread -I/usr/include -I./src/   -g -O2 -MT src/matrix.o -MD -MP -MF $depbase.Tpo -c -o src/matrix.o src/matrix.cpp &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/mkhssp.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
g++ -DHAVE_CONFIG_H -I.  -std=c++11 -pedantic -Wall -Werror -Wno-reorder -pthread -I/usr/include -I./src/   -g -O2 -MT src/mkhssp.o -MD -MP -MF $depbase.Tpo -c -o src/mkhssp.o src/mkhssp.cpp &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/progress.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
g++ -DHAVE_CONFIG_H -I.  -std=c++11 -pedantic -Wall -Werror -Wno-reorder -pthread -I/usr/include -I./src/   -g -O2 -MT src/progress.o -MD -MP -MF $depbase.Tpo -c -o src/progress.o src/progress.cpp &&\
mv -f $depbase.Tpo $depbase.Po
g++  -g -O2   -o mkhssp src/blast.o src/dssp.o src/fasta.o src/hssp-nt.o src/iocif.o src/mas.o src/matrix.o src/mkhssp.o src/primitives-3d.o src/progress.o src/structure.o src/utils.o  -lboost_date_time-mt -lboost_filesystem -lboost_iostreams-mt -lboost_program_options-mt -lboost_regex-mt -lboost_system -lboost_thread -lpthread -lboost_timer
depbase=`echo src/hssp-convert-3to1.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
g++ -DHAVE_CONFIG_H -I.  -std=c++11 -pedantic -Wall -Werror -Wno-reorder -pthread -I/usr/include -I./src/   -g -O2 -MT src/hssp-convert-3to1.o -MD -MP -MF $depbase.Tpo -c -o src/hssp-convert-3to1.o src/hssp-convert-3to1.cpp &&\
mv -f $depbase.Tpo $depbase.Po
In file included from /usr/include/boost/range/functions.hpp:18,
                 from /usr/include/boost/range/iterator_range_core.hpp:26,
                 from /usr/include/boost/lexical_cast.hpp:169,
                 from src/utils.h:16,
                 from src/hssp-convert-3to1.cpp:13:
/usr/include/boost/range/begin.hpp: In instantiation of ‘typename boost::range_iterator<C>::type boost::range_detail::range_begin(C&) [with C = const boost::sub_match<__gnu_cxx::__normal_iterator<const char*, std::basic_string<char> > >; typename boost::range_iterator<C>::type = __gnu_cxx::__normal_iterator<const char*, std::basic_string<char> >]’:
/usr/include/boost/range/begin.hpp:119:23:   required from ‘typename boost::range_iterator<const T>::type boost::range_adl_barrier::begin(const T&) [with T = boost::sub_match<__gnu_cxx::__normal_iterator<const char*, std::basic_string<char> > >; typename boost::range_iterator<const T>::type = __gnu_cxx::__normal_iterator<const char*, std::basic_string<char> >]’
/usr/include/boost/range/iterator_range_core.hpp:56:60:   required from ‘static IteratorT boost::iterator_range_detail::iterator_range_impl<IteratorT>::adl_begin(ForwardRange&) [with ForwardRange = const boost::sub_match<__gnu_cxx::__normal_iterator<const char*, std::basic_string<char> > >; IteratorT = __gnu_cxx::__normal_iterator<const char*, std::basic_string<char> >]’
/usr/include/boost/range/iterator_range_core.hpp:198:41:   required from ‘boost::iterator_range<IteratorT>::iterator_range(const Range&, boost::iterator_range_detail::const_range_tag) [with Range = boost::sub_match<__gnu_cxx::__normal_iterator<const char*, std::basic_string<char> > >; IteratorT = __gnu_cxx::__normal_iterator<const char*, std::basic_string<char> >]’
/usr/include/boost/range/iterator_range_core.hpp:563:19:   required from ‘boost::iterator_range<typename boost::range_iterator<const T>::type> boost::make_iterator_range(const ForwardRange&) [with ForwardRange = boost::sub_match<__gnu_cxx::__normal_iterator<const char*, std::basic_string<char> > >; typename boost::range_iterator<const T>::type = __gnu_cxx::__normal_iterator<const char*, std::basic_string<char> >]’
/usr/include/boost/range/as_literal.hpp:93:46:   required from ‘boost::iterator_range<typename boost::range_iterator<C>::type> boost::range_detail::make_range(T&, long int) [with T = const boost::sub_match<__gnu_cxx::__normal_iterator<const char*, std::basic_string<char> > >; typename boost::range_iterator<C>::type = __gnu_cxx::__normal_iterator<const char*, std::basic_string<char> >]’
/usr/include/boost/range/as_literal.hpp:109:40:   required from ‘boost::iterator_range<typename boost::range_iterator<const T>::type> boost::as_literal(const Range&) [with Range = boost::sub_match<__gnu_cxx::__normal_iterator<const char*, std::basic_string<char> > >; typename boost::range_iterator<const T>::type = __gnu_cxx::__normal_iterator<const char*, std::basic_string<char> >]’
/usr/include/boost/algorithm/string/iter_find.hpp:153:109:   required from ‘SequenceSequenceT& boost::algorithm::iter_split(SequenceSequenceT&, RangeT&, FinderT) [with SequenceSequenceT = std::vector<std::basic_string<char> >; RangeT = const boost::sub_match<__gnu_cxx::__normal_iterator<const char*, std::basic_string<char> > >; FinderT = boost::algorithm::detail::find_regexF<boost::basic_regex<char, boost::regex_traits<char> > >]’
/usr/include/boost/algorithm/string/regex.hpp:475:50:   required from ‘SequenceSequenceT& boost::algorithm::split_regex(SequenceSequenceT&, const RangeT&, const boost::basic_regex<charT, traits>&, boost::regex_constants::match_flag_type) [with SequenceSequenceT = std::vector<std::basic_string<char> >; RangeT = boost::sub_match<__gnu_cxx::__normal_iterator<const char*, std::basic_string<char> > >; CharT = char; RegexTraitsT = boost::regex_traits<char>; boost::regex_constants::match_flag_type = boost::regex_constants::_match_flags]’
src/hssp-convert-3to1.cpp:705:90:   required from here
/usr/include/boost/range/begin.hpp:49:18: error: ‘const struct boost::sub_match<__gnu_cxx::__normal_iterator<const char*, std::basic_string<char> > >’ has no member named ‘begin’
         return c.begin();
                ~~^~~~~
In file included from /usr/include/boost/range/functions.hpp:19,
                 from /usr/include/boost/range/iterator_range_core.hpp:26,
                 from /usr/include/boost/lexical_cast.hpp:169,
                 from src/utils.h:16,
                 from src/hssp-convert-3to1.cpp:13:
/usr/include/boost/range/end.hpp: In instantiation of ‘typename boost::range_iterator<C>::type boost::range_detail::range_end(C&) [with C = const boost::sub_match<__gnu_cxx::__normal_iterator<const char*, std::basic_string<char> > >; typename boost::range_iterator<C>::type = __gnu_cxx::__normal_iterator<const char*, std::basic_string<char> >]’:
/usr/include/boost/range/end.hpp:113:21:   required from ‘typename boost::range_iterator<const T>::type boost::range_adl_barrier::end(const T&) [with T = boost::sub_match<__gnu_cxx::__normal_iterator<const char*, std::basic_string<char> > >; typename boost::range_iterator<const T>::type = __gnu_cxx::__normal_iterator<const char*, std::basic_string<char> >]’
/usr/include/boost/range/iterator_range_core.hpp:62:58:   required from ‘static IteratorT boost::iterator_range_detail::iterator_range_impl<IteratorT>::adl_end(ForwardRange&) [with ForwardRange = const boost::sub_match<__gnu_cxx::__normal_iterator<const char*, std::basic_string<char> > >; IteratorT = __gnu_cxx::__normal_iterator<const char*, std::basic_string<char> >]’
/usr/include/boost/range/iterator_range_core.hpp:198:70:   required from ‘boost::iterator_range<IteratorT>::iterator_range(const Range&, boost::iterator_range_detail::const_range_tag) [with Range = boost::sub_match<__gnu_cxx::__normal_iterator<const char*, std::basic_string<char> > >; IteratorT = __gnu_cxx::__normal_iterator<const char*, std::basic_string<char> >]’
/usr/include/boost/range/iterator_range_core.hpp:563:19:   required from ‘boost::iterator_range<typename boost::range_iterator<const T>::type> boost::make_iterator_range(const ForwardRange&) [with ForwardRange = boost::sub_match<__gnu_cxx::__normal_iterator<const char*, std::basic_string<char> > >; typename boost::range_iterator<const T>::type = __gnu_cxx::__normal_iterator<const char*, std::basic_string<char> >]’
/usr/include/boost/range/as_literal.hpp:93:46:   required from ‘boost::iterator_range<typename boost::range_iterator<C>::type> boost::range_detail::make_range(T&, long int) [with T = const boost::sub_match<__gnu_cxx::__normal_iterator<const char*, std::basic_string<char> > >; typename boost::range_iterator<C>::type = __gnu_cxx::__normal_iterator<const char*, std::basic_string<char> >]’
/usr/include/boost/range/as_literal.hpp:109:40:   required from ‘boost::iterator_range<typename boost::range_iterator<const T>::type> boost::as_literal(const Range&) [with Range = boost::sub_match<__gnu_cxx::__normal_iterator<const char*, std::basic_string<char> > >; typename boost::range_iterator<const T>::type = __gnu_cxx::__normal_iterator<const char*, std::basic_string<char> >]’
/usr/include/boost/algorithm/string/iter_find.hpp:153:109:   required from ‘SequenceSequenceT& boost::algorithm::iter_split(SequenceSequenceT&, RangeT&, FinderT) [with SequenceSequenceT = std::vector<std::basic_string<char> >; RangeT = const boost::sub_match<__gnu_cxx::__normal_iterator<const char*, std::basic_string<char> > >; FinderT = boost::algorithm::detail::find_regexF<boost::basic_regex<char, boost::regex_traits<char> > >]’
/usr/include/boost/algorithm/string/regex.hpp:475:50:   required from ‘SequenceSequenceT& boost::algorithm::split_regex(SequenceSequenceT&, const RangeT&, const boost::basic_regex<charT, traits>&, boost::regex_constants::match_flag_type) [with SequenceSequenceT = std::vector<std::basic_string<char> >; RangeT = boost::sub_match<__gnu_cxx::__normal_iterator<const char*, std::basic_string<char> > >; CharT = char; RegexTraitsT = boost::regex_traits<char>; boost::regex_constants::match_flag_type = boost::regex_constants::_match_flags]’
src/hssp-convert-3to1.cpp:705:90:   required from here
/usr/include/boost/range/end.hpp:50:22: error: ‘const struct boost::sub_match<__gnu_cxx::__normal_iterator<const char*, std::basic_string<char> > >’ has no member named ‘end’
             return c.end();
                    ~~^~~
make[1]: *** [Makefile:661: src/hssp-convert-3to1.o] Error 1
make[1]: Leaving directory '/network/rit/lab/pandelab/xssp-3.0.7'
make: *** [Makefile:468: all] Error 2

[cbaakman]

What version of boost are you using?

[nschiraldi]

Here are the boost packages installed, but 1.53.0 is the version.

boost.x86_64                  1.53.0-27.el7            @oracle-7u5-x86_64-base
boost-atomic.x86_64           1.53.0-27.el7            @oracle-7u5-x86_64-base
boost-chrono.x86_64           1.53.0-27.el7            @oracle-7u5-x86_64-base
boost-context.x86_64          1.53.0-27.el7            @oracle-7u5-x86_64-base
boost-date-time.x86_64        1.53.0-27.el7            @rit-orael-7latest-x86_64
boost-devel.x86_64            1.53.0-27.el7            @oracle-7u5-x86_64-base
boost-filesystem.x86_64       1.53.0-27.el7            @oracle-7u5-x86_64-base
boost-graph.x86_64            1.53.0-27.el7            @oracle-7u5-x86_64-base
boost-iostreams.x86_64        1.53.0-27.el7            @rit-orael-7latest-x86_64
boost-locale.x86_64           1.53.0-27.el7            @oracle-7u5-x86_64-base
boost-math.x86_64             1.53.0-27.el7            @oracle-7u5-x86_64-base
boost-program-options.x86_64  1.53.0-27.el7            @oracle-7u5-x86_64-base
boost-python.x86_64           1.53.0-27.el7            @oracle-7u5-x86_64-base
boost-random.x86_64           1.53.0-27.el7            @rit-orael-7latest-x86_64
boost-regex.x86_64            1.53.0-27.el7            @oracle-7u5-x86_64-base
boost-serialization.x86_64    1.53.0-27.el7            @oracle-7u5-x86_64-base
boost-signals.x86_64          1.53.0-27.el7            @oracle-7u5-x86_64-base
boost-system.x86_64           1.53.0-27.el7            @rit-orael-7latest-x86_64
boost-test.x86_64             1.53.0-27.el7            @oracle-7u5-x86_64-base
boost-thread.x86_64           1.53.0-27.el7            @rit-orael-7latest-x86_64
boost-timer.x86_64            1.53.0-27.el7            @oracle-7u5-x86_64-base
boost-wave.x86_64             1.53.0-27.el7            @oracle-7u5-x86_64-base

[cbaakman]

It seems this problem is not in the code of xssp itself, because the error occurs at the include of a boost header. The error pointed out by the compiler is actually in one of the boost headers.

Something could have gone wrong while installing boost. I would suggest reinstalling it.

[CryoSky]

Hello same error reported, my boost version is 1.58

[cbaakman]

I think this issue is also related to #118. Are there multiple boost versions installed? Then it could be that your OS or autoconf is mixing them up.

[cbaakman]

I have put a new release online:
https://github.com/cmbi/xssp/releases/tag/3.0.11

In this release, the autogen.sh will automatically add the alternative boost directory to the makefile. All you have to do is specify the --with-boost path when running configure.

[cbaakman]

@nschiraldi
Does your problem still occur with the latest release of hssp?

[nschiraldi]

I will test this as soon as I get a chance

[biochemi]

@cbaakman
i got same errors with latest release

[cbaakman]

The installation of release 3.1.5 runs fine for me. I cannot reproduce the error.

Since this is an error ocurring in one of the boost headers, I would suggest opening a new issue on the boost repository:

https://github.com/boostorg/boost/issues