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make fails #59

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francicco opened this issue Dec 2, 2021 · 2 comments
Open

make fails #59

francicco opened this issue Dec 2, 2021 · 2 comments

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@francicco
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Hi,

I'm trying to compile portcullis. But I'm getting this error during make:

make  all-recursive
make[1]: Entering directory `/mnt/storage/scratch/tk19812/software/portcullis-Release-1.2.3'
Making all in deps/htslib-1.3
make[2]: Entering directory `/mnt/storage/scratch/tk19812/software/portcullis-Release-1.2.3/deps/htslib-1.3'
make  all-am
make[3]: Entering directory `/mnt/storage/scratch/tk19812/software/portcullis-Release-1.2.3/deps/htslib-1.3'
make[3]: Leaving directory `/mnt/storage/scratch/tk19812/software/portcullis-Release-1.2.3/deps/htslib-1.3'
make[2]: Leaving directory `/mnt/storage/scratch/tk19812/software/portcullis-Release-1.2.3/deps/htslib-1.3'
Making all in deps/ranger-0.3.8
make[2]: Entering directory `/mnt/storage/scratch/tk19812/software/portcullis-Release-1.2.3/deps/ranger-0.3.8'
make  all-am
make[3]: Entering directory `/mnt/storage/scratch/tk19812/software/portcullis-Release-1.2.3/deps/ranger-0.3.8'
  CXX      src/libranger_la-DataChar.lo
In file included from ./include/ranger/DataChar.h:35:0,
                 from src/DataChar.cpp:34:
./include/ranger/Data.h:159:35: error: '>>' should be '> >' within a nested template argument list
     std::vector<std::vector<double>> unique_data_values;
                                   ^
src/DataChar.cpp: In constructor 'DataChar::DataChar(double*, std::vector<std::__cxx11::basic_string<char> >, size_t, size_t, bool&)':
src/DataChar.cpp:42:52: warning: delegating constructors only available with -std=c++11 or -std=gnu++11
         DataChar(variable_names, num_rows, num_cols) {
                                                    ^
make[3]: *** [src/libranger_la-DataChar.lo] Error 1
make[3]: Leaving directory `/mnt/storage/scratch/tk19812/software/portcullis-Release-1.2.3/deps/ranger-0.3.8'
make[2]: *** [all] Error 2
make[2]: Leaving directory `/mnt/storage/scratch/tk19812/software/portcullis-Release-1.2.3/deps/ranger-0.3.8'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/mnt/storage/scratch/tk19812/software/portcullis-Release-1.2.3'
make: *** [all] Error 2

Any help?
Cheers
F
@francicco
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Fix that, now I have this.

Making all in src
make[2]: Entering directory `/mnt/storage/scratch/tk19812/software/portcullis-Release-1.2.3/src'
  CXX      portcullis-junction_filter.o
junction_filter.cc: In member function 'std::tuple<std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > >, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > > portcullis::JunctionFilter::find_jsons(boost::filesystem::path)':
junction_filter.cc:106:62: error: 'begin' was not declared in this scope
     for (const auto & entry : bfs::directory_iterator(ruleset)) {
                                                              ^
junction_filter.cc:106:62: note: suggested alternatives:
In file included from /mnt/storage/easybuild/software/GCCcore/7.2.0/include/c++/7.2.0/string:51:0,
                 from /mnt/storage/easybuild/software/GCCcore/7.2.0/include/c++/7.2.0/bitset:47,
                 from /mnt/storage/easybuild/software/GCCcore/7.2.0/include/c++/7.2.0/regex:39,
                 from junction_filter.cc:21:
/mnt/storage/easybuild/software/GCCcore/7.2.0/include/c++/7.2.0/bits/range_access.h:87:5: note:   'std::begin'
     begin(_Tp (&__arr)[_Nm])
     ^~~~~
In file included from /usr/include/boost/algorithm/string/trim.hpp:16:0,
                 from /usr/include/boost/algorithm/string.hpp:19,
                 from junction_filter.cc:45:
/usr/include/boost/range/begin.hpp:112:61: note:   'boost::range_adl_barrier::begin'
 inline BOOST_DEDUCED_TYPENAME range_iterator<const T>::type begin( const T& r )
                                                             ^~~~~
In file included from /usr/include/boost/mpl/list/aux_/begin_end.hpp:17:0,
                 from /usr/include/boost/mpl/list/list0.hpp:27,
                 from /usr/include/boost/mpl/list/list10.hpp:18,
                 from /usr/include/boost/mpl/list/list20.hpp:18,
                 from /usr/include/boost/mpl/list.hpp:36,
                 from /usr/include/boost/math/policies/policy.hpp:9,
                 from /usr/include/boost/math/special_functions/math_fwd.hpp:28,
                 from /usr/include/boost/math/special_functions/sign.hpp:17,
                 from /usr/include/boost/lexical_cast.hpp:167,
                 from /usr/include/boost/program_options/value_semantic.hpp:14,
                 from /usr/include/boost/program_options/options_description.hpp:13,
                 from /usr/include/boost/program_options.hpp:15,
                 from junction_filter.cc:47:
/usr/include/boost/mpl/begin_end_fwd.hpp:22:38: note:   'boost::mpl::begin'
 template< typename Sequence > struct begin;
                                      ^~~~~
In file included from /usr/include/boost/algorithm/string/trim.hpp:16:0,
                 from /usr/include/boost/algorithm/string.hpp:19,
                 from junction_filter.cc:45:
/usr/include/boost/range/begin.hpp:112:61: note:   'boost::range_adl_barrier::begin'
 inline BOOST_DEDUCED_TYPENAME range_iterator<const T>::type begin( const T& r )
                                                             ^~~~~
junction_filter.cc:106:62: error: 'end' was not declared in this scope
     for (const auto & entry : bfs::directory_iterator(ruleset)) {
                                                              ^
junction_filter.cc:106:62: note: suggested alternatives:
In file included from /mnt/storage/easybuild/software/GCCcore/7.2.0/include/c++/7.2.0/string:51:0,
                 from /mnt/storage/easybuild/software/GCCcore/7.2.0/include/c++/7.2.0/bitset:47,
                 from /mnt/storage/easybuild/software/GCCcore/7.2.0/include/c++/7.2.0/regex:39,
                 from junction_filter.cc:21:
/mnt/storage/easybuild/software/GCCcore/7.2.0/include/c++/7.2.0/bits/range_access.h:97:5: note:   'std::end'
     end(_Tp (&__arr)[_Nm])
     ^~~
In file included from /usr/include/boost/algorithm/string/trim.hpp:17:0,
                 from /usr/include/boost/algorithm/string.hpp:19,
                 from junction_filter.cc:45:
/usr/include/boost/range/end.hpp:106:61: note:   'boost::range_adl_barrier::end'
 inline BOOST_DEDUCED_TYPENAME range_iterator<const T>::type end( const T& r )
                                                             ^~~
In file included from /usr/include/boost/mpl/list/aux_/begin_end.hpp:17:0,
                 from /usr/include/boost/mpl/list/list0.hpp:27,
                 from /usr/include/boost/mpl/list/list10.hpp:18,
                 from /usr/include/boost/mpl/list/list20.hpp:18,
                 from /usr/include/boost/mpl/list.hpp:36,
                 from /usr/include/boost/math/policies/policy.hpp:9,
                 from /usr/include/boost/math/special_functions/math_fwd.hpp:28,
                 from /usr/include/boost/math/special_functions/sign.hpp:17,
                 from /usr/include/boost/lexical_cast.hpp:167,
                 from /usr/include/boost/program_options/value_semantic.hpp:14,
                 from /usr/include/boost/program_options/options_description.hpp:13,
                 from /usr/include/boost/program_options.hpp:15,
                 from junction_filter.cc:47:
/usr/include/boost/mpl/begin_end_fwd.hpp:23:38: note:   'boost::mpl::end'
 template< typename Sequence > struct end;
                                      ^~~
In file included from /usr/include/boost/algorithm/string/trim.hpp:17:0,
                 from /usr/include/boost/algorithm/string.hpp:19,
                 from junction_filter.cc:45:
/usr/include/boost/range/end.hpp:106:61: note:   'boost::range_adl_barrier::end'
 inline BOOST_DEDUCED_TYPENAME range_iterator<const T>::type end( const T& r )
                                                             ^~~
make[2]: *** [portcullis-junction_filter.o] Error 1
make[2]: Leaving directory `/mnt/storage/scratch/tk19812/software/portcullis-Release-1.2.3/src'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/mnt/storage/scratch/tk19812/software/portcullis-Release-1.2.3'
make: *** [all] Error 2

@veeraprt
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Did anyone fix the above issue?
I am having the same issue with the latest two versions of the portcullis.
any help would be appreciated!

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@francicco @veeraprt