sci-chemistry:reduce-3.16.111118:20160918-093410.log

sci-chemistry:reduce-3.16.111118:20160918-093410.log (text/plain), 34.45 KB, created by Toralf Förster on 2016-09-18 09:47:07 UTC

 * Package:    sci-chemistry/reduce-3.16.111118
 * Repository: gentoo
 * Maintainer: [e-mail]
 * USE:        abi_x86_64 amd64 elibc_glibc kernel_linux userland_GNU
 * FEATURES:   preserve-libs sandbox userpriv usersandbox
>>> Unpacking source...
>>> Unpacking reduce.3.16.111118.src.zip to /var/tmp/portage/sci-chemistry/reduce-3.16.111118/work
>>> Source unpacked in /var/tmp/portage/sci-chemistry/reduce-3.16.111118/work
>>> Preparing source in /var/tmp/portage/sci-chemistry/reduce-3.16.111118/work ...
 * Applying 3.13.080428-LDFLAGS.patch ...
 [ ok ]
 * Applying 3.14.080821-CFLAGS.patch ...
 [ ok ]
>>> Source prepared.
>>> Configuring source in /var/tmp/portage/sci-chemistry/reduce-3.16.111118/work ...
>>> Source configured.
>>> Compiling source in /var/tmp/portage/sci-chemistry/reduce-3.16.111118/work ...
make -j1 clean 
cleaning in /toolclasses...
make[1]: Entering directory '/var/tmp/portage/sci-chemistry/reduce-3.16.111118/work/toolclasses'
make[1]: Leaving directory '/var/tmp/portage/sci-chemistry/reduce-3.16.111118/work/toolclasses'
cleaning in /libpdb...
make[1]: Entering directory '/var/tmp/portage/sci-chemistry/reduce-3.16.111118/work/libpdb'
make[1]: Leaving directory '/var/tmp/portage/sci-chemistry/reduce-3.16.111118/work/libpdb'
cleaning in /reduce_src...
make[1]: Entering directory '/var/tmp/portage/sci-chemistry/reduce-3.16.111118/work/reduce_src'
make[1]: Leaving directory '/var/tmp/portage/sci-chemistry/reduce-3.16.111118/work/reduce_src'
make -j1 CC=x86_64-pc-linux-gnu-gcc CXX=x86_64-pc-linux-gnu-g++ 'OPT=-march=native -O2 -pipe' DICT_HOME=//usr/share/reduce/reduce_wwPDB_het_dict.txt DICT_OLD=//usr/share/reduce/reduce_het_dict.txt 
Start Compling:
for i in toolclasses libpdb reduce_src ;\
do \
	(cd $i ; echo "making" all "in /$i..."; \
		make -j1 'CXXDEBUGFLAGS=' all); \
done
making all in /toolclasses...
make[1]: Entering directory '/var/tmp/portage/sci-chemistry/reduce-3.16.111118/work/toolclasses'
x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe  -DCHARFUNCMACROS -DINCTEMPLATEDEFNS -DBOOLPREDEFINED -DBRACKETOPERPARMS -DLISTFRIENDFIX -c UseCount.cpp -o UseCount.o
x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe  -DCHARFUNCMACROS -DINCTEMPLATEDEFNS -DBOOLPREDEFINED -DBRACKETOPERPARMS -DLISTFRIENDFIX -c Point3d.cpp -o Point3d.o
x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe  -DCHARFUNCMACROS -DINCTEMPLATEDEFNS -DBOOLPREDEFINED -DBRACKETOPERPARMS -DLISTFRIENDFIX -c Stringclass.cpp -o Stringclass.o
x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe  -DCHARFUNCMACROS -DINCTEMPLATEDEFNS -DBOOLPREDEFINED -DBRACKETOPERPARMS -DLISTFRIENDFIX -c Hash.cpp -o Hash.o
x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe  -DCHARFUNCMACROS -DINCTEMPLATEDEFNS -DBOOLPREDEFINED -DBRACKETOPERPARMS -DLISTFRIENDFIX -c utility.cpp -o utility.o
x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe  -DCHARFUNCMACROS -DINCTEMPLATEDEFNS -DBOOLPREDEFINED -DBRACKETOPERPARMS -DLISTFRIENDFIX -c column_sprintf.cpp -o column_sprintf.o
x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe  -DCHARFUNCMACROS -DINCTEMPLATEDEFNS -DBOOLPREDEFINED -DBRACKETOPERPARMS -DLISTFRIENDFIX -c column_sscanf.cpp -o column_sscanf.o
x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe  -DCHARFUNCMACROS -DINCTEMPLATEDEFNS -DBOOLPREDEFINED -DBRACKETOPERPARMS -DLISTFRIENDFIX -c DisjointSets.cpp -o DisjointSets.o
Loading libtoolclasses.a ... 
done
make[1]: Leaving directory '/var/tmp/portage/sci-chemistry/reduce-3.16.111118/work/toolclasses'
making all in /libpdb...
make[1]: Entering directory '/var/tmp/portage/sci-chemistry/reduce-3.16.111118/work/libpdb'
x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe  -DBOOLPREDEFINED -DHASSSCANFEXTERN -c pdb_read.cpp -o pdb_read.o
x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe  -DBOOLPREDEFINED -DHASSSCANFEXTERN -c pdb_sprntf.cpp -o pdb_sprntf.o
x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe  -DBOOLPREDEFINED -DHASSSCANFEXTERN -c pdb_sscanf.cpp -o pdb_sscanf.o
x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe  -DBOOLPREDEFINED -DHASSSCANFEXTERN -c pdb_chars.cpp -o pdb_chars.o
x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe  -DBOOLPREDEFINED -DHASSSCANFEXTERN -c pdb_type.cpp -o pdb_type.o
x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe  -DBOOLPREDEFINED -DHASSSCANFEXTERN -c pdb++.cpp -o pdb++.o
x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe  -DBOOLPREDEFINED -DHASSSCANFEXTERN -c pdbinput.cpp -o pdbinput.o
Loading libpdb++.a ... 
done
make[1]: Leaving directory '/var/tmp/portage/sci-chemistry/reduce-3.16.111118/work/libpdb'
making all in /reduce_src...
make[1]: Entering directory '/var/tmp/portage/sci-chemistry/reduce-3.16.111118/work/reduce_src'
x86_64-pc-linux-gnu-g++ -c GraphToHoldScores.cpp -march=native -O2 -pipe  -DAROMATICS_ACCEPT_HBONDS -DCHARFUNCMACROS -DBOOLPREDEFINED  -DBRACKETOPERPARMS -DLEFT_JUSTIFY_NUC_RES_OK -DLISTFRIENDFIX -DINCTEMPLATEDEFNS -DHET_DICTIONARY='"//usr/share/reduce/reduce_wwPDB_het_dict.txt"' -DHET_DICTOLD='"//usr/share/reduce/reduce_het_dict.txt"' -I../libpdb -I../toolclasses 
GraphToHoldScores.cpp: In member function ‘int DegreeTwoEdge_ths::whichVertex(int) const’:
GraphToHoldScores.cpp:1152:88: error: no match for ‘operator<<’ (operand types are ‘std::basic_ostream<char>’ and ‘std::ostream {aka std::basic_ostream<char>}’)
  << "CRITICAL ERROR IN whichVertex(" << vertex_index << ") called on edge [" <<
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~
  << vertex_indices_[ 0 ] << ", " << vertex_indices_[ 1 ] << "]" << std::endl;
                                                                               
In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/iostream:39:0,
                 from ../toolclasses/Point3d.h:19,
                 from AtomDescr.h:10,
                 from GraphToHoldScores.h:11,
                 from GraphToHoldScores.cpp:1:
/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/ostream:628:5: note: candidate: std::basic_ostream<_CharT, _Traits>& std::operator<<(std::basic_ostream<_CharT, _Traits>&&, const _Tp&) [with _CharT = char; _Traits = std::char_traits<char>; _Tp = std::basic_ostream<char>] <near match>
     operator<<(basic_ostream<_CharT, _Traits>&& __os, const _Tp& __x)
     ^~~~~~~~
/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/ostream:628:5: note:   conversion of argument 1 would be ill-formed:
GraphToHoldScores.cpp:1152:64: error: cannot bind ‘std::basic_ostream<char>’ lvalue to ‘std::basic_ostream<char>&&’
  std::cerr << "CRITICAL ERROR IN whichVertex(" << vertex_index << ") called on edge [" <<
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
GraphToHoldScores.cpp:1152:88: note: candidate: operator<<(int, int) <built-in>
  << "CRITICAL ERROR IN whichVertex(" << vertex_index << ") called on edge [" <<
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~
  << vertex_indices_[ 0 ] << ", " << vertex_indices_[ 1 ] << "]" << std::endl;
                                                                               
GraphToHoldScores.cpp:1152:88: note:   no known conversion for argument 2 from ‘std::ostream {aka std::basic_ostream<char>}’ to ‘int’
In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/iostream:39:0,
                 from ../toolclasses/Point3d.h:19,
                 from AtomDescr.h:10,
                 from GraphToHoldScores.h:11,
                 from GraphToHoldScores.cpp:1:
/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/ostream:108:7: note: candidate: std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(std::basic_ostream<_CharT, _Traits>::__ostream_type& (*)(std::basic_ostream<_CharT, _Traits>::__ostream_type&)) [with _CharT = char; _Traits = std::char_traits<char>; std::basic_ostream<_CharT, _Traits>::__ostream_type = std::basic_ostream<char>]
       operator<<(__ostream_type& (*__pf)(__ostream_type&))
       ^~~~~~~~
/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/ostream:108:7: note:   no known conversion for argument 1 from ‘std::ostream {aka std::basic_ostream<char>}’ to ‘std::basic_ostream<char>::__ostream_type& (*)(std::basic_ostream<char>::__ostream_type&) {aka std::basic_ostream<char>& (*)(std::basic_ostream<char>&)}’
/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/ostream:117:7: note: candidate: std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(std::basic_ostream<_CharT, _Traits>::__ios_type& (*)(std::basic_ostream<_CharT, _Traits>::__ios_type&)) [with _CharT = char; _Traits = std::char_traits<char>; std::basic_ostream<_CharT, _Traits>::__ostream_type = std::basic_ostream<char>; std::basic_ostream<_CharT, _Traits>::__ios_type = std::basic_ios<char>]
       operator<<(__ios_type& (*__pf)(__ios_type&))
       ^~~~~~~~
/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/ostream:117:7: note:   no known conversion for argument 1 from ‘std::ostream {aka std::basic_ostream<char>}’ to ‘std::basic_ostream<char>::__ios_type& (*)(std::basic_ostream<char>::__ios_type&) {aka std::basic_ios<char>& (*)(std::basic_ios<char>&)}’
/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/ostream:127:7: note: candidate: std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(std::ios_base& (*)(std::ios_base&)) [with _CharT = char; _Traits = std::char_traits<char>; std::basic_ostream<_CharT, _Traits>::__ostream_type = std::basic_ostream<char>]
       operator<<(ios_base& (*__pf) (ios_base&))
       ^~~~~~~~
/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/ostream:127:7: note:   no known conversion for argument 1 from ‘std::ostream {aka std::basic_ostream<char>}’ to ‘std::ios_base& (*)(std::ios_base&)’
/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/ostream:166:7: note: candidate: std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(long int) [with _CharT = char; _Traits = std::char_traits<char>; std::basic_ostream<_CharT, _Traits>::__ostream_type = std::basic_ostream<char>]
       operator<<(long __n)
       ^~~~~~~~
/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/ostream:166:7: note:   no known conversion for argument 1 from ‘std::ostream {aka std::basic_ostream<char>}’ to ‘long int’
/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/ostream:170:7: note: candidate: std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(long unsigned int) [with _CharT = char; _Traits = std::char_traits<char>; std::basic_ostream<_CharT, _Traits>::__ostream_type = std::basic_ostream<char>]
       operator<<(unsigned long __n)
       ^~~~~~~~
/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/ostream:170:7: note:   no known conversion for argument 1 from ‘std::ostream {aka std::basic_ostream<char>}’ to ‘long unsigned int’
/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/ostream:174:7: note: candidate: std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(bool) [with _CharT = char; _Traits = std::char_traits<char>; std::basic_ostream<_CharT, _Traits>::__ostream_type = std::basic_ostream<char>]
       operator<<(bool __n)
       ^~~~~~~~
/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/ostream:174:7: note:   no known conversion for argument 1 from ‘std::ostream {aka std::basic_ostream<char>}’ to ‘bool’
In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/ostream:638:0,
                 from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/iostream:39,
                 from ../toolclasses/Point3d.h:19,
                 from AtomDescr.h:10,
                 from GraphToHoldScores.h:11,
                 from GraphToHoldScores.cpp:1:
/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/bits/ostream.tcc:91:5: note: candidate: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(short int) [with _CharT = char; _Traits = std::char_traits<char>]
     basic_ostream<_CharT, _Traits>::
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/bits/ostream.tcc:91:5: note:   no known conversion for argument 1 from ‘std::ostream {aka std::basic_ostream<char>}’ to ‘short int’
In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/iostream:39:0,
                 from ../toolclasses/Point3d.h:19,
                 from AtomDescr.h:10,
                 from GraphToHoldScores.h:11,
                 from GraphToHoldScores.cpp:1:
/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/ostream:181:7: note: candidate: std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(short unsigned int) [with _CharT = char; _Traits = std::char_traits<char>; std::basic_ostream<_CharT, _Traits>::__ostream_type = std::basic_ostream<char>]
       operator<<(unsigned short __n)
       ^~~~~~~~
/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/ostream:181:7: note:   no known conversion for argument 1 from ‘std::ostream {aka std::basic_ostream<char>}’ to ‘short unsigned int’
In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/ostream:638:0,
                 from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/iostream:39,
                 from ../toolclasses/Point3d.h:19,
                 from AtomDescr.h:10,
                 from GraphToHoldScores.h:11,
                 from GraphToHoldScores.cpp:1:
/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/bits/ostream.tcc:105:5: note: candidate: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(int) [with _CharT = char; _Traits = std::char_traits<char>]
     basic_ostream<_CharT, _Traits>::
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/bits/ostream.tcc:105:5: note:   no known conversion for argument 1 from ‘std::ostream {aka std::basic_ostream<char>}’ to ‘int’
In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/iostream:39:0,
                 from ../toolclasses/Point3d.h:19,
                 from AtomDescr.h:10,
                 from GraphToHoldScores.h:11,
                 from GraphToHoldScores.cpp:1:
/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/ostream:192:7: note: candidate: std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(unsigned int) [with _CharT = char; _Traits = std::char_traits<char>; std::basic_ostream<_CharT, _Traits>::__ostream_type = std::basic_ostream<char>]
       operator<<(unsigned int __n)
       ^~~~~~~~
/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/ostream:192:7: note:   no known conversion for argument 1 from ‘std::ostream {aka std::basic_ostream<char>}’ to ‘unsigned int’
/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/ostream:201:7: note: candidate: std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(long long int) [with _CharT = char; _Traits = std::char_traits<char>; std::basic_ostream<_CharT, _Traits>::__ostream_type = std::basic_ostream<char>]
       operator<<(long long __n)
       ^~~~~~~~
/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/ostream:201:7: note:   no known conversion for argument 1 from ‘std::ostream {aka std::basic_ostream<char>}’ to ‘long long int’
/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/ostream:205:7: note: candidate: std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(long long unsigned int) [with _CharT = char; _Traits = std::char_traits<char>; std::basic_ostream<_CharT, _Traits>::__ostream_type = std::basic_ostream<char>]
       operator<<(unsigned long long __n)
       ^~~~~~~~
/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/ostream:205:7: note:   no known conversion for argument 1 from ‘std::ostream {aka std::basic_ostream<char>}’ to ‘long long unsigned int’
/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/ostream:220:7: note: candidate: std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(double) [with _CharT = char; _Traits = std::char_traits<char>; std::basic_ostream<_CharT, _Traits>::__ostream_type = std::basic_ostream<char>]
       operator<<(double __f)
       ^~~~~~~~
/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/ostream:220:7: note:   no known conversion for argument 1 from ‘std::ostream {aka std::basic_ostream<char>}’ to ‘double’
/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/ostream:224:7: note: candidate: std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(float) [with _CharT = char; _Traits = std::char_traits<char>; std::basic_ostream<_CharT, _Traits>::__ostream_type = std::basic_ostream<char>]
       operator<<(float __f)
       ^~~~~~~~
/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/ostream:224:7: note:   no known conversion for argument 1 from ‘std::ostream {aka std::basic_ostream<char>}’ to ‘float’
/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/ostream:232:7: note: candidate: std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(long double) [with _CharT = char; _Traits = std::char_traits<char>; std::basic_ostream<_CharT, _Traits>::__ostream_type = std::basic_ostream<char>]
       operator<<(long double __f)
       ^~~~~~~~
/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/ostream:232:7: note:   no known conversion for argument 1 from ‘std::ostream {aka std::basic_ostream<char>}’ to ‘long double’
/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/ostream:245:7: note: candidate: std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(const void*) [with _CharT = char; _Traits = std::char_traits<char>; std::basic_ostream<_CharT, _Traits>::__ostream_type = std::basic_ostream<char>]
       operator<<(const void* __p)
       ^~~~~~~~
/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/ostream:245:7: note:   no known conversion for argument 1 from ‘std::ostream {aka std::basic_ostream<char>}’ to ‘const void*’
In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/ostream:638:0,
                 from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/iostream:39,
                 from ../toolclasses/Point3d.h:19,
                 from AtomDescr.h:10,
                 from GraphToHoldScores.h:11,
                 from GraphToHoldScores.cpp:1:
/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/bits/ostream.tcc:119:5: note: candidate: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(std::basic_ostream<_CharT, _Traits>::__streambuf_type*) [with _CharT = char; _Traits = std::char_traits<char>; std::basic_ostream<_CharT, _Traits>::__streambuf_type = std::basic_streambuf<char>]
     basic_ostream<_CharT, _Traits>::
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/bits/ostream.tcc:119:5: note:   no known conversion for argument 1 from ‘std::ostream {aka std::basic_ostream<char>}’ to ‘std::basic_ostream<char>::__streambuf_type* {aka std::basic_streambuf<char>*}’
In file included from AtomDescr.h:10:0,
                 from GraphToHoldScores.h:11,
                 from GraphToHoldScores.cpp:1:
../toolclasses/Point3d.h:154:15: note: candidate: std::ostream& operator<<(std::ostream&, const Point3d&)
 std::ostream& operator<<(std::ostream&, const Point3d&);
               ^~~~~~~~
../toolclasses/Point3d.h:154:15: note:   no known conversion for argument 2 from ‘std::ostream {aka std::basic_ostream<char>}’ to ‘const Point3d&’
../toolclasses/Point3d.h:155:15: note: candidate: std::ostream& operator<<(std::ostream&, const Matrix4d&)
 std::ostream& operator<<(std::ostream&, const Matrix4d&);
               ^~~~~~~~
../toolclasses/Point3d.h:155:15: note:   no known conversion for argument 2 from ‘std::ostream {aka std::basic_ostream<char>}’ to ‘const Matrix4d&’
In file included from GraphToHoldScores.h:11:0,
                 from GraphToHoldScores.cpp:1:
AtomDescr.h:119:15: note: candidate: std::ostream& operator<<(std::ostream&, const AtomDescr&)
 std::ostream& operator<<(std::ostream& os, const AtomDescr& A);
               ^~~~~~~~
AtomDescr.h:119:15: note:   no known conversion for argument 2 from ‘std::ostream {aka std::basic_ostream<char>}’ to ‘const AtomDescr&’
GraphToHoldScores.cpp:452:1: note: candidate: std::ostream& operator<<(std::ostream&, const DotsForAtom&)
 operator << (std::ostream & os, DotsForAtom const & dots )
 ^~~~~~~~
GraphToHoldScores.cpp:452:1: note:   no known conversion for argument 2 from ‘std::ostream {aka std::basic_ostream<char>}’ to ‘const DotsForAtom&’
In file included from PDBrec.h:33:0,
                 from AtomPositions.h:19,
                 from GraphToHoldScores.cpp:2:
../libpdb/pdb++.h:539:1: note: candidate: std::ostream& operator<<(std::ostream&, const PDB&)
 operator<<(std::ostream &s, const PDB &p)
 ^~~~~~~~
../libpdb/pdb++.h:539:1: note:   no known conversion for argument 2 from ‘std::ostream {aka std::basic_ostream<char>}’ to ‘const PDB&’
In file included from AtomPositions.h:19:0,
                 from GraphToHoldScores.cpp:2:
PDBrec.h:299:22: note: candidate: std::ostream& operator<<(std::ostream&, const PDBrec&)
 inline std::ostream& operator << (std::ostream& s, const PDBrec& pdbrec) {
                      ^~~~~~~~
PDBrec.h:299:22: note:   no known conversion for argument 2 from ‘std::ostream {aka std::basic_ostream<char>}’ to ‘const PDBrec&’
In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/iostream:39:0,
                 from ../toolclasses/Point3d.h:19,
                 from AtomDescr.h:10,
                 from GraphToHoldScores.h:11,
                 from GraphToHoldScores.cpp:1:
/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/ostream:574:5: note: candidate: template<class _Traits> std::basic_ostream<char, _Traits>& std::operator<<(std::basic_ostream<char, _Traits>&, const unsigned char*)
     operator<<(basic_ostream<char, _Traits>& __out, const unsigned char* __s)
     ^~~~~~~~
/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/ostream:574:5: note:   template argument deduction/substitution failed:
GraphToHoldScores.cpp:1153:7: note:   cannot convert ‘std::cerr’ (type ‘std::ostream {aka std::basic_ostream<char>}’) to type ‘const unsigned char*’
  std::cerr << vertex_indices_[ 0 ] << ", " << vertex_indices_[ 1 ] << "]" << std::endl;
       ^~~~
In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/iostream:39:0,
                 from ../toolclasses/Point3d.h:19,
                 from AtomDescr.h:10,
                 from GraphToHoldScores.h:11,
                 from GraphToHoldScores.cpp:1:
/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/ostream:569:5: note: candidate: template<class _Traits> std::basic_ostream<char, _Traits>& std::operator<<(std::basic_ostream<char, _Traits>&, const signed char*)
     operator<<(basic_ostream<char, _Traits>& __out, const signed char* __s)
     ^~~~~~~~
/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/ostream:569:5: note:   template argument deduction/substitution failed:
GraphToHoldScores.cpp:1153:7: note:   cannot convert ‘std::cerr’ (type ‘std::ostream {aka std::basic_ostream<char>}’) to type ‘const signed char*’
  std::cerr << vertex_indices_[ 0 ] << ", " << vertex_indices_[ 1 ] << "]" << std::endl;
       ^~~~
In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/iostream:39:0,
                 from ../toolclasses/Point3d.h:19,
                 from AtomDescr.h:10,
                 from GraphToHoldScores.h:11,
                 from GraphToHoldScores.cpp:1:
/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/ostream:556:5: note: candidate: template<class _Traits> std::basic_ostream<char, _Traits>& std::operator<<(std::basic_ostream<char, _Traits>&, const char*)
     operator<<(basic_ostream<char, _Traits>& __out, const char* __s)
     ^~~~~~~~
/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/ostream:556:5: note:   template argument deduction/substitution failed:
GraphToHoldScores.cpp:1153:7: note:   cannot convert ‘std::cerr’ (type ‘std::ostream {aka std::basic_ostream<char>}’) to type ‘const char*’
  std::cerr << vertex_indices_[ 0 ] << ", " << vertex_indices_[ 1 ] << "]" << std::endl;
       ^~~~
In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/ostream:638:0,
                 from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/iostream:39,
                 from ../toolclasses/Point3d.h:19,
                 from AtomDescr.h:10,
                 from GraphToHoldScores.h:11,
                 from GraphToHoldScores.cpp:1:
/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/bits/ostream.tcc:321:5: note: candidate: template<class _CharT, class _Traits> std::basic_ostream<_CharT, _Traits>& std::operator<<(std::basic_ostream<_CharT, _Traits>&, const char*)
     operator<<(basic_ostream<_CharT, _Traits>& __out, const char* __s)
     ^~~~~~~~
/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/bits/ostream.tcc:321:5: note:   template argument deduction/substitution failed:
GraphToHoldScores.cpp:1153:7: note:   cannot convert ‘std::cerr’ (type ‘std::ostream {aka std::basic_ostream<char>}’) to type ‘const char*’
  std::cerr << vertex_indices_[ 0 ] << ", " << vertex_indices_[ 1 ] << "]" << std::endl;
       ^~~~
In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/iostream:39:0,
                 from ../toolclasses/Point3d.h:19,
                 from AtomDescr.h:10,
                 from GraphToHoldScores.h:11,
                 from GraphToHoldScores.cpp:1:
/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/ostream:539:5: note: candidate: template<class _CharT, class _Traits> std::basic_ostream<_CharT, _Traits>& std::operator<<(std::basic_ostream<_CharT, _Traits>&, const _CharT*)
     operator<<(basic_ostream<_CharT, _Traits>& __out, const _CharT* __s)
     ^~~~~~~~
/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/ostream:539:5: note:   template argument deduction/substitution failed:
GraphToHoldScores.cpp:1153:7: note:   mismatched types ‘const _CharT*’ and ‘std::basic_ostream<char>’
  std::cerr << vertex_indices_[ 0 ] << ", " << vertex_indices_[ 1 ] << "]" << std::endl;
       ^~~~
In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/iostream:39:0,
                 from ../toolclasses/Point3d.h:19,
                 from AtomDescr.h:10,
                 from GraphToHoldScores.h:11,
                 from GraphToHoldScores.cpp:1:
/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/ostream:519:5: note: candidate: template<class _Traits> std::basic_ostream<char, _Traits>& std::operator<<(std::basic_ostream<char, _Traits>&, unsigned char)
     operator<<(basic_ostream<char, _Traits>& __out, unsigned char __c)
     ^~~~~~~~
/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/ostream:519:5: note:   template argument deduction/substitution failed:
GraphToHoldScores.cpp:1153:7: note:   cannot convert ‘std::cerr’ (type ‘std::ostream {aka std::basic_ostream<char>}’) to type ‘unsigned char’
  std::cerr << vertex_indices_[ 0 ] << ", " << vertex_indices_[ 1 ] << "]" << std::endl;
       ^~~~
In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/iostream:39:0,
                 from ../toolclasses/Point3d.h:19,
                 from AtomDescr.h:10,
                 from GraphToHoldScores.h:11,
                 from GraphToHoldScores.cpp:1:
/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/ostream:514:5: note: candidate: template<class _Traits> std::basic_ostream<char, _Traits>& std::operator<<(std::basic_ostream<char, _Traits>&, signed char)
     operator<<(basic_ostream<char, _Traits>& __out, signed char __c)
     ^~~~~~~~
/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/ostream:514:5: note:   template argument deduction/substitution failed:
GraphToHoldScores.cpp:1153:7: note:   cannot convert ‘std::cerr’ (type ‘std::ostream {aka std::basic_ostream<char>}’) to type ‘signed char’
  std::cerr << vertex_indices_[ 0 ] << ", " << vertex_indices_[ 1 ] << "]" << std::endl;
       ^~~~
In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/iostream:39:0,
                 from ../toolclasses/Point3d.h:19,
                 from AtomDescr.h:10,
                 from GraphToHoldScores.h:11,
                 from GraphToHoldScores.cpp:1:
/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/ostream:508:5: note: candidate: template<class _Traits> std::basic_ostream<char, _Traits>& std::operator<<(std::basic_ostream<char, _Traits>&, char)
     operator<<(basic_ostream<char, _Traits>& __out, char __c)
     ^~~~~~~~
/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/ostream:508:5: note:   template argument deduction/substitution failed:
GraphToHoldScores.cpp:1153:7: note:   cannot convert ‘std::cerr’ (type ‘std::ostream {aka std::basic_ostream<char>}’) to type ‘char’
  std::cerr << vertex_indices_[ 0 ] << ", " << vertex_indices_[ 1 ] << "]" << std::endl;
       ^~~~
In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/iostream:39:0,
                 from ../toolclasses/Point3d.h:19,
                 from AtomDescr.h:10,
                 from GraphToHoldScores.h:11,
                 from GraphToHoldScores.cpp:1:
/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/ostream:502:5: note: candidate: template<class _CharT, class _Traits> std::basic_ostream<_CharT, _Traits>& std::operator<<(std::basic_ostream<_CharT, _Traits>&, char)
     operator<<(basic_ostream<_CharT, _Traits>& __out, char __c)
     ^~~~~~~~
/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/ostream:502:5: note:   template argument deduction/substitution failed:
GraphToHoldScores.cpp:1153:7: note:   cannot convert ‘std::cerr’ (type ‘std::ostream {aka std::basic_ostream<char>}’) to type ‘char’
  std::cerr << vertex_indices_[ 0 ] << ", " << vertex_indices_[ 1 ] << "]" << std::endl;
       ^~~~
In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/iostream:39:0,
                 from ../toolclasses/Point3d.h:19,
                 from AtomDescr.h:10,
                 from GraphToHoldScores.h:11,
                 from GraphToHoldScores.cpp:1:
/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/ostream:497:5: note: candidate: template<class _CharT, class _Traits> std::basic_ostream<_CharT, _Traits>& std::operator<<(std::basic_ostream<_CharT, _Traits>&, _CharT)
     operator<<(basic_ostream<_CharT, _Traits>& __out, _CharT __c)
     ^~~~~~~~
/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/ostream:497:5: note:   template argument deduction/substitution failed:
GraphToHoldScores.cpp:1153:7: note:   deduced conflicting types for parameter ‘_CharT’ (‘char’ and ‘std::basic_ostream<char>’)
  std::cerr << vertex_indices_[ 0 ] << ", " << vertex_indices_[ 1 ] << "]" << std::endl;
       ^~~~
In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/bits/ios_base.h:46:0,
                 from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/ios:42,
                 from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/ostream:38,
                 from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/iostream:39,
                 from ../toolclasses/Point3d.h:19,
                 from AtomDescr.h:10,
                 from GraphToHoldScores.h:11,
                 from GraphToHoldScores.cpp:1:
/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/system_error:209:5: note: candidate: template<class _CharT, class _Traits> std::basic_ostream<_CharT, _Traits>& std::operator<<(std::basic_ostream<_CharT, _Traits>&, const std::error_code&)
     operator<<(basic_ostream<_CharT, _Traits>& __os, const error_code& __e)
     ^~~~~~~~
/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/system_error:209:5: note:   template argument deduction/substitution failed:
GraphToHoldScores.cpp:1153:7: note:   cannot convert ‘std::cerr’ (type ‘std::ostream {aka std::basic_ostream<char>}’) to type ‘const std::error_code&’
  std::cerr << vertex_indices_[ 0 ] << ", " << vertex_indices_[ 1 ] << "]" << std::endl;
       ^~~~
In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/string:52:0,
                 from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/bits/locale_classes.h:40,
                 from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/bits/ios_base.h:41,
                 from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/ios:42,
                 from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/ostream:38,
                 from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/iostream:39,
                 from ../toolclasses/Point3d.h:19,
                 from AtomDescr.h:10,
                 from GraphToHoldScores.h:11,
                 from GraphToHoldScores.cpp:1:
/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/bits/basic_string.h:5325:5: note: candidate: template<class _CharT, class _Traits, class _Alloc> std::basic_ostream<_CharT, _Traits>& std::operator<<(std::basic_ostream<_CharT, _Traits>&, const std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&)
     operator<<(basic_ostream<_CharT, _Traits>& __os,
     ^~~~~~~~
/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/bits/basic_string.h:5325:5: note:   template argument deduction/substitution failed:
GraphToHoldScores.cpp:1153:7: note:   ‘std::ostream {aka std::basic_ostream<char>}’ is not derived from ‘const std::__cxx11::basic_string<_CharT, _Traits, _Alloc>’
  std::cerr << vertex_indices_[ 0 ] << ", " << vertex_indices_[ 1 ] << "]" << std::endl;
       ^~~~
make[1]: *** [Makefile:31: GraphToHoldScores.o] Error 1
make[1]: Leaving directory '/var/tmp/portage/sci-chemistry/reduce-3.16.111118/work/reduce_src'
make: *** [Makefile:9: all] Error 2
 * ERROR: sci-chemistry/reduce-3.16.111118::gentoo failed (compile phase):
 *   emake failed
 * 
 * If you need support, post the output of `emerge --info '=sci-chemistry/reduce-3.16.111118::gentoo'`,
 * the complete build log and the output of `emerge -pqv '=sci-chemistry/reduce-3.16.111118::gentoo'`.
 * The complete build log is located at '/var/log/portage/sci-chemistry:reduce-3.16.111118:20160918-093410.log'.
 * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-chemistry/reduce-3.16.111118/temp/build.log'.
 * The ebuild environment file is located at '/var/tmp/portage/sci-chemistry/reduce-3.16.111118/temp/environment'.
 * Working directory: '/var/tmp/portage/sci-chemistry/reduce-3.16.111118/work'
 * S: '/var/tmp/portage/sci-chemistry/reduce-3.16.111118/work/'