Compiling Cufflinks 2.1.1: Fatal error

[sindrle]

Getting tired of "segmentation 11" errors I started compiling Cufflinks on osx maverick.

Im using Boost version 1.47 and everything works until the final steps:

http://cufflinks.cbcb.umd.edu/tutorial.html#boost

typeing "make" inside "cufflinks-2.2.1" gives this error:

fatal error: too many errors emitted, stopping now [-ferror-limit=]
2 warnings and 20 errors generated.
make[2]: *** [clustering.o] Error 1
make[1]: *** [all-recursive] Error 1
make: *** [all] Error 2



Any help?

[maubp]

So there were 2 warnings and 20 errors, but unless you show us the error messages we can't help you. Usually the first error is most important for solving compilation problems.

[sindrle]

Oh, sorry! Often many people have the same problem and find a way to fix it, but maybe not for this errors..

$ make
/Applications/Xcode.app/Contents/Developer/usr/bin/make all-recursive
Making all in src
if g++ -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -arch x86_64 -O3 -DNDEBUG -pthread -I/usr/local/bin/boost_1_47_0/include -I/usr/local/include -I/usr/local/include/Eigen/include -MT clustering.o -MD -MP -MF ".deps/clustering.Tpo" -c -o clustering.o clustering.cpp; \
then mv -f ".deps/clustering.Tpo" ".deps/clustering.Po"; else rm -f ".deps/clustering.Tpo"; exit 1; fi
In file included from clustering.cpp:10:
In file included from ./clustering.h:38:
In file included from ./abundances.h:23:
./hits.h:244:25: error: implicit instantiation of undefined template
'std:air<int, int>'
gaps_out.push_back(make_pair(pos...
^
/usr/local/include/boost/fusion/adapted/std_pair.hpp:18:12: note: template is
declared here
struct pair;
^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/vector:700:62: note:
passing argument to parameter '__x' here
_LIBCPP_INLINE_VISIBILITY void push_back(const_reference __x);
^
In file included from clustering.cpp:10:
In file included from ./clustering.h:38:
In file included from ./abundances.h:23:
./hits.h:419:41: error: implicit instantiation of undefined template
'std:air<std::__1::__map_iterator<std::__1::__tree_iterator<std::__1::__value_type<unsigned
long long, RefSequenceTable::SequenceInfo>,
std::__1::__tree_node<std::__1::__value_type<unsigned long long,
RefSequenceTable::SequenceInfo>, void *> *, long> >, bool>'
pair<InvertedIDTable::iterator, bool> ret =
^
/usr/local/include/boost/fusion/adapted/std_pair.hpp:18:12: note: template is
declared here
struct pair;
^
In file included from clustering.cpp:10:
In file included from ./clustering.h:38:
In file included from ./abundances.h:23:
./hits.h:817:48: warning: field '_expression_file_name' will be initialized
after field '_ifs' [-Wreorder]
HitFactory(insert_table, reference_table), _expression_file_name(exp...
^
./hits.h:1097:16: error: implicit instantiation of undefined template
'std:air<int, int>'
pair<int,int> genomic_outer_span() const
^
/usr/local/include/boost/fusion/adapted/std_pair.hpp:18:12: note: template is
declared here
struct pair;
^
In file included from clustering.cpp:10:
In file included from ./clustering.h:38:
In file included from ./abundances.h:23:
./hits.h:1101:11: error: implicit instantiation of undefined template
'std:air<int, int>'
return make_pair(left(),
^
/usr/local/include/boost/fusion/adapted/std_pair.hpp:18:12: note: template is
declared here
struct pair;
^
In file included from clustering.cpp:10:
In file included from ./clustering.h:38:
In file included from ./abundances.h:23:
./hits.h:1105:10: error: implicit instantiation of undefined template
'std:air<int, int>'
return make_pair(-1,-1);
^
/usr/local/include/boost/fusion/adapted/std_pair.hpp:18:12: note: template is
declared here
struct pair;
^
In file included from clustering.cpp:10:
In file included from ./clustering.h:38:
In file included from ./abundances.h:23:
./hits.h:1108:16: error: implicit instantiation of undefined template
'std:air<int, int>'
pair<int,int> genomic_inner_span() const
^
/usr/local/include/boost/fusion/adapted/std_pair.hpp:18:12: note: template is
declared here
struct pair;
^
In file included from clustering.cpp:10:
In file included from ./clustering.h:38:
In file included from ./abundances.h:23:
./hits.h:1112:11: error: implicit instantiation of undefined template
'std:air<int, int>'
return make_pair(_left_alignment->right(),
^
/usr/local/include/boost/fusion/adapted/std_pair.hpp:18:12: note: template is
declared here
struct pair;
^
In file included from clustering.cpp:10:
In file included from ./clustering.h:38:
In file included from ./abundances.h:23:
./hits.h:1116:10: error: implicit instantiation of undefined template
'std:air<int, int>'
return make_pair(-1,-1);
^
/usr/local/include/boost/fusion/adapted/std_pair.hpp:18:12: note: template is
declared here
struct pair;
^
In file included from clustering.cpp:10:
In file included from ./clustering.h:38:
In file included from ./abundances.h:24:
./scaffolds.h:581:17: error: implicit instantiation of undefined template
'std:air<int, int>'
g.push_back(make_pair(ops[j].g_left(), o...
^
/usr/local/include/boost/fusion/adapted/std_pair.hpp:18:12: note: template is
declared here
struct pair;
^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/vector:700:62: note:
passing argument to parameter '__x' here
_LIBCPP_INLINE_VISIBILITY void push_back(const_reference __x);
^
In file included from clustering.cpp:10:
In file included from ./clustering.h:38:
In file included from ./abundances.h:25:
In file included from ./bundles.h:22:
In file included from ./gtf_tracking.h:12:
In file included from ./gff.h:10:
In file included from ./GFaSeqGet.h:3:
In file included from ./GList.hh:8:
./GVec.hh:744:6: warning: unused variable 'result' [-Wunused-variable]
int result=-1;
^
In file included from clustering.cpp:10:
In file included from ./clustering.h:38:
In file included from ./abundances.h:25:
./bundles.h:280:46: error: implicit instantiation of undefined template
'std:air<unsigned long long,
std::__1::__wrap_iter<boost::shared_ptr<Scaffold> *> >'
_ref_scaff_offsets.push_back(make_pair((*i)->ref_id(), i));
^
/usr/local/include/boost/fusion/adapted/std_pair.hpp:18:12: note: template is
declared here
struct pair;
^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/vector:700:62: note:
passing argument to parameter '__x' here
_LIBCPP_INLINE_VISIBILITY void push_back(const_reference __x);
^
In file included from clustering.cpp:10:
In file included from ./clustering.h:38:
In file included from ./abundances.h:25:
./bundles.h:299:47: error: implicit instantiation of undefined template
'std:air<unsigned long long,
std::__1::__wrap_iter<boost::shared_ptr<Scaffold> *> >'
_mask_scaff_offsets.push_back(make_pair((*i)->ref_id(), i));
^
/usr/local/include/boost/fusion/adapted/std_pair.hpp:18:12: note: template is
declared here
struct pair;
^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/vector:700:62: note:
passing argument to parameter '__x' here
_LIBCPP_INLINE_VISIBILITY void push_back(const_reference __x);
^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/vector:448:68: error:
implicit instantiation of undefined template 'std:air<int, int>'
__alloc_traits::destroy(__alloc(), _VSTD::__to_raw_pointer(--__end_));
^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/vector:372:29: note:
in instantiation of member function
'std::__1::__vector_base<std:air<int, int>,
std::__1::allocator<std:air<int, int> > >::__destruct_at_end' requested
here
void clear() _NOEXCEPT {__destruct_at_end(__begin_);}
^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/vector:752:17: note:
in instantiation of member function
'std::__1::__vector_base<std:air<int, int>,
std::__1::allocator<std:air<int, int> > >::clear' requested here
__base::clear();
^
./hits.h:235:12: note: in instantiation of member function
'std::__1::vector<std:air<int, int>, std::__1::allocator<std:air<int,
int> > >::clear' requested here
gaps_out.clear();
^
/usr/local/include/boost/fusion/adapted/std_pair.hpp:18:12: note: template is
declared here
struct pair;
^
In file included from clustering.cpp:10:
In file included from ./clustering.h:17:
In file included from /usr/local/include/boost/graph/vector_as_graph.hpp:19:
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/vector:1540:9: error:
implicit instantiation of undefined template 'std:air<int, int>'
++this->__end_;
^
./hits.h:244:15: note: in instantiation of member function
'std::__1::vector<std:air<int, int>, std::__1::allocator<std:air<int,
int> > >:ush_back' requested here
gaps_out.push_back(make_pair(pos...
^
/usr/local/include/boost/fusion/adapted/std_pair.hpp:18:12: note: template is
declared here
struct pair;
^
In file included from clustering.cpp:10:
In file included from ./clustering.h:17:
In file included from /usr/local/include/boost/graph/vector_as_graph.hpp:19:
In file included from /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/vector:265:
In file included from /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/__bit_reference:15:
In file included from /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/algorithm:627:
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/memory:1462:36: error:
implicit instantiation of undefined template 'std:air<int, int>'
::new ((void*)__p) _Tp(__a0);
^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/vector:1538:25: note:
in instantiation of function template specialization
'std::__1::allocator_traits<std::__1::allocator<std:air<int, int> >
>::construct<std:air<int, int>, std:air<int, int> >' requested here
__alloc_traits::construct(this->__alloc(),
^
./hits.h:244:15: note: in instantiation of member function
'std::__1::vector<std:air<int, int>, std::__1::allocator<std:air<int,
int> > >:ush_back' requested here
gaps_out.push_back(make_pair(pos...
^
/usr/local/include/boost/fusion/adapted/std_pair.hpp:18:12: note: template is
declared here
struct pair;
^
In file included from clustering.cpp:10:
In file included from ./clustering.h:17:
In file included from /usr/local/include/boost/graph/vector_as_graph.hpp:19:
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/vector:375:52: error:
implicit instantiation of undefined template 'std:air<int, int>'
{return static_cast<size_type>(__end_cap() - __begin_);}
^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/vector:476:57: note:
in instantiation of member function
'std::__1::__vector_base<std:air<int, int>,
std::__1::allocator<std:air<int, int> > >::capacity' requested here
__alloc_traits::deallocate(__alloc(), __begin_, capacity());
^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/iterator:1225:53: note:
in instantiation of member function
'std::__1::__vector_base<std:air<int, int>,
std::__1::allocator<std:air<int, int> > >::~__vector_base' requested
here
template <class _Tp, class _Alloc> friend class vector;
^
/usr/local/include/boost/fusion/adapted/std_pair.hpp:18:12: note: template is
declared here
struct pair;
^
In file included from clustering.cpp:10:
In file included from ./clustering.h:17:
In file included from /usr/local/include/boost/graph/vector_as_graph.hpp:19:
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/vector:656:53: error:
implicit instantiation of undefined template 'std:air<int, int>'
{return static_cast<size_type>(this->__end_ - this->__begin_);}
^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/vector:1156:25: note:
in instantiation of member function 'std::__1::vector<std:air<int, int>,
std::__1::allocator<std:air<int, int> > >::size' requested here
size_type __n = __x.size();
^
./scaffolds.h:584:10: note: in instantiation of member function
'std::__1::vector<std:air<int, int>, std::__1::allocator<std:air<int,
int> > >::vector' requested here
return g;
^
/usr/local/include/boost/fusion/adapted/std_pair.hpp:18:12: note: template is
declared here
struct pair;
^
In file included from clustering.cpp:10:
In file included from ./clustering.h:17:
In file included from /usr/local/include/boost/graph/vector_as_graph.hpp:19:
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/vector:876:40: error:
implicit instantiation of undefined template 'std:air<int, int>'
this->__end_cap() = this->__begin_ + __n;
^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/vector:1159:9: note:
in instantiation of member function 'std::__1::vector<std:air<int, int>,
std::__1::allocator<std:air<int, int> > >::allocate' requested here
allocate(__n);
^
./scaffolds.h:584:10: note: in instantiation of member function
'std::__1::vector<std:air<int, int>, std::__1::allocator<std:air<int,
int> > >::vector' requested here
return g;
^
/usr/local/include/boost/fusion/adapted/std_pair.hpp:18:12: note: template is
declared here
struct pair;
^
In file included from clustering.cpp:10:
In file included from ./clustering.h:17:
In file included from /usr/local/include/boost/graph/vector_as_graph.hpp:19:
In file included from /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/vector:265:
In file included from /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/__bit_reference:15:
In file included from /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/algorithm:627:
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/memory:1634:33: error:
implicit instantiation of undefined template 'std:air<int, int>'
{return size_type(~0) / sizeof(_Tp);}
^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/memory:1590:25: note:
in instantiation of member function 'std::__1::allocator<std:air<int,
int> >::max_size' requested here
{return __a.max_size();}
^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/memory:1487:17: note:
in instantiation of member function
'std::__1::allocator_traits<std::__1::allocator<std:air<int, int> >
>::__max_size' requested here
{return __max_size(__has_max_size<const allocator_type>(), __a);}
^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/vector:895:50: note:
in instantiation of member function
'std::__1::allocator_traits<std::__1::allocator<std:air<int, int> >
>::max_size' requested here
return _VSTD::min<size_type>(__alloc_traits::max_size(this->__alloc(...
^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/vector:873:15: note:
in instantiation of member function 'std::__1::vector<std:air<int, int>,
std::__1::allocator<std:air<int, int> > >::max_size' requested here
if (__n > max_size())
^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/vector:1159:9: note:
in instantiation of member function 'std::__1::vector<std:air<int, int>,
std::__1::allocator<std:air<int, int> > >::allocate' requested here
allocate(__n);
^
./scaffolds.h:584:10: note: in instantiation of member function
'std::__1::vector<std:air<int, int>, std::__1::allocator<std:air<int,
int> > >::vector' requested here
return g;
^
/usr/local/include/boost/fusion/adapted/std_pair.hpp:18:12: note: template is
declared here
struct pair;
^
In file included from clustering.cpp:10:
In file included from ./clustering.h:17:
In file included from /usr/local/include/boost/graph/vector_as_graph.hpp:19:
In file included from /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/vector:265:
In file included from /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/__bit_reference:15:
In file included from /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/algorithm:627:
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/memory:1630:59: error:
implicit instantiation of undefined template 'std:air<int, int>'
{return static_cast<pointer>(:perator new(__n * sizeof(_Tp)));}
^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/memory:1435:21: note:
in instantiation of member function 'std::__1::allocator<std:air<int,
int> >::allocate' requested here
{return __a.allocate(__n);}
^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/vector:875:53: note:
in instantiation of member function
'std::__1::allocator_traits<std::__1::allocator<std:air<int, int> >
>::allocate' requested here
this->__begin_ = this->__end_ = __alloc_traits::allocate(this->__all...
^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/vector:1159:9: note:
in instantiation of member function 'std::__1::vector<std:air<int, int>,
std::__1::allocator<std:air<int, int> > >::allocate' requested here
allocate(__n);
^
./scaffolds.h:584:10: note: in instantiation of member function
'std::__1::vector<std:air<int, int>, std::__1::allocator<std:air<int,
int> > >::vector' requested here
return g;
^
/usr/local/include/boost/fusion/adapted/std_pair.hpp:18:12: note: template is
declared here
struct pair;
^
fatal error: too many errors emitted, stopping now [-ferror-limit=]
2 warnings and 20 errors generated.
make[2]: *** [clustering.o] Error 1
make[1]: *** [all-recursive] Error 1
make: *** [all] Error 2

[GenoMax]

You are brave to try this on OS X

General plea for all: If anyone on this list knows developers for tuxedo suite - Can you please ask them to check the OS X binaries? Many are having trouble with this and other programs on OS X.

[sindrle]

Yes, I agree.. Lots of errors on Osx..

Tuxedo-suite 2.1.1 works like a charm!


NB!
Wrong title, I meant 2.2.1!!! How can I update the title..

[GenoMax]

NB!
Wrong title, I meant 2.2.1!!! How can I update the title..

Edit your post --> Go Advanced --> Should be able to edit the title once there.