yoshimasaono
commented
9 years ago checking whether the Boost::System library is available... no checking whether the Boost::Serialization library is available... no checking whether the Boost::Thread library is available... no
Should be yes. Make sure boost can be found.
./configure output:
user@user-HP:~/Downloads/bioinformatics/cufflinks-master$ ./configure --with-eigen=/usr/local/include/Eigen --with-boost=/home/user/Downloads/boost_1_55 checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking for gawk... (cached) gawk 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 whether gcc understands -c and -o together... yes checking dependency style of gcc... gcc3 checking whether make sets $(MAKE)... (cached) yes checking for ranlib... ranlib checking for ar... ar checking the archiver (ar) interface... ar checking for a Python interpreter with version >= 2.4... python checking for python... /usr/bin/python checking for python version... 2.7 checking for python platform... linux2 checking for python script directory... ${prefix}/lib/python2.7/dist-packages checking for python extension module directory... ${exec_prefix}/lib/python2.7/dist-packages checking for boostlib >= 1.47.0... yes checking for bamlib... yes checking build system type... x86_64-unknown-linux-gnu checking whether the Boost::System library is available... no checking whether the Boost::Serialization library is available... no checking whether the Boost::Thread library is available... no checking how to run the C preprocessor... gcc -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /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 if zlib is wanted... yes checking for inflateEnd in -lz... yes checking zlib.h usability... yes checking zlib.h presence... yes checking for zlib.h... yes checking for inflateEnd in -lz... (cached) yes checking zlib in /usr... ok checking for eigenlib... yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for unistd.h... (cached) yes checking for stdbool.h that conforms to C99... yes checking for _Bool... yes checking for inline... inline checking for pid_t... yes checking for size_t... yes checking for ptrdiff_t... yes checking host system type... x86_64-unknown-linux-gnu checking if gcc accepts -m64... yes checking for struct sysinfo.totalram... yes checking whether sysctl is declared... yes checking whether CTL_HW is declared... no checking whether HW_PHYSMEM is declared... no checking how to create a pax tar archive... gnutar checking dependency style of gcc... (cached) gcc3 checking dependency style of g++... (cached) gcc3 checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating config.h config.status: config.h is unchanged config.status: executing depfiles commands
-- cufflinks 2.2.1 Configuration Results -- C++ compiler: g++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -m64 -O3 -DNDEBUG -I/home/user/Downloads/boost_1_55/include -I/usr/local/include -I/usr/local/include/Eigen/include
GCC version: gcc (Ubuntu 4.8.2-19ubuntu1) 4.8.2 Host System type: x86_64-unknown-linux-gnu Install prefix: /usr/local Install eprefix: ${prefix}
See config.h for further configuration information. Email cole@cs.umd.edu with questions and bug reports.
-- cufflinks 2.2.1 Configuration Results -- C++ compiler: g++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -m64 -O3 -DNDEBUG -pthread -I/usr/include -I/usr/local/include
GCC version: gcc (Ubuntu 4.8.2-19ubuntu1) 4.8.2 Host System type: x86_64-unknown-linux-gnu Install prefix: /usr/local Install eprefix: ${prefix}
See config.h for further configuration information. Email cole@cs.umd.edu with questions and bug reports.
make output:
user@user-HP:~/Downloads/bioinformatics/cufflinks-master$ make make all-recursive make[1]: Entering directory&, boost::numeric::ublas::dense_proxy_tag, boost::numeric::ublas::row_major_tag)’:
../boost/numeric/ublas/detail/matrix_assign.hpp:1262:39: warning: typedef ‘size_type’ locally defined but not used [-Wunused-local-typedefs]
typedef typename M::size_type size_type;
^
../boost/numeric/ublas/detail/matrix_assign.hpp: In function ‘void boost::numeric::ublas::matrix_swap(M&, boost::numeric::ublas::matrix_expression&, boost::numeric::ublas::dense_proxy_tag, boost::numeric::ublas::column_major_tag)’:
../boost/numeric/ublas/detail/matrix_assign.hpp:1288:39: warning: typedef ‘size_type’ locally defined but not used [-Wunused-local-typedefs]
typedef typename M::size_type size_type;
^
In file included from abundances.h:23:0,
from abundances.cpp:16:
hits.h: In constructor ‘PrecomputedExpressionHitFactory::PrecomputedExpressionHitFactory(const string&, ReadTable&, RefSequenceTable&)’:
hits.h:928:12: warning: ‘PrecomputedExpressionHitFactory::_expression_file_name’ will be initialized after [-Wreorder]
string _expression_file_name;
^
hits.h:927:19: warning: ‘std::ifstream PrecomputedExpressionHitFactory::_ifs’ [-Wreorder]
std::ifstream _ifs;
^
In file included from abundances.h:23:0,
from abundances.cpp:16:
hits.h:814:5: warning: when initialized here [-Wreorder]
PrecomputedExpressionHitFactory(const string& expression_file_name,
^
In file included from abundances.cpp:43:0:
replicates.h: In member function ‘bool ReplicatedBundleFactory::next_bundle(HitBundle&, bool)’:
replicates.h:224:57: warning: unused variable ‘s2’ [-Wunused-variable]
const vectorboost::shared_ptr& s2 = bundles[i-1]->ref_scaffolds();
^
In file included from abundances.cpp:44:0:
sampling.h: In function ‘double boost::numeric::ublas::cholesky_factorize(M&)’:
sampling.h:50:13: warning: typedef ‘matrix_type’ locally defined but not used [-Wunused-local-typedefs]
typedef M matrix_type;
^
In file included from abundances.cpp:44:0:
sampling.h: In function ‘void boost::numeric::ublas::cholesky_substitute(const M&, boost::numeric::ublas::vector_expression&)’:
sampling.h:113:19: warning: typedef ‘const_matrix_type’ locally defined but not used [-Wunused-local-typedefs]
typedef const M const_matrix_type;
^
sampling.h:114:42: warning: typedef ‘vector_type’ locally defined but not used [-Wunused-local-typedefs]
typedef vector vector_type;
^
sampling.h: In function ‘void boost::numeric::ublas::cholesky_substitute(const M&, boost::numeric::ublas::matrix_expression&)’:
sampling.h:120:19: warning: typedef ‘const_matrix_type’ locally defined but not used [-Wunused-local-typedefs]
typedef const M const_matrix_type;
^
sampling.h:121:42: warning: typedef ‘matrix_type’ locally defined but not used [-Wunused-local-typedefs]
typedef matrix matrix_type;
^
sampling.h: In function ‘void boost::numeric::ublas::cholesky_substitute_left(boost::numeric::ublas::vector_expression&, const M&)’:
sampling.h:127:19: warning: typedef ‘const_matrix_type’ locally defined but not used [-Wunused-local-typedefs]
typedef const M const_matrix_type;
^
sampling.h:128:42: warning: typedef ‘vector_type’ locally defined but not used [-Wunused-local-typedefs]
typedef vector vector_type;
^
sampling.h: In function ‘void boost::numeric::ublas::cholesky_substitute_left(boost::numeric::ublas::matrix_expression&, const M&)’:
sampling.h:134:19: warning: typedef ‘const_matrix_type’ locally defined but not used [-Wunused-local-typedefs]
typedef const M const_matrix_type;
^
sampling.h:135:42: warning: typedef ‘matrix_type’ locally defined but not used [-Wunused-local-typedefs]
typedef matrix matrix_type;
^
abundances.cpp: In constructor ‘AbundanceGroup::AbundanceGroup(const std::vectorboost::shared_ptr&, const boost::numeric::ublas::matrix&, const boost::numeric::ublas::matrix&, const boost::numeric::ublas::matrix&, const boost::numeric::ublas::matrix&, const std::set<boost::shared_ptr >&)’:
abundances.cpp:518:61: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (no_js_tests == false && _read_group_props.size() >= min_reps_for_js_test)
^
abundances.cpp: In member function ‘virtual AbundanceStatus AbundanceGroup::status() const’:
abundances.cpp:526:10: warning: variable ‘has_lowdata_member’ set but not used [-Wunused-but-set-variable]
bool has_lowdata_member = false;
^
abundances.cpp: In member function ‘void AbundanceGroup::collect_per_replicate_mass(const std::vector&, std::vectorboost::shared_ptr&)’:
abundances.cpp:1043:20: warning: unused variable ‘curr_mass’ [-Wunused-variable]
double curr_mass = inserted.first->second;
^
abundances.cpp: In function ‘void collapse_equivalent_hits(const std::vector&, std::vectorboost::shared_ptr&, std::vector&, std::vector&, bool)’:
abundances.cpp:1160:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t j = 0; j < N; ++j)
^
abundances.cpp:1347:44: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i = 0 ; i < nr_alignments.size(); ++i)
^
abundances.cpp: In function ‘AbundanceStatus bootstrap_gamma_mle(const std::vectorboost::shared_ptr&, const std::vector&, const std::vector&, boost::numeric::ublas::vector<double, boost::numeric::ublas::unbounded_array<double, std::allocator > >&, boost::numeric::ublas::matrix&, double&)’:
abundances.cpp:1488:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t i = 0; i < num_bootstrap_samples; ++i)
^
abundances.cpp:1491:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t j = 0; j < num_sample_frags; ++j)
^
abundances.cpp:1505:48: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
sample_idxs[curr_sample] >= processed_hits &&
^
abundances.cpp: In function ‘bool generate_count_assignment_samples(int, const std::vector&, const boost::numeric::ublas::matrix&, std::vector<boost::numeric::ublas::vector<double, boost::numeric::ublas::unbounded_array<double, std::allocator > > >&)’:
abundances.cpp:1693:46: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t assign_idx = 0; assign_idx < num_draws; ++assign_idx)
^
abundances.cpp: In function ‘void calculate_gamma_mle_covariance(const std::map<boost::shared_ptr, boost::shared_ptr >&, boost::numeric::ublas::vector<double, boost::numeric::ublas::unbounded_array<double, std::allocator > >&, boost::numeric::ublas::matrix&)’:
abundances.cpp:1760:64: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int j = 0; j < all_assigned_count_samples[i].size(); ++j)
^
abundances.cpp:1775:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t i = 0; i < num_transcripts; ++i)
^
abundances.cpp:1777:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t j = 0; j < num_transcripts; ++j)
^
abundances.cpp: In function ‘void calculate_fragment_assignment_distribution(const std::map<boost::shared_ptr, boost::shared_ptr >&, boost::numeric::ublas::vector<double, boost::numeric::ublas::unbounded_array<double, std::allocator > >&, boost::numeric::ublas::matrix&, std::vector<boost::numeric::ublas::vector<double, boost::numeric::ublas::unbounded_array<double, std::allocator > > >&)’:
abundances.cpp:1870:64: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int j = 0; j < all_assigned_count_samples[i].size(); ++j)
^
abundances.cpp:1885:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t i = 0; i < num_transcripts; ++i)
^
abundances.cpp:1887:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t j = 0; j < num_transcripts; ++j)
^
abundances.cpp: In member function ‘void AbundanceGroup::calculate_abundance_group_variance(const std::vectorboost::shared_ptr&, const std::map<boost::shared_ptr, boost::shared_ptr >&)’:
abundances.cpp:1968:65: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (no_js_tests == false && _read_group_props.size() >= min_reps_for_js_test)
^
abundances.cpp: In member function ‘void AbundanceGroup::aggregate_replicate_abundances(const std::map<boost::shared_ptr, boost::shared_ptr >&)’:
abundances.cpp:2070:58: warning: unused variable ‘sc_ab’ [-Wunused-variable]
const vectorboost::shared_ptr& sc_ab = itr->second->abundances();
^
abundances.cpp: In function ‘bool estimate_count_variance(long double&, double, double, double, double, double)’:
abundances.cpp:2277:17: warning: variable ‘bnb_mean’ set but not used [-Wunused-but-set-variable]
long double bnb_mean = 0.0;
^
abundances.cpp: In member function ‘void AbundanceGroup::generate_fpkm_samples()’:
abundances.cpp:2668:44: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t j = 0; j < sample.size(); ++j)
^
abundances.cpp: In member function ‘void AbundanceGroup::calculate_FPKM_covariance()’:
abundances.cpp:2783:42: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
if (length_i > 0 && length_j > 0 & M > 0)
^
abundances.cpp:2796:24: warning: unused variable ‘fpkm’ [-Wunused-variable]
double fpkm = _abundances[i]->FPKM();
^
abundances.cpp: In member function ‘void AbundanceGroup::calculate_conf_intervals()’:
abundances.cpp:2920:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t j = 0; j < N; ++j)
^
abundances.cpp:2939:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t j = 0; j < N; ++j)
^
abundances.cpp: In function ‘void calculate_assignment_probs(const VectorXd&, const MatrixXd&, const VectorXd&, Eigen::MatrixXd&)’:
abundances.cpp:3352:58: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t i = 0; i < alignment_multiplicities.size(); ++i)
^
abundances.cpp: In function ‘void calculate_average_assignment_probs(const VectorXd&, const MatrixXd&, const VectorXd&, Eigen::MatrixXd&)’:
abundances.cpp:3378:58: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t i = 0; i < alignment_multiplicities.size(); ++i)
^
abundances.cpp:3393:58: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t i = 0; i < alignment_multiplicities.size(); ++i)
^
abundances.cpp:3395:53: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t j = 0; j < proposed_gammas.size(); ++j)
^
abundances.cpp:3408:49: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t j = 0; j < proposed_gammas.size(); ++j)
^
abundances.cpp: In function ‘bool is_identifiable(M&, PM&)’:
abundances.cpp:4254:15: warning: typedef ‘matrix_type’ locally defined but not used [-Wunused-local-typedefs]
typedef M matrix_type;
^
abundances.cpp: In function ‘AbundanceStatus gamma_mle(const std::vectorboost::shared_ptr&, const std::vector&, const std::vector&, std::vector&, bool)’:
abundances.cpp:4322:48: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t j = 0; j < cond_probs.rows(); ++j)
^
abundances.cpp:4324:52: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t i = 0; i < cond_probs.cols(); ++i)
^
abundances.cpp:4318:10: warning: variable ‘logL’ set but not used [-Wunused-but-set-variable]
double logL;
^
In file included from /usr/include/c++/4.8/bits/stl_algobase.h:64:0,
from /usr/include/c++/4.8/vector:60,
from abundances.h:17,
from abundances.cpp:16:
/usr/include/c++/4.8/bits/stl_pair.h: In instantiation of ‘std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with U1 = const void; _U2 = boost::shared_ptr; T1 = const void const; _T2 = boost::shared_ptr]’:
../boost/serialization/shared_ptr_helper.hpp:181:20: required from ‘void boost::serialization::shared_ptrhelper::reset(SPT&, T ) [with T = const ReadGroupProperties; SPT = boost::shared_ptr]’
../boost/serialization/shared_ptr.hpp:171:5: required from ‘void boost::serialization::load(Archive&, boost::shared_ptr&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = const ReadGroupProperties]’
../boost/serialization/split_free.hpp:58:22: required from ‘static void boost::serialization::free_loader<Archive, T>::invoke(Archive&, T&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = boost::shared_ptr]’
../boost/serialization/split_free.hpp:74:38: required from ‘void boost::serialization::split_free(Archive&, T&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = boost::shared_ptr]’
../boost/serialization/shared_ptr.hpp:187:57: required from ‘void boost::serialization::serialize(Archive&, boost::shared_ptr&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = const ReadGroupProperties]’
../boost/serialization/serialization.hpp:128:27: [ skipping 57 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
../boost/serialization/export.hpp:86:1: required from ‘struct boost::archive::detail::ptr_serialization_support<boost::archive::binary_iarchive, AbundanceGroup>’
../boost/archive/detail/register_archive.hpp:25:8: required from ‘struct boost::archive::detail::_ptr_serialization_support<boost::archive::binary_iarchive, AbundanceGroup>’
../boost/archive/binary_iarchive.hpp:57:1: required by substitution of ‘template typename boost::archive::detail::_ptr_serialization_support<boost::archive::binary_iarchive, Serializable>::type boost::archive::detail::instantiate_ptrserialization(Serializable, boost::archive::binary_iarchive, boost::archive::detail::adl_tag) [with Serializable = AbundanceGroup]’
../boost/serialization/export.hpp:132:58: required from ‘void boost::archive::detail::extra_detail::guid_initializer::exportguid(mpl::false) const [with T = AbundanceGroup; mpl::false = mpl::bool_]’
../boost/serialization/export.hpp:142:61: required from ‘const boost::archive::detail::extra_detail::guid_initializer& boost::archive::detail::extra_detail::guid_initializer::export_guid() const [with T = AbundanceGroup]’
abundances.cpp:5162:1: required from here
/usr/include/c++/4.8/bits/stl_pair.h:119:39: error: no matching function for call to ‘boost::shared_ptr::shared_ptr(const boost::shared_ptr&)’
: first(p.first), second(p.second) { }
^
/usr/include/c++/4.8/bits/stl_pair.h:119:39: note: candidates are:
In file included from ../boost/shared_ptr.hpp:17:0,
from hits.h:19,
from abundances.h:23,
from abundances.cpp:16:
../boost/smart_ptr/shared_ptr.hpp:467:14: note: template boost::shared_ptr::shared_ptr(Ap, typename boost::detail::sp_enable_if_auto_ptr<Ap, int>::type)
explicit shared_ptr( Ap r, typename boost::detail::sp_enable_if_auto_ptr<Ap, int>::type = 0 ): px( r.get() ), pn()
^
../boost/smart_ptr/shared_ptr.hpp:467:14: note: template argument deduction/substitution failed:
../boost/smart_ptr/shared_ptr.hpp: In substitution of ‘template boost::shared_ptr::shared_ptr(Ap, typename boost::detail::sp_enable_if_auto_ptr<Ap, int>::type) [with Ap = boost::shared_ptr]’:
/usr/include/c++/4.8/bits/stl_pair.h:119:39: required from ‘std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with U1 = const void; _U2 = boost::shared_ptr; T1 = const void const; _T2 = boost::shared_ptr]’
../boost/serialization/shared_ptr_helper.hpp:181:20: required from ‘void boost::serialization::shared_ptrhelper::reset(SPT&, T ) [with T = const ReadGroupProperties; SPT = boost::shared_ptr]’
../boost/serialization/shared_ptr.hpp:171:5: required from ‘void boost::serialization::load(Archive&, boost::shared_ptr&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = const ReadGroupProperties]’
../boost/serialization/split_free.hpp:58:22: required from ‘static void boost::serialization::free_loader<Archive, T>::invoke(Archive&, T&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = boost::shared_ptr]’
../boost/serialization/split_free.hpp:74:38: required from ‘void boost::serialization::split_free(Archive&, T&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = boost::shared_ptr]’
../boost/serialization/shared_ptr.hpp:187:57: [ skipping 58 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
../boost/serialization/export.hpp:86:1: required from ‘struct boost::archive::detail::ptr_serialization_support<boost::archive::binary_iarchive, AbundanceGroup>’
../boost/archive/detail/register_archive.hpp:25:8: required from ‘struct boost::archive::detail::_ptr_serialization_support<boost::archive::binary_iarchive, AbundanceGroup>’
../boost/archive/binary_iarchive.hpp:57:1: required by substitution of ‘template typename boost::archive::detail::_ptr_serialization_support<boost::archive::binary_iarchive, Serializable>::type boost::archive::detail::instantiate_ptrserialization(Serializable, boost::archive::binary_iarchive , boost::archive::detail::adl_tag) [with Serializable = AbundanceGroup]’
../boost/serialization/export.hpp:132:58: required from ‘void boost::archive::detail::extra_detail::guid_initializer::exportguid(mpl::false) const [with T = AbundanceGroup; mpl::false = mpl::bool_]’
../boost/serialization/export.hpp:142:61: required from ‘const boost::archive::detail::extra_detail::guid_initializer& boost::archive::detail::extra_detail::guid_initializer::export_guid() const [with T = AbundanceGroup]’
abundances.cpp:5162:1: required from here
../boost/smart_ptr/shared_ptr.hpp:467:14: error: no type named ‘type’ in ‘struct boost::detail::sp_enable_if_auto_ptr<boost::shared_ptr, int>’
/usr/include/c++/4.8/bits/stl_pair.h: In instantiation of ‘std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with U1 = const void; _U2 = boost::shared_ptr; T1 = const void const; _T2 = boost::shared_ptr]’:
../boost/serialization/shared_ptr_helper.hpp:181:20: required from ‘void boost::serialization::shared_ptrhelper::reset(SPT&, T ) [with T = const ReadGroupProperties; SPT = boost::shared_ptr]’
../boost/serialization/shared_ptr.hpp:171:5: required from ‘void boost::serialization::load(Archive&, boost::shared_ptr&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = const ReadGroupProperties]’
../boost/serialization/split_free.hpp:58:22: required from ‘static void boost::serialization::free_loader<Archive, T>::invoke(Archive&, T&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = boost::shared_ptr]’
../boost/serialization/split_free.hpp:74:38: required from ‘void boost::serialization::split_free(Archive&, T&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = boost::shared_ptr]’
../boost/serialization/shared_ptr.hpp:187:57: required from ‘void boost::serialization::serialize(Archive&, boost::shared_ptr&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = const ReadGroupProperties]’
../boost/serialization/serialization.hpp:128:27: [ skipping 57 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
../boost/serialization/export.hpp:86:1: required from ‘struct boost::archive::detail::ptr_serialization_support<boost::archive::binary_iarchive, AbundanceGroup>’
../boost/archive/detail/register_archive.hpp:25:8: required from ‘struct boost::archive::detail::_ptr_serialization_support<boost::archive::binary_iarchive, AbundanceGroup>’
../boost/archive/binary_iarchive.hpp:57:1: required by substitution of ‘template typename boost::archive::detail::_ptr_serialization_support<boost::archive::binary_iarchive, Serializable>::type boost::archive::detail::instantiate_ptrserialization(Serializable, boost::archive::binary_iarchive, boost::archive::detail::adl_tag) [with Serializable = AbundanceGroup]’
../boost/serialization/export.hpp:132:58: required from ‘void boost::archive::detail::extra_detail::guid_initializer::exportguid(mpl::false) const [with T = AbundanceGroup; mpl::false = mpl::bool_]’
../boost/serialization/export.hpp:142:61: required from ‘const boost::archive::detail::extra_detail::guid_initializer& boost::archive::detail::extra_detail::guid_initializer::export_guid() const [with T = AbundanceGroup]’
abundances.cpp:5162:1: required from here
../boost/smart_ptr/shared_ptr.hpp:441:14: note: template boost::shared_ptr::shared_ptr(std::auto_ptr<_Tp1>&)
explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn()
^
../boost/smart_ptr/shared_ptr.hpp:441:14: note: template argument deduction/substitution failed:
In file included from /usr/include/c++/4.8/bits/stl_algobase.h:64:0,
from /usr/include/c++/4.8/vector:60,
from abundances.h:17,
from abundances.cpp:16:
/usr/include/c++/4.8/bits/stl_pair.h:119:39: note: types ‘std::auto_ptr’ and ‘const boost::shared_ptr’ have incompatible cv-qualifiers
: first(p.first), second(p.second) { }
^
In file included from ../boost/shared_ptr.hpp:17:0,
from hits.h:19,
from abundances.h:23,
from abundances.cpp:16:
../boost/smart_ptr/shared_ptr.hpp:434:5: note: template boost::shared_ptr::shared_ptr(const boost::shared_ptr&, boost::shared_ptr::elementtype)
shared_ptr( shared_ptr const & r, element_type * p ) BOOST_NOEXCEPT : px( p ), pn( r.pn )
^
../boost/smart_ptr/shared_ptr.hpp:434:5: note: template argument deduction/substitution failed:
In file included from /usr/include/c++/4.8/bits/stl_algobase.h:64:0,
from /usr/include/c++/4.8/vector:60,
from abundances.h:17,
from abundances.cpp:16:
/usr/include/c++/4.8/bits/stl_pair.h:119:39: note: candidate expects 2 arguments, 1 provided
: first(p.first), second(p.second) { }
^
In file included from ../boost/shared_ptr.hpp:17:0,
from hits.h:19,
from abundances.h:23,
from abundances.cpp:16:
../boost/smart_ptr/shared_ptr.hpp:420:5: note: template boost::shared_ptr::shared_ptr(const boost::shared_ptr&, typename boost::detail::sp_enable_if_convertible<Y, T>::type)
shared_ptr( shared_ptr const & r, typename boost::detail::sp_enable_if_convertible<Y,T>::type = boost::detail::sp_empty() )
^
../boost/smart_ptr/shared_ptr.hpp:420:5: note: template argument deduction/substitution failed:
../boost/smart_ptr/shared_ptr.hpp: In substitution of ‘template boost::shared_ptr::shared_ptr(const boost::shared_ptr&, typename boost::detail::sp_enable_if_convertible<Y, T>::type) [with Y = const ReadGroupProperties]’:
/usr/include/c++/4.8/bits/stl_pair.h:119:39: required from ‘std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with U1 = const void; _U2 = boost::shared_ptr; _T1 = const void* const; _T2 = boost::shared_ptr]’
../boost/serialization/shared_ptr_helper.hpp:181:20: required from ‘void boost::serialization::shared_ptrhelper::reset(SPT&, T ) [with T = const ReadGroupProperties; SPT = boost::shared_ptr]’
../boost/serialization/shared_ptr.hpp:171:5: required from ‘void boost::serialization::load(Archive&, boost::shared_ptr&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = const ReadGroupProperties]’
../boost/serialization/split_free.hpp:58:22: required from ‘static void boost::serialization::free_loader<Archive, T>::invoke(Archive&, T&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = boost::shared_ptr]’
../boost/serialization/split_free.hpp:74:38: required from ‘void boost::serialization::split_free(Archive&, T&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = boost::shared_ptr]’
../boost/serialization/shared_ptr.hpp:187:57: [ skipping 58 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
../boost/serialization/export.hpp:86:1: required from ‘struct boost::archive::detail::ptr_serialization_support<boost::archive::binary_iarchive, AbundanceGroup>’
../boost/archive/detail/register_archive.hpp:25:8: required from ‘struct boost::archive::detail::_ptr_serialization_support<boost::archive::binary_iarchive, AbundanceGroup>’
../boost/archive/binary_iarchive.hpp:57:1: required by substitution of ‘template typename boost::archive::detail::_ptr_serialization_support<boost::archive::binary_iarchive, Serializable>::type boost::archive::detail::instantiate_ptrserialization(Serializable, boost::archive::binary_iarchive , boost::archive::detail::adl_tag) [with Serializable = AbundanceGroup]’
../boost/serialization/export.hpp:132:58: required from ‘void boost::archive::detail::extra_detail::guid_initializer::exportguid(mpl::false) const [with T = AbundanceGroup; mpl::false = mpl::bool_]’
../boost/serialization/export.hpp:142:61: required from ‘const boost::archive::detail::extra_detail::guid_initializer& boost::archive::detail::extra_detail::guid_initializer::export_guid() const [with T = AbundanceGroup]’
abundances.cpp:5162:1: required from here
../boost/smart_ptr/shared_ptr.hpp:420:5: error: no type named ‘type’ in ‘struct boost::detail::sp_enable_if_convertible<const ReadGroupProperties, void>’
/usr/include/c++/4.8/bits/stl_pair.h: In instantiation of ‘std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with U1 = const void; _U2 = boost::shared_ptr; T1 = const void const; _T2 = boost::shared_ptr]’:
../boost/serialization/shared_ptr_helper.hpp:181:20: required from ‘void boost::serialization::shared_ptrhelper::reset(SPT&, T ) [with T = const ReadGroupProperties; SPT = boost::shared_ptr]’
../boost/serialization/shared_ptr.hpp:171:5: required from ‘void boost::serialization::load(Archive&, boost::shared_ptr&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = const ReadGroupProperties]’
../boost/serialization/split_free.hpp:58:22: required from ‘static void boost::serialization::free_loader<Archive, T>::invoke(Archive&, T&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = boost::shared_ptr]’
../boost/serialization/split_free.hpp:74:38: required from ‘void boost::serialization::split_free(Archive&, T&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = boost::shared_ptr]’
../boost/serialization/shared_ptr.hpp:187:57: required from ‘void boost::serialization::serialize(Archive&, boost::shared_ptr&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = const ReadGroupProperties]’
../boost/serialization/serialization.hpp:128:27: [ skipping 57 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
../boost/serialization/export.hpp:86:1: required from ‘struct boost::archive::detail::ptr_serialization_support<boost::archive::binary_iarchive, AbundanceGroup>’
../boost/archive/detail/register_archive.hpp:25:8: required from ‘struct boost::archive::detail::_ptr_serialization_support<boost::archive::binary_iarchive, AbundanceGroup>’
../boost/archive/binary_iarchive.hpp:57:1: required by substitution of ‘template typename boost::archive::detail::_ptr_serialization_support<boost::archive::binary_iarchive, Serializable>::type boost::archive::detail::instantiate_ptrserialization(Serializable, boost::archive::binary_iarchive, boost::archive::detail::adl_tag) [with Serializable = AbundanceGroup]’
../boost/serialization/export.hpp:132:58: required from ‘void boost::archive::detail::extra_detail::guid_initializer::exportguid(mpl::false) const [with T = AbundanceGroup; mpl::false = mpl::bool_]’
../boost/serialization/export.hpp:142:61: required from ‘const boost::archive::detail::extra_detail::guid_initializer& boost::archive::detail::extra_detail::guid_initializer::export_guid() const [with T = AbundanceGroup]’
abundances.cpp:5162:1: required from here
../boost/smart_ptr/shared_ptr.hpp:408:5: note: template boost::shared_ptr::shared_ptr(const boost::weak_ptr&, boost::detail::sp_nothrow_tag)
shared_ptr( weak_ptr const & r, boost::detail::sp_nothrow_tag )
^
../boost/smart_ptr/shared_ptr.hpp:408:5: note: template argument deduction/substitution failed:
In file included from /usr/include/c++/4.8/bits/stl_algobase.h:64:0,
from /usr/include/c++/4.8/vector:60,
from abundances.h:17,
from abundances.cpp:16:
/usr/include/c++/4.8/bits/stl_pair.h:119:39: note: ‘const boost::shared_ptr’ is not derived from ‘const boost::weak_ptr’
: first(p.first), second(p.second) { }
^
In file included from ../boost/shared_ptr.hpp:17:0,
from hits.h:19,
from abundances.h:23,
from abundances.cpp:16:
../boost/smart_ptr/shared_ptr.hpp:399:14: note: template boost::shared_ptr::shared_ptr(const boost::weak_ptr&)
explicit shared_ptr( weak_ptr const & r ): pn( r.pn ) // may throw
^
../boost/smart_ptr/shared_ptr.hpp:399:14: note: template argument deduction/substitution failed:
In file included from /usr/include/c++/4.8/bits/stl_algobase.h:64:0,
from /usr/include/c++/4.8/vector:60,
from abundances.h:17,
from abundances.cpp:16:
/usr/include/c++/4.8/bits/stl_pair.h:119:39: note: ‘const boost::shared_ptr’ is not derived from ‘const boost::weak_ptr’
: first(p.first), second(p.second) { }
^
In file included from ../boost/shared_ptr.hpp:17:0,
from hits.h:19,
from abundances.h:23,
from abundances.cpp:16:
../boost/smart_ptr/shared_ptr.hpp:373:41: note: template<class Y, class D, class A> boost::shared_ptr::sharedptr(Y, D, A)
template<class Y, class D, class A> shared_ptr( Y * p, D d, A a ): px( p ), pn( p, d, a )
^
../boost/smart_ptr/shared_ptr.hpp:373:41: note: template argument deduction/substitution failed:
In file included from /usr/include/c++/4.8/bits/stl_algobase.h:64:0,
from /usr/include/c++/4.8/vector:60,
from abundances.h:17,
from abundances.cpp:16:
/usr/include/c++/4.8/bits/stlpair.h:119:39: note: mismatched types ‘Y’ and ‘boost::shared_ptr’
: first(p.first), second(p.second) { }
^
In file included from ../boost/shared_ptr.hpp:17:0,
from hits.h:19,
from abundances.h:23,
from abundances.cpp:16:
../boost/smart_ptr/shared_ptr.hpp:358:32: note: template<class Y, class D> boost::shared_ptr::sharedptr(Y, D)
template<class Y, class D> shared_ptr( Y * p, D d ): px( p ), pn( p, d )
^
../boost/smart_ptr/shared_ptr.hpp:358:32: note: template argument deduction/substitution failed:
In file included from /usr/include/c++/4.8/bits/stl_algobase.h:64:0,
from /usr/include/c++/4.8/vector:60,
from abundances.h:17,
from abundances.cpp:16:
/usr/include/c++/4.8/bits/stlpair.h:119:39: note: mismatched types ‘Y’ and ‘boost::shared_ptr’
: first(p.first), second(p.second) { }
^
In file included from ../boost/shared_ptr.hpp:17:0,
from hits.h:19,
from abundances.h:23,
from abundances.cpp:16:
../boost/smart_ptr/shared_ptr.hpp:347:14: note: template boost::shared_ptr::sharedptr(Y)
explicit shared_ptr( Y * p ): px( p ), pn() // Y must be complete
^
../boost/smart_ptr/shared_ptr.hpp:347:14: note: template argument deduction/substitution failed:
In file included from /usr/include/c++/4.8/bits/stl_algobase.h:64:0,
from /usr/include/c++/4.8/vector:60,
from abundances.h:17,
from abundances.cpp:16:
/usr/include/c++/4.8/bits/stlpair.h:119:39: note: mismatched types ‘Y’ and ‘boost::shared_ptr’
: first(p.first), second(p.second) { }
^
In file included from ../boost/shared_ptr.hpp:17:0,
from hits.h:19,
from abundances.h:23,
from abundances.cpp:16:
../boost/smart_ptr/shared_ptr.hpp:334:5: note: boost::shared_ptr::shared_ptr() [with T = void]
shared_ptr() BOOST_NOEXCEPT : px( 0 ), pn() // never throws in 1.30+
^
../boost/smart_ptr/shared_ptr.hpp:334:5: note: candidate expects 0 arguments, 1 provided
../boost/smart_ptr/shared_ptr.hpp:323:25: note: boost::shared_ptr::shared_ptr(const boost::shared_ptr&)
template class shared_ptr
^
../boost/smart_ptr/shared_ptr.hpp:323:25: note: no known conversion for argument 1 from ‘const boost::shared_ptr’ to ‘const boost::shared_ptr&’
In file included from /usr/include/c++/4.8/bits/stl_algobase.h:64:0,
from /usr/include/c++/4.8/vector:60,
from abundances.h:17,
from abundances.cpp:16:
/usr/include/c++/4.8/bits/stl_pair.h: In instantiation of ‘std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with U1 = const void; _U2 = boost::shared_ptr; T1 = const void const; _T2 = boost::shared_ptr]’:
../boost/serialization/shared_ptr_helper.hpp:181:20: required from ‘void boost::serialization::shared_ptrhelper::reset(SPT&, T ) [with T = const EmpDist; SPT = boost::shared_ptr]’
../boost/serialization/shared_ptr.hpp:171:5: required from ‘void boost::serialization::load(Archive&, boost::shared_ptr&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = const EmpDist]’
../boost/serialization/split_free.hpp:58:22: required from ‘static void boost::serialization::free_loader<Archive, T>::invoke(Archive&, T&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = boost::shared_ptr]’
../boost/serialization/split_free.hpp:74:38: required from ‘void boost::serialization::split_free(Archive&, T&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = boost::shared_ptr]’
../boost/serialization/shared_ptr.hpp:187:57: required from ‘void boost::serialization::serialize(Archive&, boost::shared_ptr&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = const EmpDist]’
../boost/serialization/serialization.hpp:128:27: [ skipping 105 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
../boost/serialization/export.hpp:86:1: required from ‘struct boost::archive::detail::ptr_serialization_support<boost::archive::binary_iarchive, AbundanceGroup>’
../boost/archive/detail/register_archive.hpp:25:8: required from ‘struct boost::archive::detail::_ptr_serialization_support<boost::archive::binary_iarchive, AbundanceGroup>’
../boost/archive/binary_iarchive.hpp:57:1: required by substitution of ‘template typename boost::archive::detail::_ptr_serialization_support<boost::archive::binary_iarchive, Serializable>::type boost::archive::detail::instantiate_ptrserialization(Serializable, boost::archive::binary_iarchive , boost::archive::detail::adl_tag) [with Serializable = AbundanceGroup]’
../boost/serialization/export.hpp:132:58: required from ‘void boost::archive::detail::extra_detail::guid_initializer::exportguid(mpl::false) const [with T = AbundanceGroup; mpl::false = mpl::bool_]’
../boost/serialization/export.hpp:142:61: required from ‘const boost::archive::detail::extra_detail::guid_initializer& boost::archive::detail::extra_detail::guid_initializer::export_guid() const [with T = AbundanceGroup]’
abundances.cpp:5162:1: required from here
/usr/include/c++/4.8/bits/stl_pair.h:119:39: error: no matching function for call to ‘boost::shared_ptr::shared_ptr(const boost::shared_ptr&)’
: first(p.first), second(p.second) { }
^
/usr/include/c++/4.8/bits/stl_pair.h:119:39: note: candidates are:
In file included from ../boost/shared_ptr.hpp:17:0,
from hits.h:19,
from abundances.h:23,
from abundances.cpp:16:
../boost/smart_ptr/shared_ptr.hpp:467:14: note: template boost::shared_ptr::shared_ptr(Ap, typename boost::detail::sp_enable_if_auto_ptr<Ap, int>::type)
explicit shared_ptr( Ap r, typename boost::detail::sp_enable_if_auto_ptr<Ap, int>::type = 0 ): px( r.get() ), pn()
^
../boost/smart_ptr/shared_ptr.hpp:467:14: note: template argument deduction/substitution failed:
../boost/smart_ptr/shared_ptr.hpp: In substitution of ‘template boost::shared_ptr::shared_ptr(Ap, typename boost::detail::sp_enable_if_auto_ptr<Ap, int>::type) [with Ap = boost::shared_ptr]’:
/usr/include/c++/4.8/bits/stl_pair.h:119:39: required from ‘std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with U1 = const void; _U2 = boost::shared_ptr; T1 = const void const; _T2 = boost::shared_ptr]’
../boost/serialization/shared_ptr_helper.hpp:181:20: required from ‘void boost::serialization::shared_ptrhelper::reset(SPT&, T ) [with T = const EmpDist; SPT = boost::shared_ptr]’
../boost/serialization/shared_ptr.hpp:171:5: required from ‘void boost::serialization::load(Archive&, boost::shared_ptr&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = const EmpDist]’
../boost/serialization/split_free.hpp:58:22: required from ‘static void boost::serialization::free_loader<Archive, T>::invoke(Archive&, T&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = boost::shared_ptr]’
../boost/serialization/split_free.hpp:74:38: required from ‘void boost::serialization::split_free(Archive&, T&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = boost::shared_ptr]’
../boost/serialization/shared_ptr.hpp:187:57: [ skipping 106 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
../boost/serialization/export.hpp:86:1: required from ‘struct boost::archive::detail::ptr_serialization_support<boost::archive::binary_iarchive, AbundanceGroup>’
../boost/archive/detail/register_archive.hpp:25:8: required from ‘struct boost::archive::detail::_ptr_serialization_support<boost::archive::binary_iarchive, AbundanceGroup>’
../boost/archive/binary_iarchive.hpp:57:1: required by substitution of ‘template typename boost::archive::detail::_ptr_serialization_support<boost::archive::binary_iarchive, Serializable>::type boost::archive::detail::instantiate_ptrserialization(Serializable, boost::archive::binary_iarchive, boost::archive::detail::adl_tag) [with Serializable = AbundanceGroup]’
../boost/serialization/export.hpp:132:58: required from ‘void boost::archive::detail::extra_detail::guid_initializer::exportguid(mpl::false) const [with T = AbundanceGroup; mpl::false = mpl::bool_]’
../boost/serialization/export.hpp:142:61: required from ‘const boost::archive::detail::extra_detail::guid_initializer& boost::archive::detail::extra_detail::guid_initializer::export_guid() const [with T = AbundanceGroup]’
abundances.cpp:5162:1: required from here
../boost/smart_ptr/shared_ptr.hpp:467:14: error: no type named ‘type’ in ‘struct boost::detail::sp_enable_if_auto_ptr<boost::shared_ptr, int>’
/usr/include/c++/4.8/bits/stl_pair.h: In instantiation of ‘std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with U1 = const void; _U2 = boost::shared_ptr; T1 = const void const; _T2 = boost::shared_ptr]’:
../boost/serialization/shared_ptr_helper.hpp:181:20: required from ‘void boost::serialization::shared_ptrhelper::reset(SPT&, T ) [with T = const EmpDist; SPT = boost::shared_ptr]’
../boost/serialization/shared_ptr.hpp:171:5: required from ‘void boost::serialization::load(Archive&, boost::shared_ptr&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = const EmpDist]’
../boost/serialization/split_free.hpp:58:22: required from ‘static void boost::serialization::free_loader<Archive, T>::invoke(Archive&, T&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = boost::shared_ptr]’
../boost/serialization/split_free.hpp:74:38: required from ‘void boost::serialization::split_free(Archive&, T&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = boost::shared_ptr]’
../boost/serialization/shared_ptr.hpp:187:57: required from ‘void boost::serialization::serialize(Archive&, boost::shared_ptr&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = const EmpDist]’
../boost/serialization/serialization.hpp:128:27: [ skipping 105 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
../boost/serialization/export.hpp:86:1: required from ‘struct boost::archive::detail::ptr_serialization_support<boost::archive::binary_iarchive, AbundanceGroup>’
../boost/archive/detail/register_archive.hpp:25:8: required from ‘struct boost::archive::detail::_ptr_serialization_support<boost::archive::binary_iarchive, AbundanceGroup>’
../boost/archive/binary_iarchive.hpp:57:1: required by substitution of ‘template typename boost::archive::detail::_ptr_serialization_support<boost::archive::binary_iarchive, Serializable>::type boost::archive::detail::instantiate_ptrserialization(Serializable, boost::archive::binary_iarchive , boost::archive::detail::adl_tag) [with Serializable = AbundanceGroup]’
../boost/serialization/export.hpp:132:58: required from ‘void boost::archive::detail::extra_detail::guid_initializer::exportguid(mpl::false) const [with T = AbundanceGroup; mpl::false = mpl::bool_]’
../boost/serialization/export.hpp:142:61: required from ‘const boost::archive::detail::extra_detail::guid_initializer& boost::archive::detail::extra_detail::guid_initializer::export_guid() const [with T = AbundanceGroup]’
abundances.cpp:5162:1: required from here
../boost/smart_ptr/shared_ptr.hpp:441:14: note: template boost::shared_ptr::shared_ptr(std::auto_ptr<_Tp1>&)
explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn()
^
../boost/smart_ptr/shared_ptr.hpp:441:14: note: template argument deduction/substitution failed:
In file included from /usr/include/c++/4.8/bits/stl_algobase.h:64:0,
from /usr/include/c++/4.8/vector:60,
from abundances.h:17,
from abundances.cpp:16:
/usr/include/c++/4.8/bits/stl_pair.h:119:39: note: types ‘std::auto_ptr’ and ‘const boost::shared_ptr’ have incompatible cv-qualifiers
: first(p.first), second(p.second) { }
^
In file included from ../boost/shared_ptr.hpp:17:0,
from hits.h:19,
from abundances.h:23,
from abundances.cpp:16:
../boost/smart_ptr/shared_ptr.hpp:434:5: note: template boost::shared_ptr::shared_ptr(const boost::shared_ptr&, boost::shared_ptr::elementtype)
shared_ptr( shared_ptr const & r, element_type * p ) BOOST_NOEXCEPT : px( p ), pn( r.pn )
^
../boost/smart_ptr/shared_ptr.hpp:434:5: note: template argument deduction/substitution failed:
In file included from /usr/include/c++/4.8/bits/stl_algobase.h:64:0,
from /usr/include/c++/4.8/vector:60,
from abundances.h:17,
from abundances.cpp:16:
/usr/include/c++/4.8/bits/stl_pair.h:119:39: note: candidate expects 2 arguments, 1 provided
: first(p.first), second(p.second) { }
^
In file included from ../boost/shared_ptr.hpp:17:0,
from hits.h:19,
from abundances.h:23,
from abundances.cpp:16:
../boost/smart_ptr/shared_ptr.hpp:420:5: note: template boost::shared_ptr::shared_ptr(const boost::shared_ptr&, typename boost::detail::sp_enable_if_convertible<Y, T>::type)
shared_ptr( shared_ptr const & r, typename boost::detail::sp_enable_if_convertible<Y,T>::type = boost::detail::sp_empty() )
^
../boost/smart_ptr/shared_ptr.hpp:420:5: note: template argument deduction/substitution failed:
../boost/smart_ptr/shared_ptr.hpp: In substitution of ‘template boost::shared_ptr::shared_ptr(const boost::shared_ptr&, typename boost::detail::sp_enable_if_convertible<Y, T>::type) [with Y = const EmpDist]’:
/usr/include/c++/4.8/bits/stl_pair.h:119:39: required from ‘std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with U1 = const void; _U2 = boost::shared_ptr; _T1 = const void* const; _T2 = boost::shared_ptr]’
../boost/serialization/shared_ptr_helper.hpp:181:20: required from ‘void boost::serialization::shared_ptrhelper::reset(SPT&, T ) [with T = const EmpDist; SPT = boost::shared_ptr]’
../boost/serialization/shared_ptr.hpp:171:5: required from ‘void boost::serialization::load(Archive&, boost::shared_ptr&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = const EmpDist]’
../boost/serialization/split_free.hpp:58:22: required from ‘static void boost::serialization::free_loader<Archive, T>::invoke(Archive&, T&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = boost::shared_ptr]’
../boost/serialization/split_free.hpp:74:38: required from ‘void boost::serialization::split_free(Archive&, T&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = boost::shared_ptr]’
../boost/serialization/shared_ptr.hpp:187:57: [ skipping 106 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
../boost/serialization/export.hpp:86:1: required from ‘struct boost::archive::detail::ptr_serialization_support<boost::archive::binary_iarchive, AbundanceGroup>’
../boost/archive/detail/register_archive.hpp:25:8: required from ‘struct boost::archive::detail::_ptr_serialization_support<boost::archive::binary_iarchive, AbundanceGroup>’
../boost/archive/binary_iarchive.hpp:57:1: required by substitution of ‘template typename boost::archive::detail::_ptr_serialization_support<boost::archive::binary_iarchive, Serializable>::type boost::archive::detail::instantiate_ptrserialization(Serializable, boost::archive::binary_iarchive, boost::archive::detail::adl_tag) [with Serializable = AbundanceGroup]’
../boost/serialization/export.hpp:132:58: required from ‘void boost::archive::detail::extra_detail::guid_initializer::exportguid(mpl::false) const [with T = AbundanceGroup; mpl::false = mpl::bool_]’
../boost/serialization/export.hpp:142:61: required from ‘const boost::archive::detail::extra_detail::guid_initializer& boost::archive::detail::extra_detail::guid_initializer::export_guid() const [with T = AbundanceGroup]’
abundances.cpp:5162:1: required from here
../boost/smart_ptr/shared_ptr.hpp:420:5: error: no type named ‘type’ in ‘struct boost::detail::sp_enable_if_convertible<const EmpDist, void>’
/usr/include/c++/4.8/bits/stl_pair.h: In instantiation of ‘std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with U1 = const void; _U2 = boost::shared_ptr; T1 = const void const; _T2 = boost::shared_ptr]’:
../boost/serialization/shared_ptr_helper.hpp:181:20: required from ‘void boost::serialization::shared_ptrhelper::reset(SPT&, T ) [with T = const EmpDist; SPT = boost::shared_ptr]’
../boost/serialization/shared_ptr.hpp:171:5: required from ‘void boost::serialization::load(Archive&, boost::shared_ptr&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = const EmpDist]’
../boost/serialization/split_free.hpp:58:22: required from ‘static void boost::serialization::free_loader<Archive, T>::invoke(Archive&, T&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = boost::shared_ptr]’
../boost/serialization/split_free.hpp:74:38: required from ‘void boost::serialization::split_free(Archive&, T&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = boost::shared_ptr]’
../boost/serialization/shared_ptr.hpp:187:57: required from ‘void boost::serialization::serialize(Archive&, boost::shared_ptr&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = const EmpDist]’
../boost/serialization/serialization.hpp:128:27: [ skipping 105 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
../boost/serialization/export.hpp:86:1: required from ‘struct boost::archive::detail::ptr_serialization_support<boost::archive::binary_iarchive, AbundanceGroup>’
../boost/archive/detail/register_archive.hpp:25:8: required from ‘struct boost::archive::detail::_ptr_serialization_support<boost::archive::binary_iarchive, AbundanceGroup>’
../boost/archive/binary_iarchive.hpp:57:1: required by substitution of ‘template typename boost::archive::detail::_ptr_serialization_support<boost::archive::binary_iarchive, Serializable>::type boost::archive::detail::instantiate_ptrserialization(Serializable, boost::archive::binary_iarchive , boost::archive::detail::adl_tag) [with Serializable = AbundanceGroup]’
../boost/serialization/export.hpp:132:58: required from ‘void boost::archive::detail::extra_detail::guid_initializer::exportguid(mpl::false) const [with T = AbundanceGroup; mpl::false = mpl::bool_]’
../boost/serialization/export.hpp:142:61: required from ‘const boost::archive::detail::extra_detail::guid_initializer& boost::archive::detail::extra_detail::guid_initializer::export_guid() const [with T = AbundanceGroup]’
abundances.cpp:5162:1: required from here
../boost/smart_ptr/shared_ptr.hpp:408:5: note: template boost::shared_ptr::shared_ptr(const boost::weak_ptr&, boost::detail::sp_nothrow_tag)
shared_ptr( weak_ptr const & r, boost::detail::sp_nothrow_tag )
^
../boost/smart_ptr/shared_ptr.hpp:408:5: note: template argument deduction/substitution failed:
In file included from /usr/include/c++/4.8/bits/stl_algobase.h:64:0,
from /usr/include/c++/4.8/vector:60,
from abundances.h:17,
from abundances.cpp:16:
/usr/include/c++/4.8/bits/stl_pair.h:119:39: note: ‘const boost::shared_ptr’ is not derived from ‘const boost::weak_ptr’
: first(p.first), second(p.second) { }
^
In file included from ../boost/shared_ptr.hpp:17:0,
from hits.h:19,
from abundances.h:23,
from abundances.cpp:16:
../boost/smart_ptr/shared_ptr.hpp:399:14: note: template boost::shared_ptr::shared_ptr(const boost::weak_ptr&)
explicit shared_ptr( weak_ptr const & r ): pn( r.pn ) // may throw
^
../boost/smart_ptr/shared_ptr.hpp:399:14: note: template argument deduction/substitution failed:
In file included from /usr/include/c++/4.8/bits/stl_algobase.h:64:0,
from /usr/include/c++/4.8/vector:60,
from abundances.h:17,
from abundances.cpp:16:
/usr/include/c++/4.8/bits/stl_pair.h:119:39: note: ‘const boost::shared_ptr’ is not derived from ‘const boost::weak_ptr’
: first(p.first), second(p.second) { }
^
In file included from ../boost/shared_ptr.hpp:17:0,
from hits.h:19,
from abundances.h:23,
from abundances.cpp:16:
../boost/smart_ptr/shared_ptr.hpp:373:41: note: template<class Y, class D, class A> boost::shared_ptr::sharedptr(Y, D, A)
template<class Y, class D, class A> shared_ptr( Y * p, D d, A a ): px( p ), pn( p, d, a )
^
../boost/smart_ptr/shared_ptr.hpp:373:41: note: template argument deduction/substitution failed:
In file included from /usr/include/c++/4.8/bits/stl_algobase.h:64:0,
from /usr/include/c++/4.8/vector:60,
from abundances.h:17,
from abundances.cpp:16:
/usr/include/c++/4.8/bits/stlpair.h:119:39: note: mismatched types ‘Y’ and ‘boost::shared_ptr’
: first(p.first), second(p.second) { }
^
In file included from ../boost/shared_ptr.hpp:17:0,
from hits.h:19,
from abundances.h:23,
from abundances.cpp:16:
../boost/smart_ptr/shared_ptr.hpp:358:32: note: template<class Y, class D> boost::shared_ptr::sharedptr(Y, D)
template<class Y, class D> shared_ptr( Y * p, D d ): px( p ), pn( p, d )
^
../boost/smart_ptr/shared_ptr.hpp:358:32: note: template argument deduction/substitution failed:
In file included from /usr/include/c++/4.8/bits/stl_algobase.h:64:0,
from /usr/include/c++/4.8/vector:60,
from abundances.h:17,
from abundances.cpp:16:
/usr/include/c++/4.8/bits/stlpair.h:119:39: note: mismatched types ‘Y’ and ‘boost::shared_ptr’
: first(p.first), second(p.second) { }
^
In file included from ../boost/shared_ptr.hpp:17:0,
from hits.h:19,
from abundances.h:23,
from abundances.cpp:16:
../boost/smart_ptr/shared_ptr.hpp:347:14: note: template boost::shared_ptr::sharedptr(Y)
explicit shared_ptr( Y * p ): px( p ), pn() // Y must be complete
^
../boost/smart_ptr/shared_ptr.hpp:347:14: note: template argument deduction/substitution failed:
In file included from /usr/include/c++/4.8/bits/stl_algobase.h:64:0,
from /usr/include/c++/4.8/vector:60,
from abundances.h:17,
from abundances.cpp:16:
/usr/include/c++/4.8/bits/stlpair.h:119:39: note: mismatched types ‘Y’ and ‘boost::shared_ptr’
: first(p.first), second(p.second) { }
^
In file included from ../boost/shared_ptr.hpp:17:0,
from hits.h:19,
from abundances.h:23,
from abundances.cpp:16:
../boost/smart_ptr/shared_ptr.hpp:334:5: note: boost::shared_ptr::shared_ptr() [with T = void]
shared_ptr() BOOST_NOEXCEPT : px( 0 ), pn() // never throws in 1.30+
^
../boost/smart_ptr/shared_ptr.hpp:334:5: note: candidate expects 0 arguments, 1 provided
../boost/smart_ptr/shared_ptr.hpp:323:25: note: boost::shared_ptr::shared_ptr(const boost::shared_ptr&)
template class shared_ptr
^
../boost/smart_ptr/shared_ptr.hpp:323:25: note: no known conversion for argument 1 from ‘const boost::shared_ptr’ to ‘const boost::shared_ptr&’
In file included from ../boost/system/system_error.hpp:14:0,
from ../boost/thread/exceptions.hpp:22,
from ../boost/thread/pthread/thread_data.hpp:10,
from ../boost/thread/thread_only.hpp:17,
from ../boost/thread/thread.hpp:12,
from ../boost/thread.hpp:13,
from common.h:47,
from hits.h:23,
from abundances.h:23,
from abundances.cpp:16:
../boost/system/error_code.hpp: At global scope:
../boost/system/error_code.hpp:221:36: warning: ‘boost::system::posix_category’ defined but not used [-Wunused-variable]
static const error_category & posix_category = generic_category();
^
../boost/system/error_code.hpp:222:36: warning: ‘boost::system::errno_ecat’ defined but not used [-Wunused-variable]
static const error_category & errno_ecat = generic_category();
^
../boost/system/error_code.hpp:223:36: warning: ‘boost::system::native_ecat’ defined but not used [-Wunused-variable]
static const error_category & native_ecat = system_category();
^
make[2]: * [abundances.o] Error 1
make[2]: Leaving directory `/home/user/Downloads/bioinformatics/cufflinks-master/src'
make[1]: * [all-recursive] Error 1
make[1]: Leaving directory`/home/user/Downloads/bioinformatics/cufflinks-master'
make: *\ [all] Error 2
/home/user/Downloads/bioinformatics/cufflinks-master' Making all in src make[2]: Entering directory/home/user/Downloads/bioinformatics/cufflinks-master/src' g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -m64 -O3 -DNDEBUG -pthread -I/home/user/Downloads/boost_1_55/include -I/usr/local/include -I/usr/local/include/Eigen/include -MT abundances.o -MD -MP -MF .deps/abundances.Tpo -c -o abundances.o abundances.cpp In file included from ../boost/numeric/ublas/matrix.hpp:20:0, from abundances.h:18, from abundances.cpp:16: ../boost/numeric/ublas/detail/matrix_assign.hpp: In function ‘void boost::numeric::ublas::matrix_swap(M&, boost::numeric::ublas::matrix_expression