./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 [email protected] 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: ${prefix}
See config.h for further configuration information.
Email [email protected] with questions and bug reports.
make output:
user@user-HP:~/Downloads/bioinformatics/cufflinks-master$ make
make all-recursive
make[1]: Entering directory /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&, 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_ptr_helper::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_ptr_serialization(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::export_guid(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_ptr_helper::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_ptr_serialization(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::export_guid(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_ptr_helper::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_ptr_serialization(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::export_guid(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::element_type)
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_ptr_helper::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_ptr_serialization(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::export_guid(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_ptr_helper::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_ptr_serialization(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::export_guid(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::shared_ptr(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/stl_pair.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::shared_ptr(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/stl_pair.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::shared_ptr(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/stl_pair.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_ptr_helper::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_ptr_serialization(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::export_guid(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_ptr_helper::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_ptr_serialization(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::export_guid(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_ptr_helper::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_ptr_serialization(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::export_guid(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::element_type)
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_ptr_helper::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_ptr_serialization(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::export_guid(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_ptr_helper::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_ptr_serialization(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::export_guid(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::shared_ptr(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/stl_pair.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::shared_ptr(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/stl_pair.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::shared_ptr(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/stl_pair.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