* installing *source* package ‘shaman’ ...
** this is package ‘shaman’ version ‘2.1.0’
** package ‘shaman’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
specified C++17
using C++ compiler: ‘g++ (GCC) 16.2.1 20260819 (Red Hat 16.2.1-2)’
using C++17
make[1]: Entering directory '/data/localhost/ripley/R/packages/tests-devel/shaman/src'
g++ -std=gnu++17 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -pthread -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c ContactShuffler.cpp -o ContactShuffler.o
g++ -std=gnu++17 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -pthread -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c GenomeGridLog.cpp -o GenomeGridLog.o
g++ -std=gnu++17 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -pthread -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c Parser.cpp -o Parser.o
g++ -std=gnu++17 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -pthread -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c Random.cpp -o Random.o
g++ -std=gnu++17 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -pthread -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -pthread -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c hic_matrix_shuffler.cpp -o hic_matrix_shuffler.o
g++ -std=gnu++17 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -pthread -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c merge_ks.cpp -o merge_ks.o
ContactShuffler.cpp: In member function ‘int ContactShuffler::save_contacts(const char*, bool, bool)’:
ContactShuffler.cpp:133:60: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=]
133 | p = to_chars(p, buf_end + 64, b).ptr; *p++ = '\n';
| ~~~~~^~~~~~
In file included from /usr/include/c++/16/x86_64-redhat-linux/bits/c++allocator.h:33,
from /usr/include/c++/16/bits/allocator.h:46,
from /usr/include/c++/16/vector:65,
from ContactShuffler.h:10,
from ContactShuffler.cpp:8:
In member function ‘_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]’,
inlined from ‘static _Tp* std::allocator_traits<std::allocator<_Tp1> >::allocate(allocator_type&, size_type) [with _Tp = char]’ at /usr/include/c++/16/bits/alloc_traits.h:638:28,
inlined from ‘std::_Vector_base<_Tp, _Alloc>::pointer std::_Vector_base<_Tp, _Alloc>::_M_allocate(std::size_t) [with _Tp = char; _Alloc = std::allocator<char>]’ at /usr/include/c++/16/bits/stl_vector.h:389:33,
inlined from ‘void std::_Vector_base<_Tp, _Alloc>::_M_create_storage(std::size_t) [with _Tp = char; _Alloc = std::allocator<char>]’ at /usr/include/c++/16/bits/stl_vector.h:407:44,
inlined from ‘std::_Vector_base<_Tp, _Alloc>::_Vector_base(std::size_t, const allocator_type&) [with _Tp = char; _Alloc = std::allocator<char>]’ at /usr/include/c++/16/bits/stl_vector.h:341:26,
inlined from ‘std::vector<_Tp, _Alloc>::vector(size_type, const allocator_type&) [with _Tp = char; _Alloc = std::allocator<char>]’ at /usr/include/c++/16/bits/stl_vector.h:577:47,
inlined from ‘int ContactShuffler::save_contacts(const char*, bool, bool)’ at ContactShuffler.cpp:122:26:
/usr/include/c++/16/bits/new_allocator.h:162:75: note: at offset 1048576 into destination object of size 1048576 allocated by ‘operator new’
162 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp)));
| ^
ContactShuffler.cpp: In member function ‘int ContactShuffler::save_contacts(const char*, bool, bool)’:
ContactShuffler.cpp:132:60: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=]
132 | p = to_chars(p, buf_end + 64, a).ptr; *p++ = '\t';
| ~~~~~^~~~~~
In member function ‘_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]’,
inlined from ‘static _Tp* std::allocator_traits<std::allocator<_Tp1> >::allocate(allocator_type&, size_type) [with _Tp = char]’ at /usr/include/c++/16/bits/alloc_traits.h:638:28,
inlined from ‘std::_Vector_base<_Tp, _Alloc>::pointer std::_Vector_base<_Tp, _Alloc>::_M_allocate(std::size_t) [with _Tp = char; _Alloc = std::allocator<char>]’ at /usr/include/c++/16/bits/stl_vector.h:389:33,
inlined from ‘void std::_Vector_base<_Tp, _Alloc>::_M_create_storage(std::size_t) [with _Tp = char; _Alloc = std::allocator<char>]’ at /usr/include/c++/16/bits/stl_vector.h:407:44,
inlined from ‘std::_Vector_base<_Tp, _Alloc>::_Vector_base(std::size_t, const allocator_type&) [with _Tp = char; _Alloc = std::allocator<char>]’ at /usr/include/c++/16/bits/stl_vector.h:341:26,
inlined from ‘std::vector<_Tp, _Alloc>::vector(size_type, const allocator_type&) [with _Tp = char; _Alloc = std::allocator<char>]’ at /usr/include/c++/16/bits/stl_vector.h:577:47,
inlined from ‘int ContactShuffler::save_contacts(const char*, bool, bool)’ at ContactShuffler.cpp:122:26:
/usr/include/c++/16/bits/new_allocator.h:162:75: note: at offset 1048576 into destination object of size 1048576 allocated by ‘operator new’
162 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp)));
| ^
ContactShuffler.cpp: In member function ‘int ContactShuffler::save_contacts(const char*, bool, bool)’:
ContactShuffler.cpp:133:60: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=]
133 | p = to_chars(p, buf_end + 64, b).ptr; *p++ = '\n';
| ~~~~~^~~~~~
In member function ‘_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]’,
inlined from ‘static _Tp* std::allocator_traits<std::allocator<_Tp1> >::allocate(allocator_type&, size_type) [with _Tp = char]’ at /usr/include/c++/16/bits/alloc_traits.h:638:28,
inlined from ‘std::_Vector_base<_Tp, _Alloc>::pointer std::_Vector_base<_Tp, _Alloc>::_M_allocate(std::size_t) [with _Tp = char; _Alloc = std::allocator<char>]’ at /usr/include/c++/16/bits/stl_vector.h:389:33,
inlined from ‘void std::_Vector_base<_Tp, _Alloc>::_M_create_storage(std::size_t) [with _Tp = char; _Alloc = std::allocator<char>]’ at /usr/include/c++/16/bits/stl_vector.h:407:44,
inlined from ‘std::_Vector_base<_Tp, _Alloc>::_Vector_base(std::size_t, const allocator_type&) [with _Tp = char; _Alloc = std::allocator<char>]’ at /usr/include/c++/16/bits/stl_vector.h:341:26,
inlined from ‘std::vector<_Tp, _Alloc>::vector(size_type, const allocator_type&) [with _Tp = char; _Alloc = std::allocator<char>]’ at /usr/include/c++/16/bits/stl_vector.h:577:47,
inlined from ‘int ContactShuffler::save_contacts(const char*, bool, bool)’ at ContactShuffler.cpp:122:26:
/usr/include/c++/16/bits/new_allocator.h:162:75: note: at offset 1048576 into destination object of size 1048576 allocated by ‘operator new’
162 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp)));
| ^
ContactShuffler.cpp: In member function ‘int ContactShuffler::save_contacts(const char*, bool, bool)’:
ContactShuffler.cpp:135:68: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=]
135 | p = to_chars(p, buf_end + 64, b).ptr; *p++ = '\t';
| ~~~~~^~~~~~
In member function ‘_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]’,
inlined from ‘static _Tp* std::allocator_traits<std::allocator<_Tp1> >::allocate(allocator_type&, size_type) [with _Tp = char]’ at /usr/include/c++/16/bits/alloc_traits.h:638:28,
inlined from ‘std::_Vector_base<_Tp, _Alloc>::pointer std::_Vector_base<_Tp, _Alloc>::_M_allocate(std::size_t) [with _Tp = char; _Alloc = std::allocator<char>]’ at /usr/include/c++/16/bits/stl_vector.h:389:33,
inlined from ‘void std::_Vector_base<_Tp, _Alloc>::_M_create_storage(std::size_t) [with _Tp = char; _Alloc = std::allocator<char>]’ at /usr/include/c++/16/bits/stl_vector.h:407:44,
inlined from ‘std::_Vector_base<_Tp, _Alloc>::_Vector_base(std::size_t, const allocator_type&) [with _Tp = char; _Alloc = std::allocator<char>]’ at /usr/include/c++/16/bits/stl_vector.h:341:26,
inlined from ‘std::vector<_Tp, _Alloc>::vector(size_type, const allocator_type&) [with _Tp = char; _Alloc = std::allocator<char>]’ at /usr/include/c++/16/bits/stl_vector.h:577:47,
inlined from ‘int ContactShuffler::save_contacts(const char*, bool, bool)’ at ContactShuffler.cpp:122:26:
/usr/include/c++/16/bits/new_allocator.h:162:75: note: at offset 1048576 into destination object of size 1048576 allocated by ‘operator new’
162 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp)));
| ^
ContactShuffler.cpp: In member function ‘int ContactShuffler::save_contacts(const char*, bool, bool)’:
ContactShuffler.cpp:133:60: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=]
133 | p = to_chars(p, buf_end + 64, b).ptr; *p++ = '\n';
| ~~~~~^~~~~~
In member function ‘_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]’,
inlined from ‘static _Tp* std::allocator_traits<std::allocator<_Tp1> >::allocate(allocator_type&, size_type) [with _Tp = char]’ at /usr/include/c++/16/bits/alloc_traits.h:638:28,
inlined from ‘std::_Vector_base<_Tp, _Alloc>::pointer std::_Vector_base<_Tp, _Alloc>::_M_allocate(std::size_t) [with _Tp = char; _Alloc = std::allocator<char>]’ at /usr/include/c++/16/bits/stl_vector.h:389:33,
inlined from ‘void std::_Vector_base<_Tp, _Alloc>::_M_create_storage(std::size_t) [with _Tp = char; _Alloc = std::allocator<char>]’ at /usr/include/c++/16/bits/stl_vector.h:407:44,
inlined from ‘std::_Vector_base<_Tp, _Alloc>::_Vector_base(std::size_t, const allocator_type&) [with _Tp = char; _Alloc = std::allocator<char>]’ at /usr/include/c++/16/bits/stl_vector.h:341:26,
inlined from ‘std::vector<_Tp, _Alloc>::vector(size_type, const allocator_type&) [with _Tp = char; _Alloc = std::allocator<char>]’ at /usr/include/c++/16/bits/stl_vector.h:577:47,
inlined from ‘int ContactShuffler::save_contacts(const char*, bool, bool)’ at ContactShuffler.cpp:122:26:
/usr/include/c++/16/bits/new_allocator.h:162:75: note: at offset 1048576 into destination object of size 1048576 allocated by ‘operator new’
162 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp)));
| ^
ContactShuffler.cpp: In member function ‘int ContactShuffler::save_contacts(const char*, bool, bool)’:
ContactShuffler.cpp:135:68: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=]
135 | p = to_chars(p, buf_end + 64, b).ptr; *p++ = '\t';
| ~~~~~^~~~~~
In member function ‘_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]’,
inlined from ‘static _Tp* std::allocator_traits<std::allocator<_Tp1> >::allocate(allocator_type&, size_type) [with _Tp = char]’ at /usr/include/c++/16/bits/alloc_traits.h:638:28,
inlined from ‘std::_Vector_base<_Tp, _Alloc>::pointer std::_Vector_base<_Tp, _Alloc>::_M_allocate(std::size_t) [with _Tp = char; _Alloc = std::allocator<char>]’ at /usr/include/c++/16/bits/stl_vector.h:389:33,
inlined from ‘void std::_Vector_base<_Tp, _Alloc>::_M_create_storage(std::size_t) [with _Tp = char; _Alloc = std::allocator<char>]’ at /usr/include/c++/16/bits/stl_vector.h:407:44,
inlined from ‘std::_Vector_base<_Tp, _Alloc>::_Vector_base(std::size_t, const allocator_type&) [with _Tp = char; _Alloc = std::allocator<char>]’ at /usr/include/c++/16/bits/stl_vector.h:341:26,
inlined from ‘std::vector<_Tp, _Alloc>::vector(size_type, const allocator_type&) [with _Tp = char; _Alloc = std::allocator<char>]’ at /usr/include/c++/16/bits/stl_vector.h:577:47,
inlined from ‘int ContactShuffler::save_contacts(const char*, bool, bool)’ at ContactShuffler.cpp:122:26:
/usr/include/c++/16/bits/new_allocator.h:162:75: note: at offset 1048576 into destination object of size 1048576 allocated by ‘operator new’
162 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp)));
| ^
g++ -std=gnu++17 -shared -L/usr/local/lib64 -o shaman.so ContactShuffler.o GenomeGridLog.o Parser.o Random.o RcppExports.o hic_matrix_shuffler.o merge_ks.o -pthread
make[1]: Leaving directory '/data/localhost/ripley/R/packages/tests-devel/shaman/src'
make[1]: Entering directory '/data/localhost/ripley/R/packages/tests-devel/shaman/src'
make[1]: Leaving directory '/data/localhost/ripley/R/packages/tests-devel/shaman/src'
installing to /data/localhost/ripley/R/packages/tests-devel/shaman.Rcheck/00LOCK-shaman/00new/shaman/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (shaman)