clang: error: linker command failed with exit code 1 (use -v to see invocation)

[Cactusolo]

Hi,

I tried to installed phlawd_db_maker on my own Mac following the instructions. It seems working all the way until the last step:

1 warning generated.
[100%] Linking CXX executable phlawd_db_maker
Undefined symbols for architecture x86_64:
"Query::get_result(std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > const&)", referenced from:
SQLiteDBController::initiate() in SQLiteDBController.cpp.o
SQLiteDBController::load_seqs(std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator >, bool) in SQLiteDBController.cpp.o
"Database::Database(std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > const&, IError*)", referenced from:
SQLiteDBController::initiate() in SQLiteDBController.cpp.o
SQLiteDBController::load_seqs(std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator >, bool) in SQLiteDBController.cpp.o
"std::__cxx11::basic_string<char, std::char_traits, std::allocator >::_M_replace(unsigned long, unsigned long, char const*, unsigned long)", referenced from:
Query::get_string(std::__cxx11::basic_string<char, std::char_traits, std::allocator > const&) in libsqlitewrapped.a(Query.o)
"std::__cxx11::basic_string<char, std::char_traits, std::allocator >::reserve(unsigned long)", referenced from:
std::__cxx11::basic_string<char, std::char_traits, std::allocator > std::operator+<char, std::char_traits, std::allocator >(char const*, std::__cxx11::basic_string<char, std::char_traits, std::allocator > const&) in libsqlitewrapped.a(Query.o)
"std::__cxx11::basic_string<char, std::char_traits, std::allocator >::_M_append(char const*, unsigned long)", referenced from:
std::__cxx11::basic_string<char, std::char_traits, std::allocator > std::operator+<char, std::char_traits, std::allocator >(char const*, std::__cxx11::basic_string<char, std::char_traits, std::allocator > const&) in libsqlitewrapped.a(Query.o)
Database::xmlsafestr(std::__cxx11::basic_string<char, std::char_traits, std::allocator > const&) in libsqlitewrapped.a(Database.o)
"std::__cxx11::basic_string<char, std::char_traits, std::allocator >::_M_assign(std::__cxx11::basic_string<char, std::char_traits, std::allocator > const&)", referenced from:
Query::execute(std::__cxx11::basic_string<char, std::char_traits, std::allocator > const&) in libsqlitewrapped.a(Query.o)
Query::get_result(std::__cxx11::basic_string<char, std::char_traits, std::allocator > const&) in libsqlitewrapped.a(Query.o)
"std::__cxx11::basic_string<char, std::char_traits, std::allocator >::_M_create(unsigned long&, unsigned long)", referenced from:
void std::__cxx11::basic_string<char, std::char_traits, std::allocator >::_M_construct<char const*>(char const*, char const*, std::forward_iterator_tag) (.isra.43) in libsqlitewrapped.a(Query.o)
void std::__cxx11::basic_string<char, std::char_traits, std::allocator >::_M_construct<char const*>(char const*, char const*, std::forward_iterator_tag) (.isra.40) in libsqlitewrapped.a(Database.o)
"std::__cxx11::basic_string<char, std::char_traits, std::allocator >::_M_mutate(unsigned long, unsigned long, char const*, unsigned long)", referenced from:
Database::safestr(std::__cxx11::basic_string<char, std::char_traits, std::allocator > const&) in libsqlitewrapped.a(Database.o)
Database::xmlsafestr(std::__cxx11::basic_string<char, std::char_traits, std::allocator > const&) in libsqlitewrapped.a(Database.o)
"std::__detail::_List_node_base::_M_hook(std::__detail::_List_node_base*)", referenced from:
Database::grabdb() in libsqlitewrapped.a(Database.o)
"std::__detail::_List_node_base::_M_unhook()", referenced from:
Database::~Database() in libsqlitewrapped.a(Database.o)
"std::_Rb_tree_decrement(std::_Rb_tree_node_base*)", referenced from:
std::_Rb_tree<std::__cxx11::basic_string<char, std::char_traits, std::allocator >, std::pair<std::__cxx11::basic_string<char, std::char_traits, std::allocator > const, int>, std::_Select1st<std::pair<std::__cxx11::basic_string<char, std::char_traits, std::allocator > const, int> >, std::less<std::__cxx11::basic_string<char, std::char_traits, std::allocator > >, std::allocator<std::pair<std::__cxx11::basic_string<char, std::char_traits, std::allocator > const, int> > >::_M_get_insert_unique_pos(std::__cxx11::basic_string<char, std::char_traits, std::allocator > const&) in libsqlitewrapped.a(Query.o)
std::_Rb_tree<std::__cxx11::basic_string<char, std::char_traits, std::allocator >, std::pair<std::__cxx11::basic_string<char, std::char_traits, std::allocator > const, int>, std::_Select1st<std::pair<std::__cxx11::basic_string<char, std::char_traits, std::allocator > const, int> >, std::less<std::__cxx11::basic_string<char, std::char_traits, std::allocator > >, std::allocator<std::pair<std::__cxx11::basic_string<char, std::char_traits, std::allocator > const, int> > >::_M_get_insert_hint_unique_pos(std::_Rb_tree_const_iterator<std::pair<std::__cxx11::basic_string<char, std::char_traits, std::allocator > const, int> >, std::__cxx11::basic_string<char, std::char_traits, std::allocator > const&) in libsqlitewrapped.a(Query.o)
"std::_Rb_tree_increment(std::_Rb_tree_node_base*)", referenced from:
std::_Rb_tree<std::__cxx11::basic_string<char, std::char_traits, std::allocator >, std::pair<std::__cxx11::basic_string<char, std::char_traits, std::allocator > const, int>, std::_Select1st<std::pair<std::__cxx11::basic_string<char, std::char_traits, std::allocator > const, int> >, std::less<std::__cxx11::basic_string<char, std::char_traits, std::allocator > >, std::allocator<std::pair<std::__cxx11::basic_string<char, std::char_traits, std::allocator > const, int> > >::_M_get_insert_hint_unique_pos(std::_Rb_tree_const_iterator<std::pair<std::__cxx11::basic_string<char, std::char_traits, std::allocator > const, int> >, std::__cxx11::basic_string<char, std::char_traits, std::allocator > const&) in libsqlitewrapped.a(Query.o)
"std::__throw_logic_error(char const*)", referenced from:
void std::__cxx11::basic_string<char, std::char_traits, std::allocator >::_M_construct<char const*>(char const*, char const*, std::forward_iterator_tag) (.isra.43) in libsqlitewrapped.a(Query.o)
void std::__cxx11::basic_string<char, std::char_traits, std::allocator >::_M_construct<char const*>(char const*, char const*, std::forward_iterator_tag) (.isra.40) in libsqlitewrapped.a(Database.o)
"std::__throw_length_error(char const*)", referenced from:
std::__cxx11::basic_string<char, std::char_traits, std::allocator > std::operator+<char, std::char_traits, std::allocator >(char const*, std::__cxx11::basic_string<char, std::char_traits, std::allocator > const&) in libsqlitewrapped.a(Query.o)
Database::xmlsafestr(std::__cxx11::basic_string<char, std::char_traits, std::allocator > const&) in libsqlitewrapped.a(Database.o)
"std::_Rb_tree_rebalance_for_erase(std::_Rb_tree_node_base*, std::_Rb_tree_node_base&)", referenced from:
Query::free_result() in libsqlitewrapped.a(Query.o)
"std::_Rb_tree_insert_and_rebalance(bool, std::_Rb_tree_node_base*, std::_Rb_tree_node_base*, std::_Rb_tree_node_base&)", referenced from:
std::_Rb_tree<std::__cxx11::basic_string<char, std::char_traits, std::allocator >, std::pair<std::__cxx11::basic_string<char, std::char_traits, std::allocator > const, int>, std::_Select1st<std::pair<std::__cxx11::basic_string<char, std::char_traits, std::allocator > const, int> >, std::less<std::__cxx11::basic_string<char, std::char_traits, std::allocator > >, std::allocator<std::pair<std::__cxx11::basic_string<char, std::char_traits, std::allocator > const, int> > >::_M_insert_node(std::_Rb_tree_node_base*, std::_Rb_tree_node_base*, std::_Rb_tree_node<std::pair<std::__cxx11::basic_string<char, std::char_traits, std::allocator > const, int> >*) in libsqlitewrapped.a(Query.o)
ld: symbol(s) not found for architecture x86_64

clang: error: linker command failed with exit code 1 (use -v to see invocation)
make[2]: *** [phlawd_db_maker] Error 1
make[1]: *** [CMakeFiles/phlawd_db_maker.dir/all] Error 2
make: *** [all] Error 2

Please help and let me know if you need more information. I have downloaded old pln database, however, I may also need to run the most updated database.

Thanks!

Miao

[harsimranpadam]

Hi Cactusolo, I have been running into the same problem for months now. One solution in the newer version of pyphlawd was to download the database from pyphalwd_db_maker.py in the src folder. But it required .gz files and I wasn't able to retrieve them.
Were you able to solve this?

[Cactusolo]

I have this problem too with the newer version, so I roll back to the older one, which no .gz file required. Cheers, Miao Dr. Miao Sun Web: www.sunmiao.name Email: miaosun@ ***@***.***> mail.hzau.edu.cn

…

On Fri, Nov 17, 2023 at 1:41 AM harsimranpadam ***@***.***> wrote: Hi Cactusolo, I have been running into the same problem for months now. One solution in the newer version of pyphlawd was to download the database from pyphalwd_db_maker.py in the src folder. But it required .gz files and I wasn't able to retrieve them. Were you able to solve this? — Reply to this email directly, view it on GitHub <#5 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AB3TGAHZAMS7GPQU7YVAO4TYEZF4PAVCNFSM4GEBRPM2U5DIOJSWCZC7NNSXTN2JONZXKZKDN5WW2ZLOOQ5TCOBRGQ4TEOJUGI3A> . You are receiving this because you authored the thread.Message ID: ***@***.***>

[harsimranpadam]

Hi.

So, how did you solve the problem for the previous one? I have been trying to do the same from months, and I haven't been able to yet. So, any help would be greatly appreciated.

Thanks!
Harsimran Kaur