-
Notifications
You must be signed in to change notification settings - Fork 2
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
clang: error: linker command failed with exit code 1 (use -v to see invocation) #5
Comments
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. |
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:
***@***.***>
|
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! |
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
The text was updated successfully, but these errors were encountered: