ADL: Problems while builing Vina from source

Oleg Trott trott at scripps.edu
Mon Mar 10 17:16:24 PDT 2014


Hi

As it says in the error message, it looks like you disabled
multitheading. However, Vina needs it.

On Sun, Mar 9, 2014 at 11:24 AM, Ксения Сафина <cat7mail.ru at mail.ru> wrote:
>
> Thank you, Oleg
> I rebuild 1.41 Boost once again and now it doesn't look like using v3 filesystem. However, another errors have appeared.
> noraneko at noraneko-K53SJ:~/Programs/autodock_vina_1_1_2/build/linux/release$ make/usr/bin/g++ -static -pthread -ansi -Wno-long-long -O3 -DNDEBUG -I /usr/local/include -I ../../../src/lib -o main.o -c ../../../src/main/main.cpp
> In file included from /usr/local/include/boost/thread/detail/platform.hpp:17:0,
> from /usr/local/include/boost/thread/thread.hpp:12,
> from ../../../src/main/main.cpp:32:
> /usr/local/include/boost/config/requires_threads.hpp:29:4: error: #error "Threading support unavaliable: it has been explicitly disabled with BOOST_DISABLE_THREADS"
> In file included from /usr/local/include/boost/thread/thread.hpp:12:0,
> from ../../../src/main/main.cpp:32:
> /usr/local/include/boost/thread/detail/platform.hpp:67:9: error: #error "Sorry, no boost threads are available for this platform."
> ..
> from ../../../src/main/main.cpp:32:
> /usr/local/include/boost/thread/xtime.hpp:23:5: error: expected identifier before numeric constant
> /usr/local/include/boost/thread/xtime.hpp:23:5: error: expected ‘}’ before numeric constant
> /usr/local/include/boost/thread/xtime.hpp:23:5: error: expected unqualified-id before numeric constant
> /usr/local/include/boost/thread/xtime.hpp:46:14: error: expected type-specifier before ‘system_time’
> ..
> In file included from /usr/local/include/boost/thread/xtime.hpp:14:0,
> from /usr/local/include/boost/thread/detail/thread.hpp:12,
> from /usr/local/include/boost/thread/thread.hpp:22,
> from ../../../src/main/main.cpp:32:
> /usr/local/include/boost/thread/thread_time.hpp:18:24: note: ‘boost::get_system_time’
> In file included from /usr/local/include/boost/thread/detail/thread.hpp:12:0,
> from /usr/local/include/boost/thread/thread.hpp:22,
> from ../../../src/main/main.cpp:32:
> /usr/local/include/boost/thread/xtime.hpp: At global scope:
> /usr/local/include/boost/thread/xtime.hpp:88:1: error: expected declaration before ‘}’ token
> make: *** [main.o] Error 1
>
> I've found the same error with xtime.hpp file in google, and have changed TIME_UTC to TIME_UTC_ in /usr/include/boost/thread/xtime.hpp file. After this replacement I've got another errors:
> noraneko at noraneko-K53SJ:~/Programs/autodock_vina_1_1_2/build/linux/release$ make/usr/bin/g++ -static -pthread -ansi -Wno-long-long -O3 -DNDEBUG -I /usr/local/include -I ../../../src/lib -o main.o -c ../../../src/main/main.cpp
> In file included from /usr/local/include/boost/thread/detail/platform.hpp:17:0,
> from /usr/local/include/boost/thread/thread.hpp:12,
> from ../../../src/main/main.cpp:32:
> /usr/local/include/boost/config/requires_threads.hpp:29:4: error: #error "Threading support unavaliable: it has been explicitly disabled with BOOST_DISABLE_THREADS"
> In file included from /usr/local/include/boost/thread/thread.hpp:12:0,
> from ../../../src/main/main.cpp:32:
> /usr/local/include/boost/thread/detail/platform.hpp:67:9: error: #error "Sorry, no boost threads are available for this platform."
> In file included from ../../../src/main/main.cpp:32:0:
> /usr/local/include/boost/thread/thread.hpp:19:2: error: #error "Boost threads unavailable on this platform"
> ..
> /usr/local/include/boost/thread/detail/thread_group.hpp:38:52: note: (if you use ‘-fpermissive’, G++ will accept your code, but allowing the use of an undeclared name is deprecated)
> /usr/local/include/boost/thread/detail/thread_group.hpp: In member function ‘void boost::thread_group::add_thread(boost::thread*)’:
> /usr/local/include/boost/thread/detail/thread_group.hpp:48:17: error: ‘lock_guard’ is not a member of ‘boost’
> /usr/local/include/boost/thread/detail/thread_group.hpp:48:35: error: ‘shared_mutex’ was not declared in this scope
> /usr/local/include/boost/thread/detail/thread_group.hpp:48:55: error: ‘m’ was not declared in this scope
> /usr/local/include/boost/thread/detail/thread_group.hpp:48:56: error: ‘guard’ was not declared in this scope
> ..
> /usr/local/include/boost/thread/detail/thread_group.hpp: In member function ‘size_t boost::thread_group::size() const’:
> /usr/local/include/boost/thread/detail/thread_group.hpp:89:13: error: ‘shared_lock’ is not a member of ‘boost’
> /usr/local/include/boost/thread/detail/thread_group.hpp:89:32: error: ‘shared_mutex’ was not declared in this scope
> /usr/local/include/boost/thread/detail/thread_group.hpp:89:52: error: ‘m’ was not declared in this scope
> /usr/local/include/boost/thread/detail/thread_group.hpp:89:53: error: ‘guard’ was not declared in this scope
> make: *** [main.o] Error 1
>
> Does the above imply that there some problems with the Boost I've built? Or is there something else?
> And the question still remains why does 'makedepend' look for some subdirectories in lib, main and split directories ("makedepend -f dependencies_tmp -Y -I ../../../src/lib ../../../src/lib/*.cpp ../../../src/tests/*.cpp ../../../src/design/*.cpp ../../../src/main/*.cpp ../../../src/split/*.cpp ../../../src/tune/*.cpp")
> Ksenia
> Суббота,  8 марта 2014, 13:00 +04:00 от Ксения Сафина <cat7mail.ru at mail.ru>:
>>Hi everyone,
>>
>>I'm trying to build Vina from source. I want to change some parameters in main.cpp so I need a source package.
>>I've installed Boost 1.41, makedepend utility but after 'make depend' I've got a huge amount of warnings like this one:
>>
>>makedepend: warning: ../../../src/split/split.cpp, line 32: cannot find include file "boost/filesystem/exception.hpp"
>>not in ../../../src/lib/boost/filesystem/exception.hpp
>>
>>I don't actually understand why exception.hpp must be in ../../../src/lib/boost/filesystem/. There isn't any subdirectories in lib, main or split directories but I have exception.hpp in /usr/local/include/boost/filesystem. Should all these files be placed into lib directory?
>>
>>After 'make' command I've got
>>noraneko at noraneko-K53SJ:~/Programs/autodock_vina_1_1_2/build/linux/release$ make/usr/bin/g++ -static -pthread -ansi -Wno-long-long -O3 -DNDEBUG -I /usr/local/include/boost -I ../../../src/lib -o main.o -c ../../../src/main/main.cpp
>>../../../src/main/main.cpp: In function ‘path make_path(const string&)’:
>>../../../src/main/main.cpp:50:44: error: invalid conversion from ‘bool (*)(const string&) {aka bool (*)(const std::basic_string<char>&)}’ to ‘boost::enable_if_c<true, void>::type* {aka void*}’ [-fpermissive]
>>In file included from /usr/include/boost/filesystem/v3/fstream.hpp:21:0,
>>from /usr/include/boost/filesystem/fstream.hpp:31,
>>from ../../../src/main/main.cpp:29:
>>/usr/include/boost/filesystem/v3/path.hpp:131:5: error: initializing argument 2 of ‘boost::filesystem3::path::path(const Source&, typename boost::enable_if<boost::filesystem3::path_traits::is_pathable<typename boost::decay<Source>::type> >::type*) [with Source = std::basic_string<char>; typename boost::enable_if<boost::filesystem3::path_traits::is_pathable<typename boost::decay<Source>::type> >::type = void]’ [-fpermissive]
>>../../../src/main/main.cpp: In function ‘int main(int, char**)’:
>>../../../src/main/main.cpp:664:57: error: ‘path’ has no member named ‘native_file_string’
>>../../../src/main/main.cpp:676:80: error: ‘path’ has no member named ‘native_file_string’
>>make: *** [main.o] Error 1
>> There is some disagreement between paths or versions, as it seems to me. I have any experience with Boost libraries and c++ language at all so these errors are quite dark for me.
>>
>>Could you help me, please?
>>
>>________________________________________________
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> ________________________________________________
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-- 
Oleg Trott, Ph.D. (Columbia University)

Staff Scientist in the Olson Lab
The Scripps Research Institute

http://olegtrott.com



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