ADL: Problems while builing Vina from source

Oleg Trott trott at scripps.edu
Tue Mar 11 13:58:58 PDT 2014


Hi

makedepend should work despite the missing directories.

Those directories contained some unreleased software, like the
software used for training the scoring function. They are not needed
for building vina or vina_split.


On Mon, Mar 10, 2014 at 11:54 PM, Ксения Сафина <cat7mail.ru at mail.ru> wrote:
>  Yes, it seems that Boost 1.41 has some problems with gcc 4.7.3. Now I'm going to try an older version of compiler.
> Sorry for my importunity but I have to understand the 'makedepend' error. Why does '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"' command need some strange files and directories like design/, tune/ and so on? There is no such files in scr/ directory.
>
> Thank you for your replies,
>
> Ksenia
>
> Понедельник, 10 марта 2014, 17:16 -07:00 от Oleg Trott <trott at scripps.edu>:
>>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
>>
>>________________________________________________
>>--- ADL: AutoDock List  ---  http://autodock.scripps.edu/mailing_list ---
> ________________________________________________
> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---

-- 
Oleg Trott, Ph.D. (Columbia University)

Staff Scientist in the Olson Lab
The Scripps Research Institute

http://olegtrott.com



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