Re: [Seqan-dev] seqan 2 system_condition problems on windows

["Siragusa, Enrico" <Enrico.Siragusa@fu-berlin.de>]

Hi Daniel,

We decided to drop mingw.

See https://github.com/seqan/seqan/blob/master/README.rst#prerequisites for a list of supported platform.

I would suggest Visual Studio 12 on Windows…

Enrico

On Feb 19, 2015, at 12:44 AM, Bartha Dániel <daniel.bartha@gmail.com> wrote:

Hi Everyone,

I'm trying to work with seqan 2 on windows. This is pain-in-the-ass as usual, but now there is something that grinds my nervs, and has to do with the lib self.

Here my program, simply stolen from the docs:

#include <iostream>

#include <seqan/sequence.h>

#include <seqan/seq_io.h>

using namespace seqan;

int main()

{

    CharString id;

    Dna5String seq;

    CharString qual;

    SeqFileIn seqFileIn("E:/some.fastq");

    readRecord(id, seq, qual, seqFileIn);

} 

Not that big deal. But somehow I get a list of undefined references in the 'system_condition.h'. See the error log below. Do anyone have an idea, where the problem is? I assume that its either seqan or the compilation parameters, since the code itself is primitive.

Regards: Daniel

00:20:19: Starting: "C:\Qt\Tools\mingw491_32\bin\mingw32-make.exe"

C:/Qt/Tools/mingw491_32/bin/mingw32-make -f Makefile.Release

mingw32-make[1]: Entering directory 'E:/dev/build-console_1-Desktop_Qt_5_4_0_MinGW_32bit-Release'

g++ -c -pipe -fno-keep-inline-dllexport -O2 -frtti -Wall -Wextra -fexceptions -mthreads -I..\console_1 -I"C:\seqan-library-2.0.0\include" -I"." -I"C:\Qt\5.4\mingw491_32\mkspecs\win32-g++" -o release\main.o ..\console_1\main.cpp

In file included from C:\seqan-library-2.0.0\include/seqan/parallel.h:56:0,

from C:\seqan-library-2.0.0\include/seqan/modifier.h:48,

from C:\seqan-library-2.0.0\include/seqan/file.h:59,

from C:\seqan-library-2.0.0\include/seqan/stream.h:62,

from C:\seqan-library-2.0.0\include/seqan/seq_io.h:45,

from ..\console_1\main.cpp:3:

C:\seqan-library-2.0.0\include/seqan/system/system_condition.h: In constructor 'seqan::Condition::Condition(seqan::CriticalSection&)':

C:\seqan-library-2.0.0\include/seqan/system/system_condition.h:57:47: error: 'InitializeConditionVariable' was not declared in this scope

InitializeConditionVariable(&data_cond);

^

C:\seqan-library-2.0.0\include/seqan/system/system_condition.h: In destructor 'seqan::Condition::~Condition()':

C:\seqan-library-2.0.0\include/seqan/system/system_condition.h:62:44: error: 'WakeAllConditionVariable' was not declared in this scope

WakeAllConditionVariable(&data_cond);

^

C:\seqan-library-2.0.0\include/seqan/system/system_condition.h: In function 'void seqan::waitFor(seqan::Condition&)':

C:\seqan-library-2.0.0\include/seqan/system/system_condition.h:98:92: error: 'SleepConditionVariableCS' was not declared in this scope

BOOL success = SleepConditionVariableCS(&cond.data_cond, &cond.csPtr->data_cs, INFINITE);

^

C:\seqan-library-2.0.0\include/seqan/system/system_condition.h: In function 'void seqan::waitFor(seqan::Condition&, long int, bool&)':

C:\seqan-library-2.0.0\include/seqan/system/system_condition.h:112:98: error: 'SleepConditionVariableCS' was not declared in this scope

inProgress = (SleepConditionVariableCS(&cond.data_cond, &cond.csPtr->data_cs, timeoutMilliSec) == 0);

^

C:\seqan-library-2.0.0\include/seqan/system/system_condition.h: In function 'void seqan::signal(seqan::Condition&)':

C:\seqan-library-2.0.0\include/seqan/system/system_condition.h:137:45: error: 'WakeAllConditionVariable' was not declared in this scope

WakeAllConditionVariable(&cond.data_cond);

^

In file included from C:\seqan-library-2.0.0\include/seqan/basic/basic_debug.h:52:0,

from C:\seqan-library-2.0.0\include/seqan/basic.h:49,

from C:\seqan-library-2.0.0\include/seqan/sequence.h:51,

from ..\console_1\main.cpp:2:

C:\seqan-library-2.0.0\include/seqan/basic/debug_test_system.h: In instantiation of 'bool seqan::ClassTest::testEqual(const char*, int, const T1&, const char*, const T2&, const char*, const char*, ...) [with T1 = long unsigned int; T2 = long int]':

C:\seqan-library-2.0.0\include/seqan/basic/debug_test_system.h:1014:77: required from 'bool seqan::ClassTest::testEqual(const char*, int, const T1&, const char*, const T2&, const char*) [with T1 = long unsigned int; T2 = long int]'

C:\seqan-library-2.0.0\include/seqan/system/system_condition.h:114:9: required from here

C:\seqan-library-2.0.0\include/seqan/basic/debug_test_system.h:955:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]

if (!(value1 == value2))

^

In file included from C:\seqan-library-2.0.0\include/seqan/basic.h:61:0,

from C:\seqan-library-2.0.0\include/seqan/sequence.h:51,

from ..\console_1\main.cpp:2:

C:\seqan-library-2.0.0\include/seqan/basic/basic_exception.h: At global scope:

C:\seqan-library-2.0.0\include/seqan/basic/basic_exception.h:358:37: warning: 'seqan::_globalExceptionHandler' defined but not used [-Wunused-variable]

static const std::terminate_handler _globalExceptionHandler = std::set_terminate(globalExceptionHandler);

^

Makefile.Release:485: recipe for target 'release/main.o' failed

mingw32-make[1]: *** [release/main.o] Error 1

mingw32-make[1]: Leaving directory 'E:/dev/build-console_1-Desktop_Qt_5_4_0_MinGW_32bit-Release'

makefile:34: recipe for target 'release' failed

mingw32-make: *** [release] Error 2

00:20:22: The process "C:\Qt\Tools\mingw491_32\bin\mingw32-make.exe" exited with code 2.

Error while building/deploying project console_1 (kit: Desktop Qt 5.4.0 MinGW 32bit)

When executing step "Make"

00:20:22: Elapsed time: 00:03.

Live long and prosper

Bartha Dániel

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