dridk
commented
6 years ago After setting :
DEFINES += "SEQAN_ASYNC_IO=0"I pass the aio.h error and get a new one :
error: sys/mman.h: No such file or directoryClosed dridk closed 5 years ago
dridk
commented
6 years ago After setting :
DEFINES += "SEQAN_ASYNC_IO=0"I pass the aio.h error and get a new one :
error: sys/mman.h: No such file or directoryAfter removing :
// #include <sys/mman.h> I get lot a new error :
D:/Qt/Tools/mingw530_32/bin/mingw32-make -f Makefile.Debug
mingw32-make[1]: Entering directory 'C:/Users/home/Documents/GitHub/build-bamviewer-Desktop_Qt_5_9_1_MinGW_32bit-Debug'
g++ -c -fno-keep-inline-dllexport -pipe -W -Wall -Wno-long-long -pedantic -Wno-variadic-macros -g -std=gnu++1y -Wextra -Wall -W -fexceptions -mthreads -DUNICODE -DQT_DEPRECATED_WARNINGS -DSEQAN_HAS_ZLIB=1 -DSEQAN_ENABLE_DEBUG=1 -DDSEQAN_ENABLE_TESTING=1 -DSEQAN_ASYNC_IO=0 -DNDEBUG -DQT_QML_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_NEEDS_QMAIN -I..\bamviewer-poc -I. -I..\bamviewer-poc -I..\bamviewer-poc\track -ID:\Qt\5.9.1\mingw53_32\include -ID:\Qt\5.9.1\mingw53_32\include\QtWidgets -ID:\Qt\5.9.1\mingw53_32\include\QtGui -ID:\Qt\5.9.1\mingw53_32\include\QtANGLE -ID:\Qt\5.9.1\mingw53_32\include\QtCore -Idebug -I. -ID:\Qt\5.9.1\mingw53_32\mkspecs\win32-g++ -o debug\abstracttrack.o ..\bamviewer-poc\track\abstracttrack.cpp
In file included from D:/Qt/Tools/mingw530_32/i686-w64-mingw32/include/crtdefs.h:10:0,
from D:/Qt/Tools/mingw530_32/i686-w64-mingw32/include/stddef.h:7,
from D:/Qt/Tools/mingw530_32/lib/gcc/i686-w64-mingw32/5.3.0/include/stddef.h:1,
from D:/Qt/Tools/mingw530_32/i686-w64-mingw32/include/c++/cstddef:45,
from D:\Qt\5.9.1\mingw53_32\include\QtCore/qglobal.h:46,
from D:\Qt\5.9.1\mingw53_32\include\QtCore/QtCore:4,
from ..\bamviewer-poc\track\abstracttrack.h:3,
from ..\bamviewer-poc\track\abstracttrack.cpp:1:
..\bamviewer-poc/seqan/platform.h:290:17: error: declaration does not declare anything [-fpermissive]
typedef int64_t __int64; // nolint
^
..\bamviewer-poc/seqan/platform.h:292:17: error: multiple types in one declaration
typedef int32_t __int32; // nolint
^
..\bamviewer-poc/seqan/platform.h:292:17: error: declaration does not declare anything [-fpermissive]
..\bamviewer-poc/seqan/platform.h:294:17: error: declaration does not declare anything [-fpermissive]
typedef int16_t __int16; // nolint
^
..\bamviewer-poc/seqan/platform.h:296:16: error: multiple types in one declaration
typedef int8_t __int8; // nolint
^
..\bamviewer-poc/seqan/platform.h:296:16: error: declaration does not declare anything [-fpermissive]
In file included from ..\bamviewer-poc/seqan/basic/basic_debug.h:52:0,
from ..\bamviewer-poc/seqan/basic.h:49,
from ..\bamviewer-poc/seqan/seq_io.h:44,
from ..\bamviewer-poc/trackviewer.h:6,
from ..\bamviewer-poc\track\abstracttrack.h:5,
from ..\bamviewer-poc\track\abstracttrack.cpp:1:
..\bamviewer-poc/seqan/basic/debug_test_system.h: In function 'const char* seqan::ClassTest::tempFileName()':
..\bamviewer-poc/seqan/basic/debug_test_system.h:709:31: error: too many arguments to function 'int mkdir(const char*)'
mkdir(fileNameBuffer, 0777);
^
In file included from D:/Qt/Tools/mingw530_32/i686-w64-mingw32/include/unistd.h:10:0,
from ..\bamviewer-poc/seqan/basic/debug_test_system.h:165,
from ..\bamviewer-poc/seqan/basic/basic_debug.h:52,
from ..\bamviewer-poc/seqan/basic.h:49,
from ..\bamviewer-poc/seqan/seq_io.h:44,
from ..\bamviewer-poc/trackviewer.h:6,
from ..\bamviewer-poc\track\abstracttrack.h:5,
from ..\bamviewer-poc\track\abstracttrack.cpp:1:
D:/Qt/Tools/mingw530_32/i686-w64-mingw32/include/io.h:271:15: note: declared here
int __cdecl mkdir (const char *) __MINGW_ATTRIB_DEPRECATED_MSVC2005;
^
In file included from ..\bamviewer-poc/seqan/system.h:84:0,
from ..\bamviewer-poc/seqan/file.h:73,
from ..\bamviewer-poc/seqan/stream.h:62,
from ..\bamviewer-poc/seqan/seq_io.h:45,
from ..\bamviewer-poc/trackviewer.h:6,
from ..\bamviewer-poc\track\abstracttrack.h:5,
from ..\bamviewer-poc\track\abstracttrack.cpp:1:
..\bamviewer-poc/seqan/system/file_sync.h: In member function 'bool seqan::File<seqan::Sync<TSpec> >::openTemp(int)':
..\bamviewer-poc/seqan/system/file_sync.h:322:21: error: there are no arguments to 'getuid' that depend on a template parameter, so a declaration of 'getuid' must be available [-fpermissive]
if ((getuid() == geteuid()) && (getgid() == getegid()))
^
..\bamviewer-poc/seqan/system/file_sync.h:322:21: note: (if you use '-fpermissive', G++ will accept your code, but allowing the use of an undeclared name is deprecated)
..\bamviewer-poc/seqan/system/file_sync.h:322:34: error: there are no arguments to 'geteuid' that depend on a template parameter, so a declaration of 'geteuid' must be available [-fpermissive]
if ((getuid() == geteuid()) && (getgid() == getegid()))
^
..\bamviewer-poc/seqan/system/file_sync.h:322:48: error: there are no arguments to 'getgid' that depend on a template parameter, so a declaration of 'getgid' must be available [-fpermissive]
if ((getuid() == geteuid()) && (getgid() == getegid()))
^
..\bamviewer-poc/seqan/system/file_sync.h:322:61: error: there are no arguments to 'getegid' that depend on a template parameter, so a declaration of 'getegid' must be available [-fpermissive]
if ((getuid() == geteuid()) && (getgid() == getegid()))
^
In file included from ..\bamviewer-poc/seqan/file.h:83:0,
from ..\bamviewer-poc/seqan/stream.h:62,
from ..\bamviewer-poc/seqan/seq_io.h:45,
from ..\bamviewer-poc/trackviewer.h:6,
from ..\bamviewer-poc\track\abstracttrack.h:5,
from ..\bamviewer-poc\track\abstracttrack.cpp:1:
..\bamviewer-poc/seqan/file/file_page.h: In function 'bool seqan::mapReadPage(seqan::Buffer<TValue, seqan::PageFrame<TFile, TSpec> >&, TFile&, TSize)':
..\bamviewer-poc/seqan/file/file_page.h:698:63: error: 'PROT_READ' was not declared in this scope
pf.begin = (TValue*)mmap(NULL, size * sizeof(TValue), PROT_READ | PROT_WRITE, MAP_PRIVATE, file.handle, (TPos)pf.pageNo * (TPos)capacity(pf) * (TPos)sizeof(TValue));
^
..\bamviewer-poc/seqan/file/file_page.h:698:75: error: 'PROT_WRITE' was not declared in this scope
pf.begin = (TValue*)mmap(NULL, size * sizeof(TValue), PROT_READ | PROT_WRITE, MAP_PRIVATE, file.handle, (TPos)pf.pageNo * (TPos)capacity(pf) * (TPos)sizeof(TValue));
^
..\bamviewer-poc/seqan/file/file_page.h:698:87: error: 'MAP_PRIVATE' was not declared in this scope
pf.begin = (TValue*)mmap(NULL, size * sizeof(TValue), PROT_READ | PROT_WRITE, MAP_PRIVATE, file.handle, (TPos)pf.pageNo * (TPos)capacity(pf) * (TPos)sizeof(TValue));
^
..\bamviewer-poc/seqan/file/file_page.h:700:25: error: 'MAP_FAILED' was not declared in this scope
if (pf.begin == MAP_FAILED)
^
..\bamviewer-poc/seqan/file/file_page.h: In function 'bool seqan::mapWritePage(seqan::Buffer<TValue, seqan::PageFrame<TFile, TSpec> >&, TFile&, TSize)':
..\bamviewer-poc/seqan/file/file_page.h:723:63: error: 'PROT_READ' was not declared in this scope
pf.begin = (TValue*)mmap(NULL, size * sizeof(TValue), PROT_READ | PROT_WRITE, MAP_SHARED, file.handle, (TPos)pf.pageNo * (TPos)capacity(pf) * (TPos)sizeof(TValue));
^
..\bamviewer-poc/seqan/file/file_page.h:723:75: error: 'PROT_WRITE' was not declared in this scope
pf.begin = (TValue*)mmap(NULL, size * sizeof(TValue), PROT_READ | PROT_WRITE, MAP_SHARED, file.handle, (TPos)pf.pageNo * (TPos)capacity(pf) * (TPos)sizeof(TValue));
^
..\bamviewer-poc/seqan/file/file_page.h:723:87: error: 'MAP_SHARED' was not declared in this scope
pf.begin = (TValue*)mmap(NULL, size * sizeof(TValue), PROT_READ | PROT_WRITE, MAP_SHARED, file.handle, (TPos)pf.pageNo * (TPos)capacity(pf) * (TPos)sizeof(TValue));
^
..\bamviewer-poc/seqan/file/file_page.h:725:25: error: 'MAP_FAILED' was not declared in this scope
if (pf.begin == MAP_FAILED)
^
In file included from ..\bamviewer-poc/seqan/file.h:84:0,
from ..\bamviewer-poc/seqan/stream.h:62,
from ..\bamviewer-poc/seqan/seq_io.h:45,
from ..\bamviewer-poc/trackviewer.h:6,
from ..\bamviewer-poc\track\abstracttrack.h:5,
from ..\bamviewer-poc\track\abstracttrack.cpp:1:
..\bamviewer-poc/seqan/file/file_mapping.h: At global scope:
..\bamviewer-poc/seqan/file/file_mapping.h:117:18: error: 'POSIX_MADV_NORMAL' was not declared in this scope
MAP_NORMAL = POSIX_MADV_NORMAL,
^
..\bamviewer-poc/seqan/file/file_mapping.h:118:18: error: 'POSIX_MADV_RANDOM' was not declared in this scope
MAP_RANDOM = POSIX_MADV_RANDOM,
^
..\bamviewer-poc/seqan/file/file_mapping.h:119:22: error: 'POSIX_MADV_SEQUENTIAL' was not declared in this scope
MAP_SEQUENTIAL = POSIX_MADV_SEQUENTIAL,
^
..\bamviewer-poc/seqan/file/file_mapping.h:120:20: error: 'POSIX_MADV_WILLNEED' was not declared in this scope
MAP_WILLNEED = POSIX_MADV_WILLNEED,
^
..\bamviewer-poc/seqan/file/file_mapping.h:121:20: error: 'POSIX_MADV_DONTNEED' was not declared in this scope
MAP_DONTNEED = POSIX_MADV_DONTNEED
^
..\bamviewer-poc/seqan/file/file_mapping.h: In function 'bool seqan::flushFileSegment(seqan::FileMapping<TSpec>&, void*, TPos, TSize)':
..\bamviewer-poc/seqan/file/file_mapping.h:565:62: error: 'MS_SYNC' was not declared in this scope
return (msync(static_cast<char*>(addr) + beginPos, size, MS_SYNC) == 0);
^
..\bamviewer-poc/seqan/file/file_mapping.h: In function 'bool seqan::cancelFileSegment(seqan::FileMapping<TSpec>&, void*, TPos, TSize)':
..\bamviewer-poc/seqan/file/file_mapping.h:594:41: error: 'MS_INVALIDATE' was not declared in this scope
return (msync(addr, size + fileOfs, MS_INVALIDATE) == 0);
^
..\bamviewer-poc/seqan/file/file_mapping.h: In function 'void* seqan::mapFileSegment(seqan::FileMapping<TSpec>&, TPos, TSize, TFileMappingMode)':
..\bamviewer-poc/seqan/file/file_mapping.h:677:36: error: 'PROT_READ' was not declared in this scope
if (mode & MAP_RDONLY) prot |= PROT_READ;
^
..\bamviewer-poc/seqan/file/file_mapping.h:678:36: error: 'PROT_WRITE' was not declared in this scope
if (mode & MAP_WRONLY) prot |= PROT_WRITE;
^
..\bamviewer-poc/seqan/file/file_mapping.h:682:18: error: 'MAP_PRIVATE' was not declared in this scope
flags |= MAP_PRIVATE;
^
..\bamviewer-poc/seqan/file/file_mapping.h:684:18: error: 'MAP_SHARED' was not declared in this scope
flags |= MAP_SHARED;
^
..\bamviewer-poc/seqan/file/file_mapping.h:695:17: error: 'MAP_FAILED' was not declared in this scope
if (addr == MAP_FAILED)
^
Makefile.Debug:2646: recipe for target 'debug/abstracttrack.o' failed
mingw32-make[1]: Leaving directory 'C:/Users/home/Documents/GitHub/build-bamviewer-Desktop_Qt_5_9_1_MinGW_32bit-Debug'
mingw32-make[1]: *** [debug/abstracttrack.o] Error 1
Makefile:36: recipe for target 'debug' failed
mingw32-make: *** [debug] Error 2
02:13:34: The process "D:\Qt\Tools\mingw530_32\bin\mingw32-make.exe" exited with code 2.
Error while building/deploying project bamviewer (kit: Desktop Qt 5.9.1 MinGW 32bit)
When executing step "Make"
02:13:34: Elapsed time: 00:11I finally success to compile win mingw32 by removing uncompiled codes from seqan... It's ugly, and I don't know what it does. If you want to see what I changed in seqan :
h-2
commented
6 years ago @dridk Thanks for working on this! We would be interested in merging this, but only if you can provide a clean pull-request against our develop-branch and all tests pass (in edge cases some tests might also be be disabled, but not only for very minor things).
h-2
commented
5 years ago We are working on MinGW support in SeqAn3. If you want this in SeqAn2, please open a pull request!
Hi,
I didn't success to compile a"Qt hello word" with seqan. Here is my try : https://github.com/dridk/seqanwinqt Bellow are my compile error. If you resolve my issue, you win all my respect :D
Using mingw 5.3 32 bits :
Using MSVC2015 64 bits