#24 Qt and toAmos_new

[Lizzy Wilbanks]

Hi folks,

I'm having two issues, not clear if they're related though.

1) Despite my best efforts, Qt4 won't play nicely with AMOS. I passed the path to my Qt 4.8.4 installation (also have tried putting qmake directly in my path). During configuration step, it finds Qt4 but fails the working test. Configure finishes OK but with a blurb about how Qt is malfunctioning. So far as I can tell qmake works fine when I run independently - what's going wrong here?
...
checking for Qt4... yes
checking whether Qt4 works... no

2) error running make.

Making all in Converters
make[3]: Entering directory `/home/ewilbanks/software/amos-3.1.0/src/Converters'
g++ -DHAVE_CONFIG_H -I. -I../.. -I/home/ewilbanks/software/wgs-7.0/Linux-amd64//../src -I/home/ewilbanks/software/wgs-7.0/Linux-amd64//../src/AS_MSG -I/home/ewilbanks/software/wgs-7.0/Linux-amd64//../src/AS_UTL -DAMOS_HAVE_CA -I../../src/AMOS -I../../src/Common -g -O2 -MT toAmos_new-toAmos_new.o -MD -MP -MF .deps/toAmos_new-toAmos_new.Tpo -c -o toAmos_new-toAmos_new.o `test -f 'toAmos_new.cc' || echo './'`toAmos_new.cc
In file included from /home/ewilbanks/software/wgs-7.0/Linux-amd64//../src/AS_MSG/AS_MSG_pmesg.h:33,
from toAmos_new.cc:38:
/home/ewilbanks/software/wgs-7.0/Linux-amd64//../src/AS_global.h:102:2: error: #error UINT32_MAX not defined; if new code, AS_global.h must be the first include
toAmos_new.cc: In function 'bool parseMatesFile(std::ifstream&)':
toAmos_new.cc:764: warning: converting to 'AMOS::Pos_t' from 'float'
toAmos_new.cc:765: warning: converting to 'AMOS::SD_t' from 'float'
toAmos_new.cc: In function 'bool parseFrgFile(std::string)':
toAmos_new.cc:856: warning: converting to 'AMOS::Pos_t' from 'double'
toAmos_new.cc:857: warning: converting to 'AMOS::SD_t' from 'double'
toAmos_new.cc:879: warning: converting to 'AMOS::Pos_t' from 'double'
toAmos_new.cc:880: warning: converting to 'AMOS::SD_t' from 'double'
toAmos_new.cc: In function 'bool parseAsmFile(std::string)':
toAmos_new.cc:1237: warning: passing 'double' for argument 1 to 'void AMOS::Link_t::setSize(AMOS::Size_t)'
toAmos_new.cc:1238: warning: passing 'double' for argument 1 to 'void AMOS::Link_t::setSD(AMOS::SD_t)'
toAmos_new.cc:1252: warning: passing 'double' for argument 1 to 'void AMOS::Link_t::setSize(AMOS::Size_t)'
toAmos_new.cc:1253: warning: passing 'double' for argument 1 to 'void AMOS::Link_t::setSD(AMOS::SD_t)'
toAmos_new.cc:1270: warning: passing 'double' for argument 1 to 'void AMOS::Link_t::setSize(AMOS::Size_t)'
toAmos_new.cc:1271: warning: passing 'double' for argument 1 to 'void AMOS::Link_t::setSD(AMOS::SD_t)'
toAmos_new.cc:1310: warning: converting to 'int32_t' from 'double'
make[3]: *** [toAmos_new-toAmos_new.o] Error 1
make[3]: Leaving directory `/home/ewilbanks/software/amos-3.1.0/src/Converters'
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory `/home/ewilbanks/software/amos-3.1.0/src'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/home/ewilbanks/software/amos-3.1.0'
make: *** [all] Error 2

My CA installation was built from source with the modification to AS_GLOBAL.h for pacbio reads
https://sourceforge.net/apps/mediawiki/wgs-assembler/index.php?title=Check_out_and_Compile

Could this be related to the make issue?

Thanks
Lizzy

[Sergey Koren]

Hi,

The cause of the Converter build error is that CA 7.0 made a change that is
not compatible with AMOS 3.1.0. You can patch the code in
src/Coverters/toAmos_new.cc to add
#ifdef AMOS_HAVE_CA
#include "AS_global.h"
#endif

to the beginning (before extern "C" {).
The repository of AMOS also fixes this bug.