GapPipeline v1.0 on Mac OS X 10.5.5

[kwebb]

I am trying to compile GapPipeline v1.0 on a mac pro os x 10.5.5. I have gotten several errors - first I had to change all "unit" to "int" in several files. Now I am stuck on this error:

make --directory=QCalibration all
g++ -c -I../CommonUtils -I../MathUtils -I../Firecrest \
-I../IPAR -DHAVE_ZLIB -DHAVE_BZLIB -O2 -o Use_Bases.o ../CommonUtils/Use_Bases.cpp
/var/tmp//ccKqA13V.s:851:non-relocatable subtraction expression, "__Z7toupperi" minus "L00000000007$pb"
/var/tmp//ccKqA13V.s:851:symbol: "__Z7toupperi" can't be undefined in a subtraction expression
make[1]: *** [Use_Bases.o] Error 1
make: *** [QCalibration] Error 2


Has anyone encountered this problem or have any ideas?

[cgb]

this looks like it in the ipar code, which you dont need. is there a compile option for --no-ipar ? otherwise modify the makefiles.

[coxtonyj]

Here is my wild guess. I suspect the Mac is not liking line 90 of CommonUtils/UseBases.cpp, which uses a pointer to the C standard library function 'toupper' as a template argument.

It looks like the code is expecting the function prototype to be "int toupper(int c)" and for #include<cctype> to make that prototype visible to the compiler. So maybe you need to change the #include or maybe write a little wrapper to the Mac version of the function.

Failing that, it looks like line 90 is just converting the string useBasesOut to upper case, just replace that with another line that does it another way.

[kwebb]

Illumina directed us to this site:

http://samanthacooper.dreamhosters.com/mywiki/index.php?title=ModificationsForGAPipeline-1.0rc4

which describes the same error and a fix.

Thanks for the help!