BFAST - Help

[nilshomer]

Hi,
I can't install bfast in Ubuntu. Thanks for any help.

Same answer, install the necessary packages listed above. I am adding this to the new BFAST FAQ: https://sourceforge.net/apps/mediawi....php?title=FAQ

[Krosh]

Thank you!

[hkg]

Hi,

I am also having some problems building bfast (0.7.0a) on mac osx 10.8.5 with xcode version 3.2.6.

I am able to run the autogen.sh and ./configure successfully, but I get the following error during the make:

Undefined symbols for architecture x86_64:
"_AlignNTSpaceFillInCell", referenced from:
_AlignNTSpaceGappedBounded in AlignNTSpace.o
_AlignNTSpaceGappedConstrained in AlignNTSpace.o
"_ScoringMatrixGetColorScore", referenced from:
_AlignExact in Align.o
_AlignColorSpaceUngappedGetBest in AlignColorSpace.o
_AlignColorSpaceFillInCell in AlignColorSpace.o
_AlignColorSpaceGappedConstrained in AlignColorSpace.o
"_ScoringMatrixGetNTScore", referenced from:
_AlignExact in Align.o
_AlignNTSpaceUngapped in AlignNTSpace.o
_AlignNTSpaceGappedConstrained in AlignNTSpace.o
_AlignColorSpaceUngappedGetBest in AlignColorSpace.o
_AlignColorSpaceFillInCell in AlignColorSpace.o
_AlignColorSpaceGappedConstrained in AlignColorSpace.o
"_ToUpper", referenced from:
_AlignedReadConvertPrintAlignedEntryToCIGAR in AlignedReadConvert.o
_RGBinaryRead in RGBinary.o
_RGMatchCheck in RGMatch.o
_AlignExact in Align.o
(maybe you meant: _ToUpperRead)
ld: symbol(s) not found for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make[2]: *** [bfast] Error 1
make[1]: *** [all-recursive] Error 1
make: *** [all] Error 2

Searching online leads me to believe that it is a problem in the linking stage, but I don't know how to fix it myself. If anyone has any tips for me, or if I need to post more information, then please let me know.