Problems Building Illumina Pipeline 1.4 on Mac OS 10.5.7

[charliew]

Hi,
I'm attempting to build the new pipeline on a mac and it is failing with the errors listed below. Has anyone had any luck figuring out the modifications needed to get it to build?
thanks
charlie

-- Build files have been written to: /Users/charliew/GAPipeline-1.4.0/build
make --directory build
[ 0%] Building CXX object c++/common/CMakeFiles/ga_common.dir/Alignment.cpp.o
/Users/charliew/GAPipeline-1.4.0/c++/common/Sequence.hh:60: error: 'uint' was not declared in this scope
/Users/charliew/GAPipeline-1.4.0/c++/common/Sequence.hh:60: error: template argument 1 is invalid
/Users/charliew/GAPipeline-1.4.0/c++/common/Sequence.hh:60: error: template argument 2 is invalid
/Users/charliew/GAPipeline-1.4.0/c++/common/Alignment.cpp: In function 'Target boost::lexical_cast(const Source&) [with Target = ga::common::Match::NonMatchReason, Source = std::string]':
/Users/charliew/GAPipeline-1.4.0/c++/common/Alignment.cpp:42: error: 'uint' was not declared in this scope
/Users/charliew/GAPipeline-1.4.0/c++/common/Alignment.cpp:42: error: expected `;' before 'num_exact'
/Users/charliew/GAPipeline-1.4.0/c++/common/Alignment.cpp:44: error: 'num_exact' was not declared in this scope
/Users/charliew/GAPipeline-1.4.0/c++/common/Alignment.cpp:44: error: 'num_single' was not declared in this scope
/Users/charliew/GAPipeline-1.4.0/c++/common/Alignment.cpp:44: error: 'num_double' was not declared in this scope
make[3]: *** [c++/common/CMakeFiles/ga_common.dir/Alignment.cpp.o] Error 1
make[2]: *** [c++/common/CMakeFiles/ga_common.dir/all] Error 2
make[1]: *** [all] Error 2
make: *** [all] Error 2

[rlove]

Hi

I managed to get 1.4 to compile on 10.5.7 by changing every instance of 'uint' to 'unsigned int'. You will need to do this on every .cpp (and I think one .hh) file that is used during the compile process (I think there are three or four).

Hope that helps!

[charliew]

uint to unsigned int

Hi,
Thanks a lot, I've started working thought he files. When you said 3 or 4, did you mean 3 or 4 changes total?

I'm finding lots more instances of uint than that in the:

~/GAPipeline-1.4.0/c++/programs/*cpp

folder

thanks

charlie

[rlove]

No, it's 3 or four files, within which there were many instances of 'uint' (i'm afraid!).

[charliew]

thanks very much, you have been super helpful. 1.4.0 now builds fine. I've done some preliminary testing and it looks to be working fine. Same raw cluster numbers, significantly higher PF%.

Here are some slightly more explicit instructions.

----------------
replace all instances of "uint" in the files:

~/GAPipeline-1.4.0/c++/common/Sequence.cpp
~/GAPipeline-1.4.0/c++/common/Sequence.hh
~/GAPipeline-1.4.0/c++/common/Alignment.cpp
~/GAPipeline-1.4.0/c++/alignment/pickBestPairUtils.cpp
~/GAPipeline-1.4.0/c++/alignment/pickBestPairUtils.hh
~/GAPipeline-1.4.0/c++/programs/pickBestPair.cpp

with "unsigned int"

[mmuratet]

Hi

I managed to get 1.4 to compile on 10.5.7 by changing every instance of 'uint' to 'unsigned int'. You will need to do this on every .cpp (and I think one .hh) file that is used during the compile process (I think there are three or four).

Hope that helps!

How did you get around their 'cmake' build system? (Pretty cool, though!)

[dawe]

You don't... Just install it (it is included in GAP-1.4 or via MacPorts).
BTW, I've tried GAP <= 1.3 on OS X and I had some issues with it. Unfortunately GAP relies on GNU userland tools which differ from BSD tools shipped with OS X (and FreeBSD). I had to modify goat to make it work.

d