#1 compile error

[Anonymous]

When trying to compile SNPmatic on a Linux machine
(specifically Ubuntu Linux 5.1, kernel 2.6.12, gcc 4.01),
and after setting the appropriate Makefile variables to
point to the Affymetrix File SDK, I get the following
error:

../lib/FileHandler/Normalization.cpp: In member
function ‘float CSketchNormalization::GetFactor(const
int&, const float&)’:
../lib/FileHandler/Normalization.cpp:74: error: ‘ceil’
was not declared in this scope
make: *** [../lib/FileHandler/Normalization.o] Error 1

Tracing back to the relevant file in Normalization.cpp,
here is the problem line:

int col = static_cast<int>(ceil(Intensity/m_nBinSize))

The syntax looks ok to me, any thoughts on how to fix
this? Thanks, Finny Kuruvilla (kuruvilla at molbio dot
mgh dot harvard.edu).

[Simon Cawley]

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user_id=1407936

Hi Finny,

I can't replicate that error on my system (linux 2.4.20
kernel & gcc 3.2) but I suspect that it may be alleviated by
adding "#include <math.h>" in lib/FileHandler/Normalization.h

-Simon

[Nobody/Anonymous]

Logged In: NO

Yes Simon, you are right. That does fix the problem.
Thanks, Finny

[Hin-Tak Leung]

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user_id=506848

Hmm, the correct C++ way to do it is insert
"#include <cmath>" rather than "#include <math.h".
In addition to that, "using namespace std;" is needed in
both of these two files (because you were using std::ceil
and std::log10 without the std:: in front).

lib/FileHandler/Normalization.cpp
lib/FileHandler/FileHandler.cpp

GCC 4.x probably have much stricter C++ sematic checks.

gcc --version
gcc (GCC) 4.0.2 20051125 (Red Hat 4.0.2-8)

Hi Simon, this is Hin-Tak from WTCCC/CIMR.