[SOLVED] issue with compiling pindel on OS X about pindel

[EWLameijer]

Hello Odoland,

at first sight, you seem to have done things correctly, though I'm a bit confused why you called the ./INSTALL with the samtools directory, as current versions of Pindel require the htslib directory.

Looking at the error message, it refers to clang, which means that for some reason g++ was not properly 'overruled' to gcc.

As I'm not much of an OSX expert, I can only guess to the reason - is it possible that using cd src, make clean, make CXX=g++-6 did not work properly? I would in any case try to make it four 'normal' commands (cd src [ENTER] make clean [ENTER] etc.) [this may not work, but I can't check it myself as I still need to call a OSX-expert to undestroy my compiler installation]

Perhaps Kai has some tips, but in any case I would search in the direction of how to overload clang correctly.

Best regards,

Eric-Wubbo

[odoland]

Hi, I finally got pindel to compile successfully on OS X, and I would like to share how in here for others who may be Googling the problem.

First, follow the FAQ. Install g++ and gcc (any version after 4.9 has OpenMP). Then, type the command so the compiler OS X uses is gcc-6 and not clang.

$CC=gcc-6 CXX=g++-6 ./INSTALL /path/to/htslib

I ran into another error after this on the bddata.cpp. It was:
error: call of overloaded abs is ambiguous

After an extensive google search, I found this,
http://stackoverflow.com/questions/30084577/ambiguous-call-to-abs

So I went to the bddata.cpp file (located under /htslib/src), opened it up with vim editor.

I added these libraries to the header:

#include <cmath>
#include <cstdlib>
#include <cstdint>

and then I replaced every instance of abs( in the code to fabs(
The command to find and replace with vim is
:%s/abs(/fabs(/g
Find each occurrence of 'abs(' (in all lines), and replace it with 'fabs('.

After this, it finally worked!

Best of luck!