Comments (2)
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
from pindel.
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!
from pindel.
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