3,045
edits
Changes
From Genome Analysis Wiki
Jump to navigationJump to searchno edit summary
__TOC__
__TOC__
For problems with libStatGen, see [[LibStatGen Troubleshooting]]
= Compile Problems =
= Compile Problems =
# Set CXX11_AVAIL = 0 in your environment
# Set CXX11_AVAIL = 0 in your environment
By making one of these changes, the code should compile and use map instead of unordered_map.
By making one of these changes, the code should compile and use map instead of unordered_map.
==ld: lto: could not merge in ../obj/BamExecutable.o because Unknown instruction for architecture x86_64==
: ERROR:
<pre>
ld: lto: could not merge in ../obj/BamExecutable.o because Unknown instruction for architecture x86_64
collect2: ld returned 1 exit status
make[2]: *** [../bin/bam] Error 1
make[1]: *** [src] Error 2
make: *** [bamUtil/] Error 2
</pre>
: This error was seen when running on Mac OS X 10.7.5 on a 64-bit kernel with gcc/g++: i686-apple-darwin11-llvm-g++-4.2 (GCC) 4.2.1 (Based on Apple Inc. build 5658) (LLVM build 2336.1.00)
: The error appears to be due to the default build optimization: -O4
: If you see this error, try compiling for debug (optimization -O0): <code>'''make debug'''</code>
: The debug executable is: <code>'''bamUtil/bin/debug/bam'''</code>
: If the debug compile worked and you would prefer an optimized executable (runs a little faster), then update the optimization flag to -O3:
:# Open '''libStatGen/Makefiles/Makefile.include'''
:# Change <code>OPTFLAG_OPT?=-O4</code> to <code>'''OPTFLAG_OPT?=-O3'''</code>
:# Run <code>'''make clean; make'''</code> in both libStatGen and bamUtil
:# The optimized executable is <code>'''bamUtil/bin/bam'''</code>
