I'm trying to install GMAP GSNAP on my mac following all the README.txt instructions. ./configure works fine but "make" runs for some time but eventually gives me this error message.
sarray-read.c:2407:13: error: always_inline function '_pext_u32' requires target feature 'bmi2', but would be inlined into function
'fill_positions_filtered_first' that is compiled without support for 'bmi2'
selector = _pext_u32(univ_selector,mask);
1 error generated.
make[2]: *** [gsnap_avx2-sarray-read.o] Error 1
make[1]: *** [all] Error 2
make: *** [all-recursive] Error 1
Can anybody give me a hint what these errors mean. Thank you,
1 answer
Are you perhaps using an outdated compiler? You can check the version using
gcc --version
oh right, missed the mac part
Here is what I get for gcc version.
Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr --with-gxx-include-dir=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.11.sdk/usr/include/c++/4.2.1
Apple LLVM version 7.3.0 (clang-703.0.31)
Target: x86_64-apple-darwin15.5.0
Thread model: posix
InstalledDir: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin
Does that look out of date to you?
That looks like the latest Xcode.
Googling around for that error seems to indicate that this may not be a simple fix. Perhaps a C++/Clang programmer would suggest a workaround.
In a pinch you could look at this site and try the workarounds suggested: https://github.com/juliangehring/GMAP-GSNAP
From what I heard the author is very responsive in email, so contacting him might be worth trying.
Glad that your problem is solved, good luck with the analysis.
Current gcc is 6.1, but I guess that's not easy to upgrade... GMAP GSNAP works fine here, compiled using GCC 4.4.7
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Have you installed/updated to the latest Xcode and command line tools for OS X?
I think I have the latest Xcode: Version 7.3.1 (7D1014)