Compilation failed in max osx mavericks, fix provided

[thomasvangurp]

Freebayes failed to compile correctly in OSX mavericks with cmake. I got the following warning:

  * linking smithwaterman
Apple LLVM version 5.1 (clang-503.0.40) (based on LLVM 3.4svn)
Target: x86_64-apple-darwin13.3.0
Thread model: posix
clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated
 "/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/clang" -cc1 -triple x86_64-apple-macosx10.9.0 -emit-obj -disable-free -disable-llvm-verifier -main-file-name disorder.c -mrelocation-model pic -pic-level 2 -mdisable-fp-elim -masm-verbose -munwind-tables -target-cpu core2 -target-linker-version 236.3 -v -v -resource-dir /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.1 -stdlib=libc++ -O3 -Wall -fdeprecated-macro -fdebug-compilation-dir /usr/local/freebayes/vcflib/smithwaterman -ferror-limit 19 -fmessage-length 236 -stack-protector 1 -mstackrealign -fblocks -fobjc-runtime=macosx-10.9.0 -fencode-extended-block-signature -fcxx-exceptions -fexceptions -fdiagnostics-show-option -fcolor-diagnostics -vectorize-loops -vectorize-slp -o /var/tmp/disorder-c85c37.o -x c++ disorder.c
clang -cc1 version 5.1 based upon LLVM 3.4svn default target x86_64-apple-darwin13.3.0
ignoring nonexistent directory "/usr/include/c++/v1"
#include "..." search starts here:
#include <...> search starts here:
 /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1
 /usr/local/include
 /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.1/include
 /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include
 /usr/include
 /System/Library/Frameworks (framework directory)
 /Library/Frameworks (framework directory)
End of search list.
 "/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ld" -demangle -dynamic -arch x86_64 -macosx_version_min 10.9.0 -o smithwaterman -s smithwaterman.o BandedSmithWaterman.o SmithWatermanGotoh.o Repeats.o /var/tmp/disorder-c85c37.o LeftAlign.o IndelAllele.o disorder.o -lc++ -lSystem /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.1/lib/darwin/libclang_rt.osx.a
ld: warning: option -s is obsolete and being ignored
ld: internal error: atom not found in symbolIndex(__ZNKSt3__16vectorINS_4pairIicEENS_9allocatorIS2_EEE8max_sizeEv) for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)

commenting out the -s flag from the MakeFile in /vcflib/smithwaterman like this:
LDFLAGS=-Wl,-v #-s
fixed the issue.

[tseemann]

Looks like I rediscovered this: ekg/smithwaterman#4

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[github-actions]

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