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Makefile broken on OSX - linker ld options #4

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tseemann opened this issue Apr 11, 2015 · 1 comment
Open

Makefile broken on OSX - linker ld options #4

tseemann opened this issue Apr 11, 2015 · 1 comment

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@tseemann
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Erik, another minor fix to help vcflib compile on OSX:

  * linking smithwaterman
ld: warning: option -s is obsolete and being ignored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)
make: *** [smithwaterman] Error 1

This is the error command:

c++ -Wl,-s -Wall -O3 -o smithwaterman smithwaterman.o BandedSmithWaterman.o SmithWatermanGotoh.o Repeats.o LeftAlign.o IndelAllele.o disorder.o

It works if you remove the ",-s" in the LDFLAGS which I think in Linux/GCC just strips the symbol table.

LDFLAGS=-Wl,-s => LDFLAGS=-Wl

@SHuang-Broad
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Same linker error with similar error message. The fix proposed worked.

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