Re: [Samtools-help] warnings with htslib on MacOS

[Robert D. <rm...@sa...>]

On Sat, 16 Jun 2018, Richard Durbin wrote:

> Hello Shane and Rob,
>
> I am fixing a problem with pbwt, and now I get link warnings for htslib with a current github install:
>
> [Richards-MacBook-Pro:~/tmp/pbwt] rd% make
> cc -g -O3 -I../htslib   pbwtMain.o pbwtCore.o pbwtSample.o pbwtIO.o pbwtMatch.o pbwtImpute.o pbwtPaint.o pbwtLikelihood.o pbwtMerge.o pbwtGeneticMap.o pbwtHtslib.o hash.o dict.o array.o utils.o -lpthread ../htslib/libhts.a -lz -lm -lbz2 -llzma -o pbwt
> ld: warning: could not create compact unwind for _vcf_parse_format.isra.19: stack subq instruction is too different from dwarf stack size
> ld: warning: could not create compact unwind for _cram_populate_ref: stack subq instruction is too different from dwarf stack size
> ld: warning: could not create compact unwind for _rans_uncompress_O0: stack subq instruction is too different from dwarf stack size
>
> I haven’t seen this before.  Should I just ignore these, or is there a way to remove them?

A web search suggests that this warning shows up when linking using real 
gcc (not the gcc wrapper around llvm that comes with Xcode).  It looks 
like there are a couple of solutions:

1. Use clang instead of gcc

2. Use the -no_compact_unwind linker option.  To do this with htslib, the 
best way would be:

./configure LDFLAGS='-Wl,-no_compact_unwind'
make

This linker option appears to be harmless when used with clang and the 
llvm gcc wrapper.  Unfortunately I haven't been able to test real gcc yet 
as homebrew appears to want to build it from scratch, which takes rather a 
long time.

To see if you're using the real gcc, run `gcc -v`.  If it says 'Apple 
LLVM' somewhere then it's the wrapper and not the real thing.

Rob Davies              rm...@sa...
The Sanger Institute    http://www.sanger.ac.uk/
Hinxton, Cambs.,        Tel. +44 (1223) 834244
CB10 1SA, U.K.          Fax. +44 (1223) 494919


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