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 r...@sanger.ac.uk
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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