Thanks. I am confused about the llvm and gcc status of my gcc. Whatever it
is, it seems to mess up gdb for me. The output of `gcc -v` is below.
However, given that it seems to work despite the warnings, my current view is
that life is too short to sort this out, so I am going to carry on ignoring it
until my world descends into dependency chaos.
Richard
[Richards-MacBook-Pro:~/src] rd% gcc -v
Using built-in specs.
COLLECT_GCC=gcc
COLLECT_LTO_WRAPPER=/opt/local/libexec/gcc/x86_64-apple-darwin16/4.9.4/lto-wrapper
Target: x86_64-apple-darwin16
Configured with:
/opt/local/var/macports/build/_opt_bblocal_var_buildworker_ports_build_ports_lang_gcc49/gcc49/work/gcc-4.9.4/configure
--prefix=/opt/local --build=x86_64-apple-darwin16
--enable-languages=c,c++,objc,obj-c++,lto,fortran,java
--libdir=/opt/local/lib/gcc49 --includedir=/opt/local/include/gcc49
--infodir=/opt/local/share/info --mandir=/opt/local/share/man
--datarootdir=/opt/local/share/gcc-4.9 --with-local-prefix=/opt/local
--with-system-zlib --disable-nls --program-suffix=-mp-4.9
--with-gxx-include-dir=/opt/local/include/gcc49/c++/ --with-gmp=/opt/local
--with-mpfr=/opt/local --with-mpc=/opt/local --with-isl=/opt/local
--disable-isl-version-check --with-cloog=/opt/local
--disable-cloog-version-check --enable-stage1-checking --disable-multilib
--enable-lto --enable-libstdcxx-time --with-build-config=bootstrap-debug
--with-as=/opt/local/bin/as --with-ld=/opt/local/bin/ld
--with-ar=/opt/local/bin/ar --with-bugurl=https://trac.macports.org/newticket
--disable-tls --with-pkgversion='MacPorts gcc49 4.9.4_2'
--with-build-config=bootstrap-debug
Thread model: posix
gcc version 4.9.4 (MacPorts gcc49 4.9.4_2)
> On 18 Jun 2018, at 17:34, Robert Davies <r...@sanger.ac.uk> wrote:
>
> 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
>
>
> --
> The Wellcome Sanger Institute is operated by Genome Research Limited, a
> charity registered in England with number 1021457 and a company registered in
> England with number 2742969, whose registered office is 215 Euston Road,
> London, NW1 2BE.
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