search

mcveanlab / mccortex

De novo genome assembly and multisample variant calling
https://github.com/mcveanlab/mccortex/wiki
MIT License
113 stars 25 forks source link

bcftools doesn't compile with gcc 4.9 on MacOSX #31

Closed rec3141 closed 7 years ago

rec3141 commented 8 years ago

a la https://stackoverflow.com/questions/29534519/why-gcc-doesnt-recognize-rdynamic-option

make all | grep bcftools

cd bcftools && /Applications/Xcode.app/Contents/Developer/usr/bin/make
gcc -rdynamic  -o bcftools main.o vcfindex.o tabix.o vcfstats.o vcfisec.o vcfmerge.o vcfquery.o vcffilter.o filter.o vcfsom.o vcfnorm.o vcfgtcheck.o vcfview.o vcfannotate.o vcfroh.o vcfconcat.o vcfcall.o mcall.o vcmp.o gvcf.o reheader.o convert.o vcfconvert.o tsv2vcf.o vcfcnv.o HMM.o vcfplugin.o consensus.o ploidy.o version.o ccall.o em.o prob1.o kmin.o  ../htslib/libhts.a -lpthread -lz -lm -ldl  
gcc: error: unrecognized command line option '-rdynamic'
make[2]: *** [bcftools] Error 1
make[1]: *** [bcftools] Error 2
make: *** [libs-other] Error 2

gcc -v

Using built-in specs.
COLLECT_GCC=gcc
COLLECT_LTO_WRAPPER=/opt/local/libexec/gcc/x86_64-apple-darwin13/4.9.3/lto-wrapper
Target: x86_64-apple-darwin13
Configured with: /opt/local/var/macports/build/_opt_mports_dports_lang_gcc49/gcc49/work/gcc-4.9.3/configure --prefix=/opt/local --build=x86_64-apple-darwin13 --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-as=/opt/local/bin/as --with-ld=/opt/local/bin/ld --with-ar=/opt/local/bin/ar --with-bugurl=https://trac.macports.org/newticket --with-pkgversion='MacPorts gcc49 4.9.3_0'
Thread model: posix
gcc version 4.9.3 (MacPorts gcc49 4.9.3_0)
rec3141 commented 8 years ago

Same with samtools.

Edited libs/bcftools/Makefile and libs/samtools/Makefile to remove the flag and it compiled.

noporpoise commented 8 years ago

Thanks @rec3141. This is discussed on the bcftools issues page: samtools/bcftools#388

I'm not sure how best to fix this. I'd rather not maintain my own fork of bcftools just to fix this compilation issue. Hopefully the samtools team can provide a fix. In the meantime, you have to remove the -rdynamic flags manually from libs/bcftools/Makefile and libs/samtools/Makefile.

noporpoise commented 8 years ago

Is this still an issue?