Build fails on linking libbwa (Mac OS X) about sparkbwa HOT 3 CLOSED

Issue solved by changing the line into
LIBBWA_LIBS =

cd bwa/bwa-0.07.15
make clean
make
and the build of bwa is executed with success.

Is this option needed ?

Martijn

from sparkbwa.

Now the make fails during linking.

cp ./bwa/bwa-0.7.15/.o build
gcc -shared -o build/libbwa.so build/.o
Undefined symbols for architecture x86_64:
"_gzclose", referenced from:
_bamlite_gzclose in bamlite.o
_main_maxk in maxk.o
_err_gzclose in utils.o
(maybe you meant: _bamlite_gzclose, _err_gzclose )
"_gzdopen", referenced from:
_bamlite_gzopen in bamlite.o
_main_mem in fastmap.o
_main_maxk in maxk.o
_main_pemerge in pemerge.o
_err_xzopen_core in utils.o
"_gzerror", referenced from:
_bamlite_gzread in bamlite.o
_kseq_read in utils.o
_ks_getuntil2 in utils.o
_err_gzread in utils.o
"_gzopen", referenced from:
_bamlite_gzopen in bamlite.o
_main_maxk in maxk.o
_main_pemerge in pemerge.o
_err_xzopen_core in utils.o
(maybe you meant: _bamlite_gzopen)
"_gzread", referenced from:
_bamlite_gzread in bamlite.o
_kseq_read in utils.o
_ks_getuntil2 in utils.o
_err_gzread in utils.o
(maybe you meant: _err_gzread, _bamlite_gzread )
"_zError", referenced from:
_bamlite_gzclose in bamlite.o
_err_gzclose in utils.o
ld: symbol(s) not found for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [libbwa.so] Error 1

from sparkbwa.

Changed Makefile.common
LIBBWA_LIBS = -lz

Now the build fails on wget spark :)

I will close this issue and make a dockerfile for setup with linux.

from sparkbwa.