Hello. everyone
I downloaded the bwa version 5.7 and cannot compile it on Macbook Pro (10.6.3).
I challenged following steps.
On make command, I can not continue the installation.
I think The linker is complaining that it cannot find the math library. I am not sure why this may happen. One thing I tried to remove the "-m64" option on the CFLAG line in Makefile. But I could not remove this error.
Any idea what the problem on my pc ?
And error message desribed below(Here, I did not removed -m64 option).
------------------------------------------------------
gcc -Wall -m64 -fPIC -g -O2 -o bwa is.o bwtmisc.o bwtindex.o simple_dp.o bwape.o bwtsw2_core.o bwtsw2_main.o bwtsw2_aux.o bwt_lite.o bwtsw2_chain.o main.o bwt_gen/libbwtgen.a libbwacore.a -lpthread -lz -lm
Undefined symbols:
"_egzclose", referenced from:
_bwa_index in bwtindex.o
_bwa_index in bwtindex.o
_bwa_stdsw in simple_dp.o
_bwa_stdsw in simple_dp.o
_bsw2_aln in bwtsw2_aux.o
_bwa_fa2pac in libbwacore.a(bntseq.o)
_bwa_seq_close in libbwacore.a(bwaseqio.o)
"_egzopen", referenced from:
_err_xzopen_core in libbwacore.a(utils.o)
"_egzread", referenced from:
_ks_getuntil in simple_dp.o
_kseq_read in simple_dp.o
_kseq_read in simple_dp.o
_kseq_read in simple_dp.o
_kseq_read in simple_dp.o
_ks_getuntil in bwtsw2_aux.o
_bsw2_aln in bwtsw2_aux.o
_bsw2_aln in bwtsw2_aux.o
_bsw2_aln in bwtsw2_aux.o
_bsw2_aln in bwtsw2_aux.o
_ks_getuntil in libbwacore.a(bntseq.o)
_bns_fasta2bntseq in libbwacore.a(bntseq.o)
_bns_fasta2bntseq in libbwacore.a(bntseq.o)
_bns_fasta2bntseq in libbwacore.a(bntseq.o)
_bns_fasta2bntseq in libbwacore.a(bntseq.o)
_ks_getuntil in libbwacore.a(bwaseqio.o)
_bwa_read_seq in libbwacore.a(bwaseqio.o)
_bwa_read_seq in libbwacore.a(bwaseqio.o)
_bwa_read_seq in libbwacore.a(bwaseqio.o)
_bwa_read_seq in libbwacore.a(bwaseqio.o)
"_egzdopen", referenced from:
_err_xzopen_core in libbwacore.a(utils.o)
ld: symbol(s) not found
collect2: ld returned 1 exit status
make[2]: *** [bwa] Error 1
make[1]: *** [all-recursive] Error 1
make: *** [all] Error 2
I downloaded the bwa version 5.7 and cannot compile it on Macbook Pro (10.6.3).
I challenged following steps.
- 1. tar -xvf bwa-0.5.7.tar.bz2
- 2. cd /bwa-0.5.7
- 3. sh autogen.sh
- 4. ./configure
- 5. make
On make command, I can not continue the installation.
I think The linker is complaining that it cannot find the math library. I am not sure why this may happen. One thing I tried to remove the "-m64" option on the CFLAG line in Makefile. But I could not remove this error.
Any idea what the problem on my pc ?
And error message desribed below(Here, I did not removed -m64 option).
------------------------------------------------------
gcc -Wall -m64 -fPIC -g -O2 -o bwa is.o bwtmisc.o bwtindex.o simple_dp.o bwape.o bwtsw2_core.o bwtsw2_main.o bwtsw2_aux.o bwt_lite.o bwtsw2_chain.o main.o bwt_gen/libbwtgen.a libbwacore.a -lpthread -lz -lm
Undefined symbols:
"_egzclose", referenced from:
_bwa_index in bwtindex.o
_bwa_index in bwtindex.o
_bwa_stdsw in simple_dp.o
_bwa_stdsw in simple_dp.o
_bsw2_aln in bwtsw2_aux.o
_bwa_fa2pac in libbwacore.a(bntseq.o)
_bwa_seq_close in libbwacore.a(bwaseqio.o)
"_egzopen", referenced from:
_err_xzopen_core in libbwacore.a(utils.o)
"_egzread", referenced from:
_ks_getuntil in simple_dp.o
_kseq_read in simple_dp.o
_kseq_read in simple_dp.o
_kseq_read in simple_dp.o
_kseq_read in simple_dp.o
_ks_getuntil in bwtsw2_aux.o
_bsw2_aln in bwtsw2_aux.o
_bsw2_aln in bwtsw2_aux.o
_bsw2_aln in bwtsw2_aux.o
_bsw2_aln in bwtsw2_aux.o
_ks_getuntil in libbwacore.a(bntseq.o)
_bns_fasta2bntseq in libbwacore.a(bntseq.o)
_bns_fasta2bntseq in libbwacore.a(bntseq.o)
_bns_fasta2bntseq in libbwacore.a(bntseq.o)
_bns_fasta2bntseq in libbwacore.a(bntseq.o)
_ks_getuntil in libbwacore.a(bwaseqio.o)
_bwa_read_seq in libbwacore.a(bwaseqio.o)
_bwa_read_seq in libbwacore.a(bwaseqio.o)
_bwa_read_seq in libbwacore.a(bwaseqio.o)
_bwa_read_seq in libbwacore.a(bwaseqio.o)
"_egzdopen", referenced from:
_err_xzopen_core in libbwacore.a(utils.o)
ld: symbol(s) not found
collect2: ld returned 1 exit status
make[2]: *** [bwa] Error 1
make[1]: *** [all-recursive] Error 1
make: *** [all] Error 2
Comment