Vcftools Installation Error

Question

[Luke Noble]

Hi,

Can anyone help make sense of the following make error (multiple versions of vcftools), onto OS X 10.6... I've seen this over on SeqAnswers too so apparently I'm not the only one.

g++ -O2 -Wall -Wextra vcftools.cpp vcf_file.cpp vcf_entry.cpp vcf_entry_getters.cpp vcf_entry_setters.cpp vcf_file_filters.cpp vcf_file_output.cpp vcf_file_format_convert.cpp vcf_file_diff.cpp parameters.cpp output_log.cpp -o vcftools -lz Undefined symbols: "_gzbuffer", referenced from: vcf_file::open() in ccwWxKh6.o ld: symbol(s) not found collect2: ld returned 1 exit status make[1]: * [vcftools] Error 1 /bin/sh: line 0: cd: perl: No such file or directory make: * [install] Error 1

Cheers

Answer 1

[Peter Stockwell]

There seems to be an issue with picking up an inappropriate zlib version. To fix, in the cpp dir edit the Makefile so that the line

LIB= -lz

becomes

LIB = -L/usr/local/lib -lz

Then return the top level dir and define BINDIR to be the local bin:

export BINDIR=pwd/bin

and do the 'make'

Cheers

[Peter Stockwell]

This thing has trashed my line for BINDIR - the pwd has backward single quotes around it.

[Click downvote]

Thank you! Ps. I did not have to BINDIR.

Answer 2

[Pascal]

I'm not 100% sure but it seems that "_gzbuffer" is part of zlib library.

Can you install this library in your system?

Cheers