Question: (Closed) Vcf Tools Installation Error
0
gravatar for Matteo
6.9 years ago by
Matteo200
Matteo200 wrote:

Hi all,

I'm trying to install the latest version of vcf-tools but i'm facing with this error:

g++ -O2 -Wall -Wextra vcftools.cpp vcffile.cpp vcfentry.cpp vcfentrygetters.cpp vcfentrysetters.cpp vcffilefilters.cpp vcffileoutput.cpp vcffileformatconvert.cpp vcffilediff.cpp parameters.cpp vcffileindex.cpp outputlog.cpp -o vcftools -lz /tmp/ccvTYIPP.o: In function vcf_file::output_as_LDhat_unphased(std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)': vcf_file_format_convert.cpp:(.text+0x18d3): warning: the use oftmpnam' is dangerous, better use mkstemp' /tmp/cccloweC.o: In functionvcffile::open()': vcffile.cpp:(.text+0xed2): undefined reference to gzbuffer' collect2: ld returned 1 exit status make[1]: *** [vcftools] Error 1 make[1]: Leaving directory/opt/NGS/VCFTOOLS/vcftools_latest/cpp' cd: 2: can't cd to perl make: * [install] Error 2

How can solve it? Any suggestions?

Matteo

installation vcftools • 3.0k views
ADD COMMENTlink written 6.9 years ago by Matteo200
1
gravatar for Istvan Albert
6.9 years ago by
Istvan Albert ♦♦ 80k
University Park, USA
Istvan Albert ♦♦ 80k wrote:

Your zlib development library is missing or is not installed properly.

ADD COMMENTlink written 6.9 years ago by Istvan Albert ♦♦ 80k
3

This, if it is installed then you make need to set your the LDFLAGS to include -L <path to=""/>

edit: In the newest version of vcf-tools in cpp/Makefile on line 18:

17 LIB = -lz                                                                                                                                                                                                 
18 #LIB = -lz -I/opt/local/include/ -L/opt/local/lib/

You may need to comment out line 17 and uncomment line 18, fixing the paths for the -I and -L flags to point to where ever they are on your system.

ADD REPLYlink modified 6.9 years ago • written 6.9 years ago by geoffreycolburn50
1

Thanks a lot! This solve the issue.

ADD REPLYlink written 6.9 years ago by Matteo200

" fixing the paths for the -I and -L flags to point to where ever they are on your system", what do you mean by "they", zlib ? or those directories ? I do not have either of them !

ADD REPLYlink written 5.5 years ago by User 1933340

search for: how to install the zlib library (for your linux system)

ADD REPLYlink written 5.5 years ago by Istvan Albert ♦♦ 80k
Please log in to add an answer.
The thread is closed. No new answers may be added.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 883 users visited in the last hour