Patch is already applied on the github version after port from sourceforge:

https://github.com/samtools/tabix

Hi!
I have the following error when installing cgpVcf 2.02 (but also with previous releases) in a Ubuntu 14.04 machine:

#   Failed test 'use Sanger::CGP::Vcf;'
#   at t/1_pm_compile.t line 66.
#     Tried to use 'Sanger::CGP::Vcf'.
#     Error:  Subroutine _dclone redefined at /home/xxx/software/cgpVcf-2.0.2/lib/perl5/Const/Fast.pm line 14.
# Compilation failed in require at /home/xxx/software/cgpVcf-2.0.2/blib/lib/Sanger/CGP/Vcf.pm line 37.
# BEGIN failed--compilation aborted at /home/xxx/software/cgpVcf-2.0.2/blib/lib/Sanger/CGP/Vcf.pm line 37.
# Compilation failed in require at (eval 192) line 2.
# BEGIN failed--compilation aborted at (eval 192) line 2.
Bailout called.  Further testing stopped:  Unable to 'use' module Sanger::CGP::Vcf
# Tests were run but no plan was declared and done_testing() was not seen.
FAILED--Further testing stopped: Unable to 'use' module Sanger::CGP::Vcf
make: *** [test_dynamic] Error 255

Best,
Francesco

I have the following fail bellow in the end of compillation, any suggestion? I have installed Specio::Library::String.

Error belown:

Failed test 'use perl5::Specio::Library::String;'

at t/1_pm_compile.t line 66.

Tried to use 'perl5::Specio::Library::String'.

Error: The Specio::Library::String package already has a type named NonEmptySimpleStr at /usr/local/cgpVcf-2.0.4/lib/perl5/Specio/Declare.pm line 84.

Compilation failed in require at t/1_pm_compile.t line 66.

BEGIN failed--compilation aborted at t/1_pm_compile.t line 66.

Bailout called. Further testing stopped: Unable to 'use' module perl5::Specio::Library::String
FAILED--Further testing stopped: Unable to 'use' module perl5::Specio::Library::String
make: *** [test_dynamic] Error 255

Hi there I have a compilation error I dont understand, any help much appreciated.

system: 
ubuntu 16.04
perl (v5.16.3) built for x86_64-linux-thread-multi

commands
git clone https://github.com/cancerit/cgpVcf.git
cd cgpVcf/
./setup.sh .

error:
#   Failed test 'use perl5::Specio::Library::Builtins;'
#   at t/1_pm_compile.t line 66.
#     Tried to use 'perl5::Specio::Library::Builtins'.
#     Error:  The Specio::Library::Builtins package already has a type named Item at /mnt/scratch/DGE/MOPOPGEN/jstudd/jstudd/Programs/cgpVcf/lib/perl5/Specio/Declare.pm line 84.
# Compilation failed in require at (eval 464) line 2.
# BEGIN failed--compilation aborted at (eval 464) line 2.
Bailout called.  Further testing stopped:  Unable to 'use' module perl5::Specio::Library::Builtins
# Tests were run but no plan was declared and done_testing() was not seen.
FAILED--Further testing stopped: Unable to 'use' module perl5::Specio::Library::Builtins

https://github.com/cancerit/cgpVcf/blob/dev/lib/Sanger/CGP/Vcf/BamUtil.pm#L100

https://github.com/cancerit/cgpVcf/blob/dev/lib/Sanger/CGP/Vcf/VcfUtil.pm#L200

$vcf->add_header_line(\%input_hash, append => 1);

Need to record cell burden of first state and optional second state for:

cancerit/cgpBattenberg#16

Just add it to the string here:

https://github.com/cancerit/cgpVcf/blob/dev/lib/Sanger/CGP/Vcf/VCFCNConverter.pm#L109

I want to install packages cgpVcf. And it stopped with "Installing cgpVcf ...Writing Makefile for cgpVcf Writing MYMETA.yml and MYMETA.json Makefile:12943: *** multiple target patterns. Stop."

My code is as follows:

wget -c https://github.com/cancerit/cgpVcf/archive/v2.0.4.tar.gz

tar -xzvf v2.0.4.tar.gz

rm v2.0.4.tar.gz

cd cgpVcf-2.0.4/

./setup.sh cgpVcf
What's wrong with it? Thanks for your help.

Hi,
I was trying to install cgpVcf-2.0.1 on a Centos 6.6 machine.
It gave me the following errors:

gcc -g -O2 -I. -fpic -c -o hfile_libcurl.pico hfile_libcurl.c
hfile_libcurl.c: In function ‘easy_errno’:
hfile_libcurl.c:93: error: ‘CURLE_NOT_BUILT_IN’ undeclared (first use in this function)
hfile_libcurl.c:93: error: (Each undeclared identifier is reported only once
hfile_libcurl.c:93: error: for each function it appears in.)
make[1]: *** [hfile_libcurl.pico] Error 1
make[1]: Leaving directory `/opt/cgpVcf-2.0.1/install_tmp/samtools/htslib-1.3'
make: *** [all-htslib] Error 2

Could you please help me solve these errors? Thank you very much!

Python: v2.6.6
Perl: v5.10.1
gcc: 4.4.7

In VcfUtil.pm, it is localtime.

But in vcftools, it is gmtime.
https://github.com/vcftools/vcftools/blob/master/src/perl/Vcf.pm#L732C18-L732C24

Data::UUID is missing from Makefile.PL, probably missed as full CGP stack will get this from PCAP-core.