Error in installing version 2.*

[FraMatMan]

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

[keiranmraine]

Hi,

Please can you provide more information?

I don't see this problem on an AWS Ubuntu 14.04, or using a docker image based on Ubuntu 14.04.

Are you running:

./setup.sh /install/path

Regards, Keiran

[FraMatMan]

Thanks Keiran to answer so quickly. Yes, I am running

./setup.sh /install/path

I am trying to install ASCATNGS in my Ubuntu 14.04 LTS machine. Its dependencies are: PCAP, cgpVcf and alleleCount. I succeed in installing PCAP, not the others For cgpVcf and alleleCount I have the same problem in installing: it seems that cannot read the Sanger::CGP::Vcf perl module.

I thought it was a problem of file permission, but also with 777 permission and running as root I have the same error.

From previous post, I forgot the following line at the beginning: Subroutine Const::Fast::import redefined at /home/xxx/software/cgpVcf-2.0.2/lib/perl5/Sub/Exporter/Progressive.pm line 40.

I hope this is sufficient, if it is not the case make me specific question.

Best regards, Francesco

[keiranmraine]

Hi,

Sorry this has been left for so long. Could you tell me what perl version you are using?

perl -v

Thanks, K

[brainstorm]

This seems to be a duplicate of https://github.com/ICGC-TCGA-PanCancer/PCAP-core/issues/144. @fmancuso, does this happen to you when trying to install via i.e:

cpanm https://github.com/cancerit/cgpVcf/archive/v2.0.4.tar.gz?

[FraMatMan]

Hi brainstorm, I just tried the cpanm you suggest and the installation failed.

Best, Fra

[brainstorm]

@fmancuso And with cpanm --notests https://github.com/cancerit/cgpVcf/archive/v2.0.4.tar.gz?

[FraMatMan]

With --notest it has been installed.

cpanm --notest https://github.com/cancerit/cgpVcf/archive/v2.0.4.tar.gz --> Working on https://github.com/cancerit/cgpVcf/archive/v2.0.4.tar.gz Fetching https://github.com/cancerit/cgpVcf/archive/v2.0.4.tar.gz ... OK Configuring cgpVcf-2.0.4 ... OK Building cgpVcf-v2.0.4 ... OK Successfully installed cgpVcf-v2.0.4 1 distribution installed

[penglbio]

@fmancuso I also cannot install the software cgpVcf-2.0.4,I follow you with --notest it has been installed. And get the same message: cpanm --notest https://github.com/cancerit/cgpVcf/archive/v2.0.4.tar.gz --> Working on https://github.com/cancerit/cgpVcf/archive/v2.0.4.tar.gz Fetching https://github.com/cancerit/cgpVcf/archive/v2.0.4.tar.gz ... OK Configuring cgpVcf-2.0.4 ... OK Building cgpVcf-v2.0.4 ... OK Successfully installed cgpVcf-v2.0.4 1 distribution installed

But where is the installed cgpVcf-v2.0.4. How can I use it?