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cancerit / cgpVcf

Vcf file utilities

Home Page:http://cancerit.github.io/cgpVcf/

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Error in installing version 2.*

FraMatMan opened this issue · comments

commented

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

commented

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

commented

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

commented

Hi,

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

perl -v

Thanks,
K

commented

This seems to be a duplicate of ICGC-TCGA-PanCancer/PCAP-core#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?

commented

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

Best,
Fra

commented

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

commented

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

commented

@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?