Question: Install/loading problems for perl module Vcf
gravatar for thijs.burg
3.1 years ago by
thijs.burg0 wrote:


I am trying to run a perl script from the dDocent pipeline using several perl modules. However for some reason the Vcf module is giving problems.

I cannot seem to download the module using cpanm:

$ cpanm Vcf --sudo
! Finding Vcf on cpanmetadb failed.
Vcf is up to date. (undef)

And I'm not sure why it mentioned that its up to date, which I guess means that I already have it.

So checking if it is working:

$ perl -e "use Vcf "
Subroutine validate redefined at /Library/Perl/5.18/ line 94.
Subroutine validate_v32 redefined at /Library/Perl/5.18/ line 117.
Subroutine new redefined at /Library/Perl/5.18/ line 147.
Subroutine throw redefined at /Library/Perl/5.18/ line 175.
Ambiguous call resolved as CORE::warn(), qualify as such or use & at /Library/Perl/5.18/ line 185.
Subroutine warn redefined at /Library/Perl/5.18/ line 181.
Ambiguous call resolved as CORE::open(), qualify as such or use & at /Library/Perl/5.18/ line 222.
Subroutine _open redefined at /Library/Perl/5.18/ line 189.
Subroutine open redefined at /Library/Perl/5.18/ line 249.
Ambiguous call resolved as CORE::close(), qualify as such or use & at /Library/Perl/5.18/ line 269.
Subroutine close redefined at /Library/Perl/5.18/ line 266.
Subroutine next_line redefined at /Library/Perl/5.18/ line 286.
Subroutine _unread_line redefined at /Library/Perl/5.18/ line 316.
Subroutine next_data_array redefined at /Library/Perl/5.18/ line 334.
Subroutine set_samples redefined at /Library/Perl/5.18/ line 358.
Subroutine _set_version redefined at /Library/Perl/5.18/ line 386.

Something is up I guess as it doesn't give back an empty output, although I don't understand what is the problem.

So thereafter I downloaded the module manually and tried to install it:

$ perl Makefile.PL
Checking if your kit is complete...
Looks good
Warning: prerequisite Vcf4_0 0 not found.
Warning: prerequisite VcfReader 0 not found.
Writing Makefile for Bio::Pipeline::Comparison
Writing MYMETA.yml and MYMETA.json

So it can't locate Vcf4_0 and VcfReader Running $make and $make test:

Test Summary Report
t/Bio/Pipeline/Comparison/Report/ParseVCFCompare.t (Wstat: 512 Tests: 21 Failed: 2)
  Failed tests:  3, 19
  Non-zero exit status: 2
Files=7, Tests=73,  5 wallclock secs ( 0.05 usr  0.02 sys +  2.98 cusr  0.57 csys =  3.62 CPU)
Result: FAIL
Failed 1/7 test programs. 2/73 subtests failed.
make: *** [test_dynamic] Error 255

As you probably already figured out I'm quite new to this and I'm not sure how to proceed from here. I do have a VCF//Reader.3pm and VCF//V4_0.3pm file in my perl5/man/man3/ folder but I don't think its looking for those.

Thanks in advance! Thijs

module perl vcf • 1.3k views
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