[Bioperl-l] compiling Bio::Perl error in Bio/Root

Wed Oct 24 02:20:39 UTC 2012

The versions of the bioperl and bioperl-run packages in ubuntu 12.04 are
1.6.901. I think it is up-to-date.

haizhou

On Wed, Oct 24, 2012 at 10:10 AM, Fields, Christopher J <
cjfields at illinois.edu> wrote:

> If this package represents the latest CPAN release, then that works.
>  Otherwise it may be quite out of date.
>
> The error in question is a bit odd, as it hasn't popped up before with
> testing (at least that I have seen).  The clone() method will alias to
> Storable's dclone() if Clone isn't installed; somehow it thinks Clone is
> present when it isn't (or there is a Clone module installed w/o the clone()
> method). Can you run 'perldoc Clone' to see if Clone is installed?
>
> chris
>
> On Oct 23, 2012, at 8:31 PM, longbow leo <longbow0 at gmail.com>
>  wrote:
>
> > Hi,
> >
> > There is a "bioperl" package in ubuntu repository. It is not need to
> > compile and install it.
> >
> > Best,
> >
> > Haizhou
> >
> > On Wed, Oct 24, 2012 at 8:42 AM, Georg Vogler <
> gvogler at sanfordburnham.org>wrote:
> >
> >> Hi!
> >>
> >> I'm having trouble compiling Bio::Perl on my Ubuntu 12.04 server. Here
> is
> >> the excerpt (I removed some lines from tests that passed) from the
> >> build.log after running "sudo cpanm Bio::Perl":
> >>
> >> Searching Bio::Perl on cpanmetadb ...
> >> --> Working on Bio::Perl
> >> Fetching
> >> http://www.cpan.org/authors/id/C/CJ/CJFIELDS/BioPerl-1.6.901.tar.gz
> >> -> OK
> >> Unpacking BioPerl-1.6.901.tar.gz
> >> Entering BioPerl-1.6.901
> >> Checking configure dependencies from META.yml
> >> Checking if you have Module::Build 0.38 ... Yes (0.4003)
> >> Configuring BioPerl-1.006901
> >> Running Build.PL
> >> Do you want to run the Bio::DB::GFF or Bio::DB::SeqFeature::Store live
> >> database tests? y/n [n]   - will not run the BioDBGFF or BioDBSeqFeature
> >> live database t
> >> ests
> >>
> >> Install [a]ll BioPerl scripts, [n]one, or choose groups [i]nteractively?
> >> [a]   - will install all scripts
> >>
> >> Do you want to run tests that require connection to servers across the
> >> internet
> >> (likely to cause some failures)? y/n [n]   - will not run
> >> internet-requiring tests
> >> Created MYMETA.yml and MYMETA.json
> >> Creating new 'Build' script for 'BioPerl' version '1.006901'
> >> -> OK
> >> Checking dependencies from MYMETA.json ...
> >> Checking if you have Test::More 0 ... Yes (0.98)
> >> Checking if you have Test::Harness 2.62 ... Yes (3.25)
> >> Checking if you have CPAN 1.81 ... Yes (1.9800)
> >> Checking if you have Module::Build 0.2805 ... Yes (0.4003)
> >> Checking if you have Scalar::Util 0 ... Yes (1.23)
> >> Checking if you have IO::String 0 ... Yes (1.08)
> >> Checking if you have Data::Stag 0.11 ... Yes (0.11)
> >> Checking if you have DB_File 0 ... Yes (1.821)
> >> Checking if you have ExtUtils::Manifest 1.52 ... Yes (1.61)
> >> Building and testing BioPerl-1.006901
> >> Building BioPerl
> >> t/Align/AlignStats.t ......................... ok
> >> t/Align/AlignUtil.t .......................... ok
> >> t/Align/Graphics.t ........................... ok
> >> t/Align/SimpleAlign.t ........................ ok
> >> t/Align/TreeBuild.t .......................... ok
> >>
> >> …
> >>
> >> t/Assembly/IO/bowtie.t ....................... skipped: The optional
> >> module Bio::Tools::Run::Samtools (or dependencies thereof) was not
> installed
> >> t/Assembly/IO/sam.t .......................... skipped: The optional
> >> module Bio::DB::Sam (or dependencies thereof) was not installed
> >>
> >> …
> >>
> >> t/Restriction/Analysis-refac.t ............... ok
> >> t/Restriction/Analysis.t ..................... ok
> >> t/Restriction/Gel.t .......................... ok
> >> t/Restriction/IO.t ........................... ok
> >> t/Root/Exception.t ........................... ok
> >> t/Root/HTTPget.t ............................. skipped: Network tests
> have
> >> not been requested
> >> Undefined subroutine &Clone::clone called at Bio/Root/Root.pm line 214.
> >> # Looks like you planned 63 tests but ran 51.
> >> # Looks like your test exited with 255 just after 51.
> >> t/Root/RootI.t ...............................
> >> Dubious, test returned 255 (wstat 65280, 0xff00)
> >> Failed 12/63 subtests
> >>
> >> …
> >>
> >>
> >> ------------- EXCEPTION: Bio::Root::Exception -------------
> >> MSG: Unallowed parameter: clone !
> >> STACK: Error::throw
> >> STACK: Bio::Root::Root::throw Bio/Root/Root.pm:472
> >> STACK: Bio::Tools::Primer3::AUTOLOAD Bio/Tools/Primer3.pm:150
> >> STACK: Bio::Tools::Primer3::next_primer Bio/Tools/Primer3.pm:338
> >> STACK: t/Tools/Primer3.t:26
> >> -----------------------------------------------------------
> >>
> >> …
> >>
> >> Test Summary Report
> >> -------------------
> >> t/Root/RootI.t                             (Wstat: 65280 Tests: 51
> Failed:
> >> 0)
> >>  Non-zero exit status: 255
> >>  Parse errors: Bad plan.  You planned 63 tests but ran 51.
> >> t/SeqFeature/Clone.t                       (Wstat: 65280 Tests: 0
> Failed:
> >> 0)
> >>  Non-zero exit status: 255
> >>  Parse errors: Bad plan.  You planned 17 tests but ran 0.
> >> t/Tools/Primer3.t                          (Wstat: 65280 Tests: 8
> Failed:
> >> 0)
> >>  Non-zero exit status: 255
> >>  Parse errors: Bad plan.  You planned 14 tests but ran 8.
> >> Files=349, Tests=22654, 157 wallclock secs ( 3.58 usr  0.73 sys + 141.69
> >> cusr  9.30 csys = 155.30 CPU)
> >> Result: FAIL
> >> Failed 3/349 test programs. 0/22654 subtests failed.
> >> -> FAIL Installing Bio::Perl failed. See /home/gvogler/.cpanm/build.log
> >> for details.
> >>
> >>
> >> Any suggestions are greatly appreciated!
> >>
> >> Many thanks,
> >>
> >> Geo
> >>
> >>
> >>
> >> _______________________________________________
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> >> Bioperl-l at lists.open-bio.org
> >> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >>
> >
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