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

Wed Oct 24 02:10:56 UTC 2012

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  Otherwise it may be quite out of date.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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>> 
> 
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