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

[longbow leo]

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
>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>