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

[Georg Vogler]

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