Bug #90819 for bioperl: problems installing BioPerl-1.6.1

>> Hello, >> >> The program I’m using is Phyla_AMPHORA, which is based on AMPHORA, and >> this problem I had when using the most recent BioPerl version. >> >> https://github.com/martinwu/AMPHORA2 >> >> >> KNOWN ISSUES >> >> Bioperl >> AMPHORA2 has been tested on Bioperl 1.6.1. People have reported >> problems running AMPHORA2 on Bioperl 1.6.9. For example, the following >> error has been reported when running Phylotyping.pl: >> >> ------------- EXCEPTION: Bio::Root::Exception ------------- >> MSG: parse error: expected ; or ) or , >> >> STACK: Error::throw >> STACK: Bio::Root::Root::throw >> /usr/local/share/perl/5.14.2/Bio/Root/Root.pm:472 >> STACK: Bio::TreeIO::NewickParser::parse_newick >> /usr/local/share/perl/5.14.2/Bio/TreeIO/NewickParser.pm:195 >> STACK: Bio::TreeIO::newick::next_tree >> /usr/local/share/perl/5.14.2/Bio/TreeIO/newick.pm:143 >> STACK: main::assign_phylotype >> /usr/local/Bioinf/AMPHORA2/Scripts/Phylotyping.pl:154 >> STACK: /usr/local/Bioinf/AMPHORA2/Scripts/Phylotyping.pl:70 >> >> Downgrading Bioperl from 1.6.9 to 1.6.1 solves the problem. >> >> I will try getting 1.6.9 in the meantime. >> >> Thanks, >> Malcolm >> >> On Nov 25, 2013, at 7:35 PM, Chris Fields via RT <bug- >> bioperl@rt.cpan.org<mailto:bug-bioperl@rt.cpan.org>> wrote: >> >> <URL: https://rt.cpan.org/Ticket/Display.html?id=90819 > >> >> The best place to ask this question is the bioperl mail list: >> >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> >> What software are you using with the problem, and what is the error >> you are getting with the updated BioPerl? The problem you are seeing >> is only fixed in the latest versions and is mainly due to a missing >> version in the Build.PL file (as the error indicates). >> >> You can also download the 1.6.1 tarball and run installation from >> that: >> >> <pre> >> perl Build.PL >> ./Build >> ./Build install >> </pre> >> >> chris >> >> On Mon Nov 25 20:49:42 2013, malcolm.zachariah@utah.edu wrote: >> Hello, >> >> I’m using perl-5.16.0 via perlbrew (I don’t have sudo rights) and I’m >> trying to install an older version of BioPerl (1.6.1). I have to use >> that version because I’m using a program which has some errors with >> BioPerl-1.6.9. >> >> The specific problem can be seen here: >> >> [. . .]$ cpanm BioPerl >> ! Finding BioPerl on cpanmetadb failed. >> --> Working on BioPerl >> Fetching http://www.cpan.org/authors/id/C/CJ/CJFIELDS/BioPerl- >> 1.6.1.tar.gz ... OK >> Configuring BioPerl-1.6.1 ... OK >> Failed to upconvert metadata to 1.1. Errors: >> Missing mandatory field, 'version' (version) [Validation: 1.0] >> at /loader/0x26b2b28/App/cpanminus/script.pm line 99. >> >> >> >> >> I also tried downloading the tar.gz file and running the makefile.pl >> script within, but it got stuck here: >> >> Could not get valid metadata. Error is: Invalid metadata structure. >> Errors: 'Perl_5' for 'license' does not have a URL scheme (resources >> -> license) [Validation: 1.2], Expected a map structure from string or >> file. (optional_features -> Bio::FeatureIO::gff -> requires) >> [Validation: 1.2], Expected a map structure from string or file. >> (optional_features -> Bio::WebAgent -> requires) [Validation: 1.2], >> Expected a map structure from string or file. (optional_features -> >> Bio::DB::EUtilParameters -> requires) [Validation: 1.2], Expected a >> map structure from string or file. (optional_features -> >> Bio::OntologyIO::InterProParser -> requires) [Validation: 1.2], >> Expected a map structure from string or file. (optional_features -> >> Bio::Biblio::IO::medlinexml -> requires) [Validation: 1.2], Expected a >> map structure from string or file. (optional_features -> >> Bio::SeqIO::strider -> requires) [Validation: 1.2], Expected a map >> structure from string or file. (optional_features -> >> Bio::PhyloNetwork::RandomFactory -> requires) [Validation: 1.2] >> . . . >> at /N/u/mzachariah/perl5/perlbrew/perls/perl- >> 5.16.0/lib/5.16.3/Module/Build/Base.pm line 4564. >> Could not create MYMETA files >> Creating new 'Build' script for 'BioPerl' version ‘1.006001' >> >> >> >> Do you know what could be the issue here? >> >> Thanks, >> Malcolm Zachariah