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Id: 90819
Status: open
Priority: 0/
Queue: bioperl

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Owner: Nobody in particular
Requestors: malcolm.zachariah [...] utah.edu
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Subject: problems installing BioPerl-1.6.1
Date: Tue, 26 Nov 2013 01:49:27 +0000
To: "bug-bioperl [...] rt.cpan.org" <bug-bioperl [...] rt.cpan.org>
From: Malcolm Zachariah <malcolm.zachariah [...] utah.edu>
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
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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: Show quoted text
> 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
Subject: Re: [rt.cpan.org #90819] problems installing BioPerl-1.6.1
Date: Tue, 26 Nov 2013 04:23:44 +0000
To: "bug-bioperl [...] rt.cpan.org" <bug-bioperl [...] rt.cpan.org>
From: Malcolm Zachariah <malcolm.zachariah [...] utah.edu>
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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
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Filed this bug report for AMPHORA2; we can't fix bugs that aren't reported, so hopefully this will end up fixing things for you in a later bioperl release. https://github.com/martinwu/AMPHORA2/issues/2 chris On Mon Nov 25 23:23:59 2013, malcolm.zachariah@utah.edu wrote: Show quoted text
> 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
Subject: Re: [rt.cpan.org #90819] problems installing BioPerl-1.6.1
Date: Tue, 26 Nov 2013 07:04:10 +0000
To: "bug-bioperl [...] rt.cpan.org" <bug-bioperl [...] rt.cpan.org>
From: Malcolm Zachariah <malcolm.zachariah [...] utah.edu>
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Thank you, Malcolm On Nov 25, 2013, at 9:41 PM, Chris Fields via RT <bug-bioperl@rt.cpan.org> wrote: Show quoted text
> <URL: https://rt.cpan.org/Ticket/Display.html?id=90819 > > > Filed this bug report for AMPHORA2; we can't fix bugs that aren't reported, so hopefully this will end up fixing things for you in a later bioperl release. > > https://github.com/martinwu/AMPHORA2/issues/2 > > chris > > On Mon Nov 25 23:23:59 2013, malcolm.zachariah@utah.edu wrote:
>> 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
> > >


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