sheenamt
sheenamt
/ gist:97286ea893dfbc5e7cc8
Created
August 26, 2014 20:55
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| { | |
| "metadata": { | |
| "name": "" | |
| }, | |
| "nbformat": 3, | |
| "nbformat_minor": 0, | |
| "worksheets": [ | |
| { | |
| "cells": [ | |
| { |
sheenamt
/ gist:1148203
Created
August 16, 2011 00:28
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| Compilation failed in require at -e line 1. | |
| # Failed test 'Bio::Coordinate::MapperI loaded ok' | |
| # at t/00-compile.t line 48. | |
| # '' | |
| # doesn't match '(?s-xim:^\s*Bio::Coordinate::MapperI ok)' | |
| Can't locate Bio/Root/Version.pm in @INC (@INC contains: lib /home/sheena-warrior/bioperl-tmp/.build/FO3G3tO_Js/blib/lib /home/sheena-warrior/bioperl-tmp/.build/FO3G3tO_Js/blib/arch /home/sheena-warrior/cpan-lib/lib/perl5/i486-linux-gnu-thread-multi /home/sheena-warrior/cpan-lib/lib/perl5/i486-linux-gnu-thread-multi /home/sheena-warrior/cpan-lib/lib/perl5 /home/sheena-warrior/cpan-lib/lib/perl5/i486-linux-gnu-thread-multi /home/sheena-warrior/cpan-lib/lib/perl5/i486-linux-gnu-thread-multi /home/sheena-warrior/cpan-lib/lib/perl5 /etc/perl /usr/local/lib/perl/5.10.1 /usr/local/share/perl/5.10.1 /usr/lib/perl5 /usr/share/perl5 /usr/lib/perl/5.10 /usr/share/perl/5.10 /usr/local/lib/site_perl .) at /home/sheena-warrior/cpan-lib/lib/perl5/Bio/Root/RootI.pm line 35. | |
| BEGIN failed--compilation aborted at /h |
sheenamt
/ gist:1148202
Created
August 16, 2011 00:27
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| Compilation failed in require at -e line 1. | |
| # Failed test 'Bio::Coordinate::MapperI loaded ok' | |
| # at t/00-compile.t line 48. | |
| # '' | |
| # doesn't match '(?s-xim:^\s*Bio::Coordinate::MapperI ok)' | |
| Can't locate Bio/Root/Version.pm in @INC (@INC contains: lib /home/sheena-warrior/bioperl-tmp/.build/FO3G3tO_Js/blib/lib /home/sheena-warrior/bioperl-tmp/.build/FO3G3tO_Js/blib/arch /home/sheena-warrior/cpan-lib/lib/perl5/i486-linux-gnu-thread-multi /home/sheena-warrior/cpan-lib/lib/perl5/i486-linux-gnu-thread-multi /home/sheena-warrior/cpan-lib/lib/perl5 /home/sheena-warrior/cpan-lib/lib/perl5/i486-linux-gnu-thread-multi /home/sheena-warrior/cpan-lib/lib/perl5/i486-linux-gnu-thread-multi /home/sheena-warrior/cpan-lib/lib/perl5 /etc/perl /usr/local/lib/perl/5.10.1 /usr/local/share/perl/5.10.1 /usr/lib/perl5 /usr/share/perl5 /usr/lib/perl/5.10 /usr/share/perl/5.10 /usr/local/lib/site_perl .) at /home/sheena-warrior/cpan-lib/lib/perl5/Bio/Root/RootI.pm line 35. | |
| BEGIN failed--compilation aborted at /h |
sheenamt
/ gist:1147524
Created
August 15, 2011 19:26
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| t/SearchIO/hmmer.t ........................... 1/299 | |
| # Failed test 'Check algorithm' | |
| # at t/SearchIO/hmmer.t line 20. | |
| # got: '' | |
| # expected: 'HMMPFAM' | |
| # Failed test 'Check num_hits' | |
| # at t/SearchIO/hmmer.t line 26. | |
| # got: '0' | |
| # expected: '2' |
sheenamt
/ gist:1135285
Created
August 9, 2011 21:47
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| sheena-warrior@sheena-warrior:~$ perl -MBio::Root::Root -E 'say $INC{"Bio/Root/Root.pm"}' | |
| Can't locate Bio/Root/Version.pm in @INC (@INC contains: /home/sheena-warrior/cpan-lib/lib/perl5/i486-linux-gnu-thread-multi /home/sheena-warrior/cpan-lib/lib/perl5/i486-linux-gnu-thread-multi /home/sheena-warrior/cpan-lib/lib/perl5 /etc/perl /usr/local/lib/perl/5.10.1 /usr/local/share/perl/5.10.1 /usr/lib/perl5 /usr/share/perl5 /usr/lib/perl/5.10 /usr/share/perl/5.10 /usr/local/lib/site_perl .) at /home/sheena-warrior/cpan-lib/lib/perl5/Bio/Root/RootI.pm line 35. | |
| BEGIN failed--compilation aborted at /home/sheena-warrior/cpan-lib/lib/perl5/Bio/Root/RootI.pm line 35. | |
| Compilation failed in require at (eval 11) line 3. | |
| ...propagated at /usr/share/perl/5.10/base.pm line 93. | |
| BEGIN failed--compilation aborted at /home/sheena-warrior/cpan-lib/lib/perl5/Bio/Root/Root.pm line 18. | |
| Compilation failed in require. | |
| BEGIN failed--compilation aborted. |
sheenamt
/ gist:1135200
Created
August 9, 2011 21:07
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| Can't find dist packages without a MANIFEST file - run 'manifest' action first at /usr/local/share/perl/5.10.1/Bio/Root/Build.pm line 605. | |
| WARNING: Possible missing or corrupt 'MANIFEST' file. | |
| Nothing to enter for 'provides' field in META.yml | |
| 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) [Validation: 1.2] | |
| at /home/sheena-warrior/cpan-lib/lib/perl5/Module/Build/Base.pm line 4559 | |
| Could not create MYMETA files | |
| Creating new 'Build' script for 'BioPerl' version '1.006902' |
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| 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) [Va |
sheenamt
/ gist:1047998
Created
June 26, 2011 21:43
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| sheena-warrior@sheena-warrior:~/Bio-Root (master *)$ dzil install | |
| [DZ] building distribution under .build/TfmigXic6B for installation | |
| [DZ] beginning to build Bio-Root | |
| [DZ] dist's main_module is lib/Bio/Root/Root.pm | |
| [DZ] extracting distribution abstract from lib/Bio/Root/Root.pm | |
| [@Bioperl/@Basic/ExtraTests] rewriting release test xt/release/pod-syntax.t | |
| [@Bioperl/@Basic/ExtraTests] rewriting release test xt/release/no-tabs.t | |
| [@Bioperl/@Basic/ExtraTests] rewriting release test xt/release/pod-coverage.t | |
| [@Bioperl/@Basic/ExtraTests] rewriting release test xt/release/eol.t | |
| [@Bioperl/Authority] skipping lib/Bio/Root/Utilities.pm: assigns to $AUTHORITY |
sheenamt
/ gist:1041686
Created
June 23, 2011 01:12
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| WARNING: the following files are missing in your kit: | |
| Bio/Das/FeatureTypeI.pm | |
| Bio/Das/SegmentI.pm | |
| Bio/Event/EventGeneratorI.pm | |
| Bio/Event/EventHandlerI.pm | |
| t/data/9K_v4.psl | |
| t/data/fishBlats.txt | |
| t/data/fishBlats_UCSC.psl | |
| t/data/O_ZNF496.blast | |
| t/data/O_ZNF496.psl |
sheenamt
/ gist:1041570
Created
June 22, 2011 23:40
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| sheena-warrior@sheena-warrior:~/Bio-Das (master *)$ dzil build | |
| [DZ] beginning to build Bio-Das | |
| [DZ] dist's main_module is lib/Bio/Das/SegmentI.pm | |
| [DZ] extracting distribution abstract from lib/Bio/Das/SegmentI.pm | |
| [@Bioperl/@Basic/ExtraTests] rewriting release test xt/release/pod-syntax.t | |
| [@Bioperl/@Basic/ExtraTests] rewriting release test xt/release/no-tabs.t | |
| [@Bioperl/@Basic/ExtraTests] rewriting release test xt/release/pod-coverage.t | |
| [@Bioperl/@Basic/ExtraTests] rewriting release test xt/release/eol.t | |
| [@Bioperl/PodWeaver] [@FLORA/Name] couldn't find abstract in lib/Bio/Das/FeatureTypeI.pm | |
| [@Bioperl/PodWeaver] [@FLORA/Name] couldn't find abstract in lib/Bio/Das/SegmentI.pm |
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