cpantestlogs/Bio::GeneDesign::Basic_genfailure.log

perl-blead
==========
cpanm (App::cpanminus) 1.7043 on perl 5.026000 built for x86_64-linux
Work directory is /home/ryan/.cpanm/work/1493529823.24731
You have make /usr/bin/make
You have LWP 6.26
You have /bin/tar: tar (GNU tar) 1.29
Copyright (C) 2015 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>.
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.

Written by John Gilmore and Jay Fenlason.
You have /usr/bin/unzip
Searching Bio::GeneDesign::Basic () on cpanmetadb ...
Unpacking Bio-GeneDesign-5.54.tar.gz
--> Working on Bio::GeneDesign::Basic
Fetching http://www.cpan.org/authors/id/N/NO/NOTDOCTOR/Bio-GeneDesign-5.54.tar.gz ... OK
Bio-GeneDesign-5.54
Bio-GeneDesign-5.54/Build.PL
Bio-GeneDesign-5.54/Changes
Bio-GeneDesign-5.54/Makefile.PL
Bio-GeneDesign-5.54/MANIFEST
Bio-GeneDesign-5.54/META.json
Bio-GeneDesign-5.54/META.yml
Bio-GeneDesign-5.54/README
Bio-GeneDesign-5.54/ToDo
Bio-GeneDesign-5.54/bin
Bio-GeneDesign-5.54/bin/GD_Filter_Enzymes.pl
Bio-GeneDesign-5.54/bin/GD_Generate_RSCU_Table.pl
Bio-GeneDesign-5.54/bin/GD_Graph_Dotplot.pl
Bio-GeneDesign-5.54/bin/GD_Graph_RSCU_Values.pl
Bio-GeneDesign-5.54/bin/GD_Juggle_Codons.pl
Bio-GeneDesign-5.54/bin/GD_List_Codon_Tables.pl
Bio-GeneDesign-5.54/bin/GD_Repeat_Smash.pl
Bio-GeneDesign-5.54/bin/GD_Reverse_Translate.pl
Bio-GeneDesign-5.54/bin/GD_Sequence_Subtraction.pl
Bio-GeneDesign-5.54/codon_tables
Bio-GeneDesign-5.54/codon_tables/Arabidopsis_thaliana.rscu
Bio-GeneDesign-5.54/codon_tables/Bacillus_subtilis.rscu
Bio-GeneDesign-5.54/codon_tables/Caenorhabditis_elegans.rscu
Bio-GeneDesign-5.54/codon_tables/Corynebacterium_glutamicum.rscu
Bio-GeneDesign-5.54/codon_tables/Deinococcus_radiodurans.rscu
Bio-GeneDesign-5.54/codon_tables/Drosophila_melanogaster.rscu
Bio-GeneDesign-5.54/codon_tables/Escherichia_coli.rscu
Bio-GeneDesign-5.54/codon_tables/Homo_sapiens.rscu
Bio-GeneDesign-5.54/codon_tables/Mycoplasma_genitalium.ct
Bio-GeneDesign-5.54/codon_tables/Mycoplasma_genitalium.rscu
Bio-GeneDesign-5.54/codon_tables/Oryza_sativa.rscu
Bio-GeneDesign-5.54/codon_tables/Saccharomyces_cerevisiae.rscu
Bio-GeneDesign-5.54/codon_tables/Standard.ct
Bio-GeneDesign-5.54/codon_tables/Unbiased.rscu
Bio-GeneDesign-5.54/codon_tables/Yarrowia_lipolytica.rscu
Bio-GeneDesign-5.54/enzymes
Bio-GeneDesign-5.54/enzymes/all_enzymes
Bio-GeneDesign-5.54/enzymes/blunts
Bio-GeneDesign-5.54/enzymes/IIB
Bio-GeneDesign-5.54/enzymes/nonpal
Bio-GeneDesign-5.54/enzymes/nonpal_and_IIB
Bio-GeneDesign-5.54/enzymes/nonpal_short
Bio-GeneDesign-5.54/enzymes/outside
Bio-GeneDesign-5.54/enzymes/standard
Bio-GeneDesign-5.54/enzymes/standard_and_IIB
Bio-GeneDesign-5.54/enzymes/test
Bio-GeneDesign-5.54/lib
Bio-GeneDesign-5.54/lib/Bio
Bio-GeneDesign-5.54/lib/Bio/GeneDesign.pm
Bio-GeneDesign-5.54/lib/Bio/GeneDesign
Bio-GeneDesign-5.54/lib/Bio/GeneDesign/Basic.pm
Bio-GeneDesign-5.54/lib/Bio/GeneDesign/CodonJuggle.pm
Bio-GeneDesign-5.54/lib/Bio/GeneDesign/Codons.pm
Bio-GeneDesign-5.54/lib/Bio/GeneDesign/Graph.pm
Bio-GeneDesign-5.54/lib/Bio/GeneDesign/Oligo.pm
Bio-GeneDesign-5.54/lib/Bio/GeneDesign/PrefixTree.pm
Bio-GeneDesign-5.54/lib/Bio/GeneDesign/Random.pm
Bio-GeneDesign-5.54/lib/Bio/GeneDesign/RestrictionEnzyme.pm
Bio-GeneDesign-5.54/lib/Bio/GeneDesign/RestrictionEnzymes.pm
Bio-GeneDesign-5.54/lib/Bio/GeneDesign/ReverseTranslate.pm
Bio-GeneDesign-5.54/t
Bio-GeneDesign-5.54/t/00-load.t
Bio-GeneDesign-5.54/t/10-basic.t
Bio-GeneDesign-5.54/t/12-io.t
Bio-GeneDesign-5.54/t/15-codons.t
Bio-GeneDesign-5.54/t/20-reverse_translate.t
Bio-GeneDesign-5.54/t/25-codon_juggle.t
Bio-GeneDesign-5.54/t/30-enzymes.t
Bio-GeneDesign-5.54/t/35-subtract_sequence.t
Bio-GeneDesign-5.54/t/40-graph.t
Bio-GeneDesign-5.54/t/60-prefix.t
Bio-GeneDesign-5.54/t/65-random.t
Bio-GeneDesign-5.54/t/boilerplate.t
Bio-GeneDesign-5.54/t/manifest.t
Bio-GeneDesign-5.54/t/pod-coverage.t
Bio-GeneDesign-5.54/t/pod.t
Bio-GeneDesign-5.54/t/testagene.fasta
Bio-GeneDesign-5.54/t/testr_GRV_yeast.gif
Entering Bio-GeneDesign-5.54
Checking configure dependencies from META.json
Checking if you have ExtUtils::Install 1.46 ... Yes (2.04)
Checking if you have Module::Build 0.38 ... Yes (0.4222)
Running Build.PL
Configuring Bio-GeneDesign-5.54 ... 
Checking prerequisites...
  requires:
    !  Bio::Root::Root (0) is installed, but we need version >= 1.006924

ERRORS/WARNINGS FOUND IN PREREQUISITES.  You may wish to install the versions
of the modules indicated above before proceeding with this installation

Where should configuration files be installed? [/etc/GeneDesign/ ]/etc/GeneDesign/ 
Where should scripts be installed? [/usr/local/bin/ ]/usr/local/bin/ 
Where should GeneDesign write tmp files? [/tmp/ ]/tmp/ 
Enable GD::Graphics support? [Y ]Y 
Configuration files will be in /etc/GeneDesign/
Scripts will be in /usr/local/bin/
Temporary files will be written to /tmp/
Installing graphics support

Created MYMETA.yml and MYMETA.json
Creating new 'Build' script for 'Bio-GeneDesign' version '5.54'

Checking dependencies from MYMETA.json ...
Checking if you have Test::More 0.8 ... Yes (1.302083)
Checking if you have Math::Combinatorics 0.09 ... Yes (0.09)
Checking if you have Text::Wrap 2009.0305 ... Yes (2013.0523)
Checking if you have Bio::Root::Root 1.006924 ... No
Checking if you have List::Util 1.22 ... Yes (1.47)
Checking if you have Test::Deep 0.1 ... Yes (1.126)
Searching Bio::Root::Root (1.006924) on cpanmetadb ...
Unpacking BioPerl-1.007001.tar.gz
OK
==> Found dependencies: Bio::Root::Root
--> Working on Bio::Root::Root
Fetching http://www.cpan.org/authors/id/C/CJ/CJFIELDS/BioPerl-1.007001.tar.gz ... OK
BioPerl-1.007001
BioPerl-1.007001/.travis.yml
BioPerl-1.007001/AUTHORS
BioPerl-1.007001/BioPerl.pm
BioPerl-1.007001/BUGS
BioPerl-1.007001/Build.PL
BioPerl-1.007001/Changes
BioPerl-1.007001/DEPENDENCIES
BioPerl-1.007001/DEPRECATED
BioPerl-1.007001/INSTALL-WIN.md
BioPerl-1.007001/INSTALL.md
BioPerl-1.007001/INSTALL.SKIP
BioPerl-1.007001/LICENSE
BioPerl-1.007001/MANIFEST
BioPerl-1.007001/META.json
BioPerl-1.007001/META.yml
BioPerl-1.007001/README.md
BioPerl-1.007001/Bio
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BioPerl-1.007001/Bio/AnalysisI.pm
BioPerl-1.007001/Bio/AnalysisParserI.pm
BioPerl-1.007001/Bio/AnalysisResultI.pm
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BioPerl-1.007001/Bio/CodonUsage/Table.pm
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BioPerl-1.007001/Bio/Tools/Phylo/Phylip
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BioPerl-1.007001/Bio/Tools/Primer
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BioPerl-1.007001/Bio/Tools/Primer/Assessor
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BioPerl-1.007001/Bio/Tools/Signalp
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BioPerl-1.007001/Bio/Tree
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BioPerl-1.007001/Bio/Tree/RandomFactory.pm
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BioPerl-1.007001/Bio/Tree/Draw
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BioPerl-1.007001/Bio/TreeIO
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BioPerl-1.007001/Bio/TreeIO/newick.pm
BioPerl-1.007001/Bio/TreeIO/NewickParser.pm
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BioPerl-1.007001/Bio/TreeIO/TreeEventBuilder.pm
BioPerl-1.007001/Bio/Variation
BioPerl-1.007001/Bio/Variation/AAChange.pm
BioPerl-1.007001/Bio/Variation/AAReverseMutate.pm
BioPerl-1.007001/Bio/Variation/Allele.pm
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BioPerl-1.007001/Bio/Variation/IO.pm
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BioPerl-1.007001/Bio/Variation/IO
BioPerl-1.007001/Bio/Variation/IO/flat.pm
BioPerl-1.007001/Bio/Variation/IO/xml.pm
BioPerl-1.007001/deobfuscator
BioPerl-1.007001/deobfuscator/makedoc.PL
BioPerl-1.007001/deobfuscator/Deobfuscator
BioPerl-1.007001/deobfuscator/Deobfuscator/Build.PL
BioPerl-1.007001/deobfuscator/Deobfuscator/Changes
BioPerl-1.007001/deobfuscator/Deobfuscator/excluded_modules.txt
BioPerl-1.007001/deobfuscator/Deobfuscator/LICENSE
BioPerl-1.007001/deobfuscator/Deobfuscator/Makefile.PL
BioPerl-1.007001/deobfuscator/Deobfuscator/MANIFEST
BioPerl-1.007001/deobfuscator/Deobfuscator/META.yml
BioPerl-1.007001/deobfuscator/Deobfuscator/README
BioPerl-1.007001/deobfuscator/Deobfuscator/bin
BioPerl-1.007001/deobfuscator/Deobfuscator/bin/deob_index.pl
BioPerl-1.007001/deobfuscator/Deobfuscator/bin/run-deobfuscator-update.pl
BioPerl-1.007001/deobfuscator/Deobfuscator/cgi-bin
BioPerl-1.007001/deobfuscator/Deobfuscator/cgi-bin/deob_detail.cgi
BioPerl-1.007001/deobfuscator/Deobfuscator/cgi-bin/deob_flowchart.png
BioPerl-1.007001/deobfuscator/Deobfuscator/cgi-bin/deob_help.html
BioPerl-1.007001/deobfuscator/Deobfuscator/cgi-bin/deob_interface.cgi
BioPerl-1.007001/deobfuscator/Deobfuscator/lib
BioPerl-1.007001/deobfuscator/Deobfuscator/lib/Deobfuscator.pm
BioPerl-1.007001/deobfuscator/Deobfuscator/t
BioPerl-1.007001/deobfuscator/Deobfuscator/t/00.load.t
BioPerl-1.007001/deobfuscator/Deobfuscator/t/pod.t
BioPerl-1.007001/examples
BioPerl-1.007001/examples/bioperl.pl
BioPerl-1.007001/examples/generate_random_seq.pl
BioPerl-1.007001/examples/longorf.pl
BioPerl-1.007001/examples/make_primers.pl
BioPerl-1.007001/examples/rev_and_trans.pl
BioPerl-1.007001/examples/revcom_dir.pl
BioPerl-1.007001/examples/subsequence.cgi
BioPerl-1.007001/examples/align
BioPerl-1.007001/examples/align/align_on_codons.pl
BioPerl-1.007001/examples/align/aligntutorial.pl
BioPerl-1.007001/examples/align/clustalw.pl
BioPerl-1.007001/examples/align/FastAlign.pl
BioPerl-1.007001/examples/align/simplealign.pl
BioPerl-1.007001/examples/Bio-DB-GFF
BioPerl-1.007001/examples/Bio-DB-GFF/load_ucsc.pl
BioPerl-1.007001/examples/cluster
BioPerl-1.007001/examples/cluster/dbsnp.pl
BioPerl-1.007001/examples/contributed
BioPerl-1.007001/examples/contributed/nmrpdb_parse.pl
BioPerl-1.007001/examples/contributed/prosite2perl.pl
BioPerl-1.007001/examples/contributed/rebase2list.pl
BioPerl-1.007001/examples/db
BioPerl-1.007001/examples/db/dbfetch
BioPerl-1.007001/examples/db/est_tissue_query.pl
BioPerl-1.007001/examples/db/gb2features.pl
BioPerl-1.007001/examples/db/get_seqs.pl
BioPerl-1.007001/examples/db/getGenBank.pl
BioPerl-1.007001/examples/db/rfetch.pl
BioPerl-1.007001/examples/db/use_registry.pl
BioPerl-1.007001/examples/liveseq
BioPerl-1.007001/examples/liveseq/change_gene.pl
BioPerl-1.007001/examples/popgen
BioPerl-1.007001/examples/popgen/parse_calc_stats.pl
BioPerl-1.007001/examples/quality
BioPerl-1.007001/examples/quality/svgtrace.pl
BioPerl-1.007001/examples/root
BioPerl-1.007001/examples/root/exceptions1.pl
BioPerl-1.007001/examples/root/exceptions2.pl
BioPerl-1.007001/examples/root/exceptions3.pl
BioPerl-1.007001/examples/root/exceptions4.pl
BioPerl-1.007001/examples/root/README
BioPerl-1.007001/examples/searchio
BioPerl-1.007001/examples/searchio/blast_example.pl
BioPerl-1.007001/examples/searchio/custom_writer.pl
BioPerl-1.007001/examples/searchio/hitwriter.pl
BioPerl-1.007001/examples/searchio/hspwriter.pl
BioPerl-1.007001/examples/searchio/htmlwriter.pl
BioPerl-1.007001/examples/searchio/psiblast_features.pl
BioPerl-1.007001/examples/searchio/psiblast_iterations.pl
BioPerl-1.007001/examples/searchio/rawwriter.pl
BioPerl-1.007001/examples/searchio/resultwriter.pl
BioPerl-1.007001/examples/searchio/waba2gff.pl
BioPerl-1.007001/examples/searchio/waba2gff3.pl
BioPerl-1.007001/examples/sirna
BioPerl-1.007001/examples/sirna/rnai_finder.cgi
BioPerl-1.007001/examples/sirna/TAG
BioPerl-1.007001/examples/structure
BioPerl-1.007001/examples/structure/structure-io.pl
BioPerl-1.007001/examples/tk
BioPerl-1.007001/examples/tk/gsequence.pl
BioPerl-1.007001/examples/tk/hitdisplay.pl
BioPerl-1.007001/examples/tools
BioPerl-1.007001/examples/tools/extract_genes.pl
BioPerl-1.007001/examples/tools/gb_to_gff.pl
BioPerl-1.007001/examples/tools/gff2ps.pl
BioPerl-1.007001/examples/tools/parse_codeml.pl
BioPerl-1.007001/examples/tools/psw.pl
BioPerl-1.007001/examples/tools/reverse-translate.pl
BioPerl-1.007001/examples/tools/run_genscan.pl
BioPerl-1.007001/examples/tools/run_primer3.pl
BioPerl-1.007001/examples/tools/seq_pattern.pl
BioPerl-1.007001/examples/tools/standaloneblast.pl
BioPerl-1.007001/examples/tree
BioPerl-1.007001/examples/tree/paup2phylip.pl
BioPerl-1.007001/ide
BioPerl-1.007001/ide/bioperl.komodo
BioPerl-1.007001/ide/bioperl-mode
BioPerl-1.007001/ide/bioperl-mode/README
BioPerl-1.007001/ide/bioperl-mode/dist
BioPerl-1.007001/ide/bioperl-mode/dist/bioperl-mode-xemacs.tar
BioPerl-1.007001/ide/bioperl-mode/dist/bioperl-mode-xemacs.tar.md5
BioPerl-1.007001/ide/bioperl-mode/dist/bioperl-mode.tar
BioPerl-1.007001/ide/bioperl-mode/dist/bioperl-mode.tar.md5
BioPerl-1.007001/ide/bioperl-mode/dist/Changes
BioPerl-1.007001/ide/bioperl-mode/dist/package-me
BioPerl-1.007001/ide/bioperl-mode/dist/SKIP
BioPerl-1.007001/ide/bioperl-mode/etc
BioPerl-1.007001/ide/bioperl-mode/etc/images
BioPerl-1.007001/ide/bioperl-mode/etc/images/bpmode-tool-dis.xpm
BioPerl-1.007001/ide/bioperl-mode/etc/images/bpmode-tool.xpm
BioPerl-1.007001/ide/bioperl-mode/site-lisp
BioPerl-1.007001/ide/bioperl-mode/site-lisp/bioperl-init.el
BioPerl-1.007001/ide/bioperl-mode/site-lisp/bioperl-mode.el
BioPerl-1.007001/ide/bioperl-mode/site-lisp/bioperl-skel.el
BioPerl-1.007001/ide/bioperl-mode/site-lisp/pod.el
BioPerl-1.007001/maintenance
BioPerl-1.007001/maintenance/authors.pl
BioPerl-1.007001/maintenance/check_NAME.pl
BioPerl-1.007001/maintenance/check_URLs.pl
BioPerl-1.007001/maintenance/cvs2cl_by_file.pl
BioPerl-1.007001/maintenance/dependencies.pl
BioPerl-1.007001/maintenance/deprecated.pl
BioPerl-1.007001/maintenance/find_mod_deps.pl
BioPerl-1.007001/maintenance/module_usage.pl
BioPerl-1.007001/maintenance/modules.pl
BioPerl-1.007001/maintenance/ncbi_blast_switches.pl
BioPerl-1.007001/maintenance/perltidy.conf
BioPerl-1.007001/maintenance/pod.pl
BioPerl-1.007001/maintenance/README
BioPerl-1.007001/maintenance/symlink_script.pl
BioPerl-1.007001/maintenance/version.pl
BioPerl-1.007001/maintenance/big_split
BioPerl-1.007001/maintenance/big_split/file_classification.csv
BioPerl-1.007001/maintenance/big_split/rbuels_notes.txt
BioPerl-1.007001/models
BioPerl-1.007001/models/biblio.dia
BioPerl-1.007001/models/bio_liveseq_variation.dia
BioPerl-1.007001/models/bio_map.dia
BioPerl-1.007001/models/bio_restriction.dia
BioPerl-1.007001/models/bioperl.dia
BioPerl-1.007001/models/coordinatemapper.dia
BioPerl-1.007001/models/map_proposal.txt
BioPerl-1.007001/models/maps_and_markers.dia
BioPerl-1.007001/models/popgen.dia
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BioPerl-1.007001/scripts/Bio-DB-GFF
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BioPerl-1.007001/scripts/DB/bp_flanks.pl
BioPerl-1.007001/scripts/DB/TAG
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BioPerl-1.007001/scripts/index
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BioPerl-1.007001/scripts/index/bp_index.pl
BioPerl-1.007001/scripts/index/bp_seqret.pl
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BioPerl-1.007001/scripts/searchio/bp_hmmer_to_table.pl
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BioPerl-1.007001/scripts/searchio/bp_search2table.pl
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BioPerl-1.007001/scripts/seq/bp_seqretsplit.pl
BioPerl-1.007001/scripts/seq/bp_split_seq.pl
BioPerl-1.007001/scripts/seq/bp_translate_seq.pl
BioPerl-1.007001/scripts/seq/bp_unflatten_seq.pl
BioPerl-1.007001/scripts/seq/TAG
BioPerl-1.007001/scripts/seqstats
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BioPerl-1.007001/scripts/seqstats/bp_chaos_plot.pl
BioPerl-1.007001/scripts/seqstats/bp_gccalc.pl
BioPerl-1.007001/scripts/seqstats/bp_oligo_count.pl
BioPerl-1.007001/scripts/seqstats/TAG
BioPerl-1.007001/scripts/taxa
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BioPerl-1.007001/scripts/taxa/bp_local_taxonomydb_query.pl
BioPerl-1.007001/scripts/taxa/bp_query_entrez_taxa.pl
BioPerl-1.007001/scripts/taxa/bp_taxid4species.pl
BioPerl-1.007001/scripts/taxa/bp_taxonomy2tree.pl
BioPerl-1.007001/scripts/taxa/TAG
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BioPerl-1.007001/scripts/tree/bp_nexus2nh.pl
BioPerl-1.007001/scripts/tree/bp_tree2pag.pl
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BioPerl-1.007001/scripts/utilities/bp_mask_by_search.pl
BioPerl-1.007001/scripts/utilities/bp_mrtrans.pl
BioPerl-1.007001/scripts/utilities/bp_mutate.pl
BioPerl-1.007001/scripts/utilities/bp_netinstall.pl
BioPerl-1.007001/scripts/utilities/bp_nrdb.pl
BioPerl-1.007001/scripts/utilities/bp_pairwise_kaks.pl
BioPerl-1.007001/scripts/utilities/bp_remote_blast.pl
BioPerl-1.007001/scripts/utilities/bp_revtrans-motif.pl
BioPerl-1.007001/scripts/utilities/bp_search2alnblocks.pl
BioPerl-1.007001/scripts/utilities/bp_search2gff.pl
BioPerl-1.007001/scripts/utilities/bp_search2tribe.pl
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BioPerl-1.007001/scripts/utilities/README
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BioPerl-1.007001/t/SeqIO
BioPerl-1.007001/t/SeqIO/abi.t
BioPerl-1.007001/t/SeqIO/ace.t
BioPerl-1.007001/t/SeqIO/agave.t
BioPerl-1.007001/t/SeqIO/alf.t
BioPerl-1.007001/t/SeqIO/asciitree.t
BioPerl-1.007001/t/SeqIO/bsml.t
BioPerl-1.007001/t/SeqIO/bsml_sax.t
BioPerl-1.007001/t/SeqIO/chadoxml.t
BioPerl-1.007001/t/SeqIO/chaos.t
BioPerl-1.007001/t/SeqIO/chaosxml.t
BioPerl-1.007001/t/SeqIO/ctf.t
BioPerl-1.007001/t/SeqIO/embl.t
BioPerl-1.007001/t/SeqIO/entrezgene.t
BioPerl-1.007001/t/SeqIO/excel.t
BioPerl-1.007001/t/SeqIO/exp.t
BioPerl-1.007001/t/SeqIO/fasta.t
BioPerl-1.007001/t/SeqIO/fastq.t
BioPerl-1.007001/t/SeqIO/flybase_chadoxml.t
BioPerl-1.007001/t/SeqIO/game.t
BioPerl-1.007001/t/SeqIO/gbxml.t
BioPerl-1.007001/t/SeqIO/gcg.t
BioPerl-1.007001/t/SeqIO/genbank.t
BioPerl-1.007001/t/SeqIO/Handler.t
BioPerl-1.007001/t/SeqIO/interpro.t
BioPerl-1.007001/t/SeqIO/kegg.t
BioPerl-1.007001/t/SeqIO/largefasta.t
BioPerl-1.007001/t/SeqIO/lasergene.t
BioPerl-1.007001/t/SeqIO/locuslink.t
BioPerl-1.007001/t/SeqIO/mbsout.t
BioPerl-1.007001/t/SeqIO/metafasta.t
BioPerl-1.007001/t/SeqIO/msout.t
BioPerl-1.007001/t/SeqIO/MultiFile.t
BioPerl-1.007001/t/SeqIO/Multiple_fasta.t
BioPerl-1.007001/t/SeqIO/nexml.t
BioPerl-1.007001/t/SeqIO/phd.t
BioPerl-1.007001/t/SeqIO/pir.t
BioPerl-1.007001/t/SeqIO/pln.t
BioPerl-1.007001/t/SeqIO/qual.t
BioPerl-1.007001/t/SeqIO/raw.t
BioPerl-1.007001/t/SeqIO/scf.t
BioPerl-1.007001/t/SeqIO/SeqBuilder.t
BioPerl-1.007001/t/SeqIO/SeqIO.t
BioPerl-1.007001/t/SeqIO/seqxml.t
BioPerl-1.007001/t/SeqIO/Splicedseq.t
BioPerl-1.007001/t/SeqIO/strider.t
BioPerl-1.007001/t/SeqIO/swiss.t
BioPerl-1.007001/t/SeqIO/tab.t
BioPerl-1.007001/t/SeqIO/table.t
BioPerl-1.007001/t/SeqIO/tigr.t
BioPerl-1.007001/t/SeqIO/tigrxml.t
BioPerl-1.007001/t/SeqIO/tinyseq.t
BioPerl-1.007001/t/SeqIO/ztr.t
BioPerl-1.007001/t/SeqTools
BioPerl-1.007001/t/SeqTools/Backtranslate.t
BioPerl-1.007001/t/SeqTools/CodonTable.t
BioPerl-1.007001/t/SeqTools/ECnumber.t
BioPerl-1.007001/t/SeqTools/GuessSeqFormat.t
BioPerl-1.007001/t/SeqTools/OddCodes.t
BioPerl-1.007001/t/SeqTools/SeqPattern.t
BioPerl-1.007001/t/SeqTools/SeqStats.t
BioPerl-1.007001/t/SeqTools/SeqUtils.t
BioPerl-1.007001/t/SeqTools/SeqWords.t
BioPerl-1.007001/t/Structure
BioPerl-1.007001/t/Structure/IO.t
BioPerl-1.007001/t/Structure/Structure.t
BioPerl-1.007001/t/Tools
BioPerl-1.007001/t/Tools/AmpliconSearch.t
BioPerl-1.007001/t/Tools/ePCR.t
BioPerl-1.007001/t/Tools/Est2Genome.t
BioPerl-1.007001/t/Tools/FootPrinter.t
BioPerl-1.007001/t/Tools/Geneid.t
BioPerl-1.007001/t/Tools/Genewise.t
BioPerl-1.007001/t/Tools/Genomewise.t
BioPerl-1.007001/t/Tools/Genpred.t
BioPerl-1.007001/t/Tools/GFF.t
BioPerl-1.007001/t/Tools/Hmmer.t
BioPerl-1.007001/t/Tools/IUPAC.t
BioPerl-1.007001/t/Tools/Lucy.t
BioPerl-1.007001/t/Tools/Match.t
BioPerl-1.007001/t/Tools/pICalculator.t
BioPerl-1.007001/t/Tools/Primer3.t
BioPerl-1.007001/t/Tools/Promoterwise.t
BioPerl-1.007001/t/Tools/Pseudowise.t
BioPerl-1.007001/t/Tools/QRNA.t
BioPerl-1.007001/t/Tools/RandDistFunctions.t
BioPerl-1.007001/t/Tools/RepeatMasker.t
BioPerl-1.007001/t/Tools/Seg.t
BioPerl-1.007001/t/Tools/Sigcleave.t
BioPerl-1.007001/t/Tools/Signalp.t
BioPerl-1.007001/t/Tools/Sim4.t
BioPerl-1.007001/t/Tools/SiRNA.t
BioPerl-1.007001/t/Tools/TandemRepeatsFinder.t
BioPerl-1.007001/t/Tools/TargetP.t
BioPerl-1.007001/t/Tools/Tmhmm.t
BioPerl-1.007001/t/Tools/tRNAscanSE.t
BioPerl-1.007001/t/Tools/Alignment
BioPerl-1.007001/t/Tools/Alignment/Consed.t
BioPerl-1.007001/t/Tools/Analysis
BioPerl-1.007001/t/Tools/Analysis/DNA
BioPerl-1.007001/t/Tools/Analysis/DNA/ESEfinder.t
BioPerl-1.007001/t/Tools/Analysis/Protein
BioPerl-1.007001/t/Tools/Analysis/Protein/Domcut.t
BioPerl-1.007001/t/Tools/Analysis/Protein/ELM.t
BioPerl-1.007001/t/Tools/Analysis/Protein/GOR4.t
BioPerl-1.007001/t/Tools/Analysis/Protein/HNN.t
BioPerl-1.007001/t/Tools/Analysis/Protein/NetPhos.t
BioPerl-1.007001/t/Tools/Analysis/Protein/Scansite.t
BioPerl-1.007001/t/Tools/Analysis/Protein/Sopma.t
BioPerl-1.007001/t/Tools/EMBOSS
BioPerl-1.007001/t/Tools/EMBOSS/Palindrome.t
BioPerl-1.007001/t/Tools/Phylo
BioPerl-1.007001/t/Tools/Phylo/Gerp.t
BioPerl-1.007001/t/Tools/Phylo/Molphy.t
BioPerl-1.007001/t/Tools/Phylo/PAML.t
BioPerl-1.007001/t/Tools/Phylo/Phylip
BioPerl-1.007001/t/Tools/Phylo/Phylip/ProtDist.t
BioPerl-1.007001/t/Tools/Run
BioPerl-1.007001/t/Tools/Run/RemoteBlast.t
BioPerl-1.007001/t/Tools/Run/RemoteBlast_rpsblast.t
BioPerl-1.007001/t/Tools/Signalp
BioPerl-1.007001/t/Tools/Signalp/ExtendedSignalp.t
BioPerl-1.007001/t/Tools/Spidey
BioPerl-1.007001/t/Tools/Spidey/Spidey.t
BioPerl-1.007001/t/Tree
BioPerl-1.007001/t/Tree/Compatible.t
BioPerl-1.007001/t/Tree/Node.t
BioPerl-1.007001/t/Tree/RandomTreeFactory.t
BioPerl-1.007001/t/Tree/Tree.t
BioPerl-1.007001/t/Tree/TreeIO.t
BioPerl-1.007001/t/Tree/TreeStatistics.t
BioPerl-1.007001/t/Tree/PhyloNetwork
BioPerl-1.007001/t/Tree/PhyloNetwork/Factory.t
BioPerl-1.007001/t/Tree/PhyloNetwork/GraphViz.t
BioPerl-1.007001/t/Tree/PhyloNetwork/MuVector.t
BioPerl-1.007001/t/Tree/PhyloNetwork/PhyloNetwork.t
BioPerl-1.007001/t/Tree/PhyloNetwork/RandomFactory.t
BioPerl-1.007001/t/Tree/PhyloNetwork/TreeFactory.t
BioPerl-1.007001/t/Tree/TreeIO
BioPerl-1.007001/t/Tree/TreeIO/lintree.t
BioPerl-1.007001/t/Tree/TreeIO/newick.t
BioPerl-1.007001/t/Tree/TreeIO/nexml.t
BioPerl-1.007001/t/Tree/TreeIO/nexus.t
BioPerl-1.007001/t/Tree/TreeIO/nhx.t
BioPerl-1.007001/t/Tree/TreeIO/phyloxml.t
BioPerl-1.007001/t/Tree/TreeIO/svggraph.t
BioPerl-1.007001/t/Tree/TreeIO/tabtree.t
BioPerl-1.007001/t/Variation
BioPerl-1.007001/t/Variation/AAChange.t
BioPerl-1.007001/t/Variation/AAReverseMutate.t
BioPerl-1.007001/t/Variation/Allele.t
BioPerl-1.007001/t/Variation/DNAMutation.t
BioPerl-1.007001/t/Variation/RNAChange.t
BioPerl-1.007001/t/Variation/SeqDiff.t
BioPerl-1.007001/t/Variation/SNP.t
BioPerl-1.007001/t/Variation/Variation_IO.t
BioPerl-1.007001/travis_scripts
BioPerl-1.007001/travis_scripts/dependency_installs
BioPerl-1.007001/travis_scripts/trigger-dockerhub.sh
Entering BioPerl-1.007001
Checking configure dependencies from META.json
Checking if you have ExtUtils::Install 1.46 ... Yes (2.04)
Checking if you have Module::Build 0.42 ... Yes (0.4222)
Running Build.PL
Configuring BioPerl-1.007001 ... Checking prerequisites...
  recommends:
    *  XML::DOM::XPath is not installed

ERRORS/WARNINGS FOUND IN PREREQUISITES.  You may wish to install the versions
of the modules indicated above before proceeding with this installation

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 tests

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 '1.007001'
Checking dependencies from MYMETA.json ...
Checking if you have IO::String 0 ... Yes (1.08)
Checking if you have Test::Harness 2.62 ... Yes (3.39)
Checking if you have Module::Build 0.42 ... Yes (0.4222)
Checking if you have Test::Most 0 ... Yes (0.35)
Checking if you have URI::Escape 0 ... Yes (3.31)
Checking if you have CPAN 1.81 ... Yes (2.16)
Checking if you have Scalar::Util 0 ... Yes (1.47)
Checking if you have Data::Stag 0.11 ... Yes (0.14)
Checking if you have ExtUtils::Manifest 1.52 ... Yes (1.70)
OK
Building and testing BioPerl-1.007001 ... 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/Align/Utilities.t .................... ok
t/AlignIO/AlignIO.t .................... ok
t/AlignIO/arp.t ........................ ok
t/AlignIO/bl2seq.t ..................... ok
t/AlignIO/clustalw.t ................... ok
t/AlignIO/emboss.t ..................... ok
t/AlignIO/fasta.t ...................... ok
t/AlignIO/largemultifasta.t ............ ok
t/AlignIO/maf.t ........................ ok
t/AlignIO/mase.t ....................... ok
t/AlignIO/mega.t ....................... ok
t/AlignIO/meme.t ....................... ok
t/AlignIO/metafasta.t .................. ok
t/AlignIO/msf.t ........................ ok
# WARNING: NeXML parsing for NeXML v0.9 is currently very experimental support
t/AlignIO/nexml.t ...................... ok
t/AlignIO/nexus.t ...................... ok
t/AlignIO/pfam.t ....................... ok
t/AlignIO/phylip.t ..................... ok
t/AlignIO/po.t ......................... ok
t/AlignIO/prodom.t ..................... ok
t/AlignIO/psi.t ........................ ok
t/AlignIO/selex.t ...................... ok
t/AlignIO/stockholm.t .................. ok
t/AlignIO/xmfa.t ....................... ok
t/Alphabet.t ........................... ok
t/Annotation/Annotation.t .............. ok
t/Annotation/AnnotationAdaptor.t ....... ok
Unescaped left brace in regex is deprecated here (and will be fatal in Perl 5.30), passed through in regex; marked by <-- HERE in m/function(\s+)([a-z0-9_]+)(\s*){ <-- HERE (.*?)}/ at /home/ryan/perl5/perlbrew/perls/perl-blead/lib/site_perl/5.26.0/Inline/Echo.pm line 25.
Unescaped left brace in regex is deprecated here (and will be fatal in Perl 5.30), passed through in regex; marked by <-- HERE in m/function(\s+)([a-z0-9_]+)(\s*){ <-- HERE (.*?)}/ at /home/ryan/perl5/perlbrew/perls/perl-blead/lib/site_perl/5.26.0/Inline/Nouse.pm line 28.
t/Assembly/ContigSpectrum.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::Tools::Run::Samtools (or dependencies thereof) was not installed
t/Assembly/core.t ...................... ok
t/Cluster/UniGene.t .................... ok
t/ClusterIO/ClusterIO.t ................ ok
t/ClusterIO/SequenceFamily.t ........... ok
t/ClusterIO/unigene.t .................. ok
t/Draw/Pictogram.t ..................... ok
t/LiveSeq/Chain.t ...................... ok
t/LiveSeq/LiveSeq.t .................... ok
t/LiveSeq/Mutation.t ................... ok
t/LiveSeq/Mutator.t .................... ok
File::Glob::glob() will disappear in perl 5.30. Use File::Glob::bsd_glob() instead. at Bio/DB/GFF.pm line 2000.

You are loading a Bio::DB::GFF database with GFF3 formatted data.
While this will likely work fine, the Bio::DB::GFF schema does not
always faithfully capture the complexity represented in GFF3 files.
Unless you have a specific reason for using Bio::DB::GFF, we suggest
that you use a Bio::DB::SeqFeature::Store database and its corresponding
loader, bp_seqfeature_load.pl.

t/LocalDB/BioDBGFF.t ................... ok
Subroutine dl_load_flags redefined at (eval 73) line 8.
Subroutine Bio::DB::IndexedBase::_strip_crnl redefined at (eval 73) line 9.
t/LocalDB/Fasta.t ...................... ok
t/LocalDB/Flat.t ....................... ok
t/LocalDB/Index/Blast.t ................ ok
t/LocalDB/Index/BlastTable.t ........... ok
t/LocalDB/Index/Index.t ................ ok
t/LocalDB/Qual.t ....................... ok
t/LocalDB/Registry.t ................... ok
t/LocalDB/SeqFeature.t ................. ok
t/LocalDB/Taxonomy/greengenes.t ........ ok
t/LocalDB/Taxonomy/silva.t ............. ok
t/LocalDB/Taxonomy/sqlite.t ............ ok
t/LocalDB/transfac_pro.t ............... ok
t/Map/Cyto.t ........................... ok
t/Map/Linkage.t ........................ ok
t/Map/Map.t ............................ ok
t/Map/MapIO.t .......................... ok
t/Map/MicrosatelliteMarker.t ........... ok
t/Map/Physical.t ....................... ok
t/Matrix/IO/masta.t .................... ok
t/Matrix/IO/psm.t ...................... ok
t/Matrix/InstanceSite.t ................ ok
t/Matrix/Matrix.t ...................... ok
t/Matrix/ProtMatrix.t .................. ok
t/Matrix/ProtPsm.t ..................... ok
t/Matrix/SiteMatrix.t .................. ok
t/Ontology/GOterm.t .................... ok
t/Ontology/GraphAdaptor.t .............. ok
t/Ontology/IO/go.t ..................... ok
t/Ontology/IO/interpro.t ............... ok
t/Ontology/IO/obo.t .................... ok
t/Ontology/Ontology.t .................. ok
t/Ontology/OntologyEngine.t ............ ok
t/Ontology/OntologyStore.t ............. skipped: Network tests have not been requested
t/Ontology/Relationship.t .............. ok
t/Ontology/RelationshipType.t .......... ok
t/Ontology/Term.t ...................... ok
t/Perl.t ............................... ok
t/Phenotype/Correlate.t ................ ok
t/Phenotype/MeSH.t ..................... ok
t/Phenotype/Measure.t .................. ok
t/Phenotype/MiniMIMentry.t ............. ok
t/Phenotype/OMIMentry.t ................ ok
t/Phenotype/OMIMentryAllelicVariant.t .. ok
t/Phenotype/OMIMparser.t ............... ok
t/Phenotype/Phenotype.t ................ ok
t/PodSyntax.t .......................... ok
t/PopGen/Coalescent.t .................. ok
t/PopGen/HtSNP.t ....................... ok
t/PopGen/MK.t .......................... ok
t/PopGen/PopGen.t ...................... ok
t/PopGen/PopGenSims.t .................. ok
t/PopGen/TagHaplotype.t ................ ok
t/RemoteDB/BioFetch.t .................. skipped: Network tests have not been requested
t/RemoteDB/CUTG.t ...................... ok
t/RemoteDB/EMBL.t ...................... skipped: Network tests have not been requested
t/RemoteDB/EntrezGene.t ................ skipped: Network tests have not been requested
t/RemoteDB/GenBank.t ................... skipped: Network tests have not been requested
t/RemoteDB/GenPept.t ................... skipped: Network tests have not been requested
t/RemoteDB/HIV/HIV.t ................... ok
t/RemoteDB/HIV/HIVAnnotProcessor.t ..... ok
t/RemoteDB/HIV/HIVQuery.t .............. ok
t/RemoteDB/HIV/HIVQueryHelper.t ........ ok
t/RemoteDB/MeSH.t ...................... skipped: Network tests have not been requested
t/RemoteDB/Query/GenBank.t ............. skipped: Network tests have not been requested
t/RemoteDB/RefSeq.t .................... ok
t/RemoteDB/SeqRead_fail.t .............. skipped: Network tests have not been requested
t/RemoteDB/SeqVersion.t ................ ok
t/RemoteDB/SwissProt.t ................. skipped: Network tests have not been requested
t/RemoteDB/Taxonomy.t .................. ok
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
t/Root/IO.t ............................ ok
t/Root/RootI.t ......................... ok
t/Root/RootIO.t ........................ skipped: Network tests have not been requested
t/Root/Storable.t ...................... ok
t/Root/Utilities.t ..................... ok
t/SearchDist.t ......................... skipped: The optional module Bio::Ext::Align (or dependencies thereof) was not installed
t/SearchIO/CigarString.t ............... ok
t/SearchIO/SearchIO.t .................. ok
t/SearchIO/SimilarityPair.t ............ ok
t/SearchIO/Tiling.t .................... ok
t/SearchIO/Writer/GbrowseGFF.t ......... ok
t/SearchIO/Writer/HSPTableWriter.t ..... ok
t/SearchIO/Writer/HTMLWriter.t ......... ok
t/SearchIO/Writer/HitTableWriter.t ..... ok
t/SearchIO/Writer/TextWriter.t ......... ok
t/SearchIO/axt.t ....................... ok
t/SearchIO/blast.t ..................... ok
t/SearchIO/blast_pull.t ................ ok
t/SearchIO/blasttable.t ................ ok
t/SearchIO/cross_match.t ............... ok
t/SearchIO/erpin.t ..................... ok
t/SearchIO/exonerate.t ................. ok
t/SearchIO/fasta.t ..................... ok
t/SearchIO/gmap_f9.t ................... ok
t/SearchIO/hmmer.t ..................... ok
t/SearchIO/hmmer_pull.t ................ ok
t/SearchIO/infernal.t .................. ok
t/SearchIO/megablast.t ................. ok
t/SearchIO/psl.t ....................... ok
t/SearchIO/rnamotif.t .................. ok
t/SearchIO/sim4.t ...................... ok
t/SearchIO/waba.t ...................... ok
t/SearchIO/wise.t ...................... ok
t/Seq/DBLink.t ......................... ok
t/Seq/EncodedSeq.t ..................... ok
t/Seq/LargeLocatableSeq.t .............. ok
t/Seq/LargePSeq.t ...................... ok
t/Seq/LocatableSeq.t ................... ok
t/Seq/MetaSeq.t ........................ ok
t/Seq/PrimaryQual.t .................... ok
t/Seq/PrimarySeq.t ..................... ok
t/Seq/PrimedSeq.t ...................... ok
t/Seq/Quality.t ........................ ok
t/Seq/Seq.t ............................ ok
t/Seq/SimulatedRead.t .................. ok
t/Seq/WithQuality.t .................... ok
t/SeqEvolution.t ....................... ok
t/SeqFeature/Amplicon.t ................ ok
t/SeqFeature/Clone.t ................... ok
t/SeqFeature/Collection.t .............. ok
t/SeqFeature/Computation.t ............. ok
t/SeqFeature/FeaturePair.t ............. ok
t/SeqFeature/Gene.t .................... ok
t/SeqFeature/Generic.t ................. ok
t/SeqFeature/Location.t ................ ok
t/SeqFeature/LocationFactory.t ......... ok
t/SeqFeature/Primer.t .................. ok
t/SeqFeature/Range.t ................... ok
t/SeqFeature/RangeI.t .................. ok
t/SeqFeature/SeqAnalysisParser.t ....... ok
t/SeqFeature/SubSeq.t .................. ok
t/SeqFeature/Unflattener.t ............. ok
t/SeqIO/Handler.t ...................... ok
t/SeqIO/MultiFile.t .................... ok
t/SeqIO/Multiple_fasta.t ............... ok
t/SeqIO/SeqBuilder.t ................... ok
t/SeqIO/SeqIO.t ........................ ok
t/SeqIO/Splicedseq.t ................... ok
t/SeqIO/abi.t .......................... skipped: The optional module Bio::SeqIO::staden::read (or dependencies thereof) was not installed
t/SeqIO/ace.t .......................... ok
t/SeqIO/agave.t ........................ ok
t/SeqIO/alf.t .......................... skipped: The optional module Bio::SeqIO::staden::read (or dependencies thereof) was not installed
t/SeqIO/asciitree.t .................... ok
t/SeqIO/bsml.t ......................... ok
t/SeqIO/bsml_sax.t ..................... ok
t/SeqIO/chadoxml.t ..................... ok
t/SeqIO/chaos.t ........................ ok
t/SeqIO/chaosxml.t ..................... ok
t/SeqIO/ctf.t .......................... skipped: The optional module Bio::SeqIO::staden::read (or dependencies thereof) was not installed
t/SeqIO/embl.t ......................... ok
t/SeqIO/entrezgene.t ................... ok
t/SeqIO/excel.t ........................ ok
t/SeqIO/exp.t .......................... skipped: The optional module Bio::SeqIO::staden::read (or dependencies thereof) was not installed
t/SeqIO/fasta.t ........................ ok
t/SeqIO/fastq.t ........................ ok
t/SeqIO/flybase_chadoxml.t ............. ok
t/SeqIO/game.t ......................... ok
t/SeqIO/gbxml.t ........................ ok
t/SeqIO/gcg.t .......................... ok
t/SeqIO/genbank.t ...................... ok
t/SeqIO/interpro.t ..................... skipped: The optional module XML::DOM::XPath (or dependencies thereof) was not installed
t/SeqIO/kegg.t ......................... ok
t/SeqIO/largefasta.t ................... ok
t/SeqIO/lasergene.t .................... ok
t/SeqIO/locuslink.t .................... ok
t/SeqIO/mbsout.t ....................... ok
t/SeqIO/metafasta.t .................... ok
t/SeqIO/msout.t ........................ ok
# WARNING: NeXML parsing for NeXML v0.9 is currently very experimental support
t/SeqIO/nexml.t ........................ ok
t/SeqIO/phd.t .......................... ok
t/SeqIO/pir.t .......................... ok
t/SeqIO/pln.t .......................... skipped: The optional module Bio::SeqIO::staden::read (or dependencies thereof) was not installed
t/SeqIO/qual.t ......................... ok
t/SeqIO/raw.t .......................... ok
t/SeqIO/scf.t .......................... ok
t/SeqIO/seqxml.t ....................... ok
t/SeqIO/strider.t ...................... ok
t/SeqIO/swiss.t ........................ ok
t/SeqIO/tab.t .......................... ok
t/SeqIO/table.t ........................ ok
t/SeqIO/tigr.t ......................... ok
t/SeqIO/tigrxml.t ...................... ok
t/SeqIO/tinyseq.t ...................... ok
t/SeqIO/ztr.t .......................... skipped: The optional module Bio::SeqIO::staden::read (or dependencies thereof) was not installed
t/SeqTools/Backtranslate.t ............. ok
t/SeqTools/CodonTable.t ................ ok
t/SeqTools/ECnumber.t .................. ok
t/SeqTools/GuessSeqFormat.t ............ ok
t/SeqTools/OddCodes.t .................. ok
t/SeqTools/SeqPattern.t ................ ok
t/SeqTools/SeqStats.t .................. ok
t/SeqTools/SeqUtils.t .................. ok
t/SeqTools/SeqWords.t .................. ok
t/Species.t ............................ ok
t/Structure/IO.t ....................... ok
t/Structure/Structure.t ................ ok
t/Symbol.t ............................. ok
t/TaxonTree.t .......................... skipped: These modules are now probably deprecated
t/Tools/Alignment/Consed.t ............. ok
t/Tools/AmpliconSearch.t ............... ok
t/Tools/Analysis/DNA/ESEfinder.t ....... skipped: Network tests have not been requested
t/Tools/Analysis/Protein/Domcut.t ...... skipped: Network tests have not been requested
t/Tools/Analysis/Protein/ELM.t ......... skipped: Network tests have not been requested
t/Tools/Analysis/Protein/GOR4.t ........ skipped: Network tests have not been requested
t/Tools/Analysis/Protein/HNN.t ......... skipped: Network tests have not been requested
t/Tools/Analysis/Protein/NetPhos.t ..... skipped: Network tests have not been requested
t/Tools/Analysis/Protein/Scansite.t .... ok
t/Tools/Analysis/Protein/Sopma.t ....... skipped: Network tests have not been requested
t/Tools/EMBOSS/Palindrome.t ............ ok
t/Tools/Est2Genome.t ................... ok
t/Tools/FootPrinter.t .................. ok
t/Tools/GFF.t .......................... ok
t/Tools/Geneid.t ....................... ok
t/Tools/Genewise.t ..................... ok
t/Tools/Genomewise.t ................... ok
t/Tools/Genpred.t ...................... ok
t/Tools/Hmmer.t ........................ ok
t/Tools/IUPAC.t ........................ ok
t/Tools/Lucy.t ......................... ok
t/Tools/Match.t ........................ ok
t/Tools/Phylo/Gerp.t ................... ok
t/Tools/Phylo/Molphy.t ................. ok
t/Tools/Phylo/PAML.t ................... ok
t/Tools/Phylo/Phylip/ProtDist.t ........ ok
t/Tools/Primer3.t ...................... ok
t/Tools/Promoterwise.t ................. ok
t/Tools/Pseudowise.t ................... ok
t/Tools/QRNA.t ......................... ok
t/Tools/RandDistFunctions.t ............ ok
t/Tools/RepeatMasker.t ................. ok
t/Tools/Run/RemoteBlast.t .............. skipped: Network tests have not been requested
t/Tools/Run/RemoteBlast_rpsblast.t ..... skipped: Network tests have not been requested
t/Tools/Seg.t .......................... ok
t/Tools/SiRNA.t ........................ ok
t/Tools/Sigcleave.t .................... ok
t/Tools/Signalp.t ...................... ok
t/Tools/Signalp/ExtendedSignalp.t ...... ok
t/Tools/Sim4.t ......................... ok
t/Tools/Spidey/Spidey.t ................ ok
t/Tools/TandemRepeatsFinder.t .......... ok
t/Tools/TargetP.t ...................... ok
t/Tools/Tmhmm.t ........................ ok
t/Tools/ePCR.t ......................... ok
t/Tools/pICalculator.t ................. ok
t/Tools/tRNAscanSE.t ................... ok
t/Tree/Compatible.t .................... ok
t/Tree/Node.t .......................... ok
t/Tree/PhyloNetwork/Factory.t .......... ok
t/Tree/PhyloNetwork/GraphViz.t ......... ok
t/Tree/PhyloNetwork/MuVector.t ......... ok
t/Tree/PhyloNetwork/PhyloNetwork.t ..... ok
t/Tree/PhyloNetwork/RandomFactory.t .... ok
t/Tree/PhyloNetwork/TreeFactory.t ...... ok
t/Tree/RandomTreeFactory.t ............. ok
t/Tree/Tree.t .......................... ok
t/Tree/TreeIO.t ........................ ok
t/Tree/TreeIO/lintree.t ................ ok
t/Tree/TreeIO/newick.t ................. ok
# WARNING: NeXML parsing for NeXML v0.9 is currently very experimental support
# Begin tests for writing tree files
t/Tree/TreeIO/nexml.t .................. ok
t/Tree/TreeIO/nexus.t .................. ok
t/Tree/TreeIO/nhx.t .................... ok
t/Tree/TreeIO/phyloxml.t ............... ok
t/Tree/TreeIO/svggraph.t ............... ok
t/Tree/TreeIO/tabtree.t ................ ok
t/Tree/TreeStatistics.t ................ ok
t/Variation/AAChange.t ................. ok
t/Variation/AAReverseMutate.t .......... ok
t/Variation/Allele.t ................... ok
t/Variation/DNAMutation.t .............. ok
t/Variation/RNAChange.t ................ ok
t/Variation/SNP.t ...................... ok
t/Variation/SeqDiff.t .................. ok
t/Variation/Variation_IO.t ............. ok
# WARNING: NeXML parsing for NeXML v0.9 is currently very experimental support
t/nexml.t .............................. ok
All tests successful.

Test Summary Report
-------------------
t/Root/IO.t                          (Wstat: 0 Tests: 154 Failed: 0)
  TODO passed:   109, 112, 115, 118
Files=325, Tests=23238, 77 wallclock secs ( 4.07 usr  1.92 sys + 68.64 cusr  5.33 csys = 79.96 CPU)
Result: PASS
Building BioPerl
Reading skip patterns from 'INSTALL.SKIP'.
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Writing /home/ryan/perl5/perlbrew/perls/perl-blead/lib/site_perl/5.26.0/x86_64-linux/auto/Bio/.packlist
OK
Successfully installed BioPerl-1.007001
Installing /home/ryan/perl5/perlbrew/perls/perl-blead/lib/site_perl/5.26.0/x86_64-linux/.meta/BioPerl-1.007001/install.json
! Installing the dependencies failed: Missing version info for module 'Bio::Root::Root'
! Bailing out the installation for Bio-GeneDesign-5.54.
1 distribution installed
Command [cpanm --reinstall --verbose Bio::GeneDesign::Basic] terminated with exit code 1 ($? = 256) under the following perl environment:
Command terminated with non-zero status.


Current perl:
  Name: perl-blead
  Path: /home/ryan/perl5/perlbrew/perls/perl-blead/bin/perl
  Config: -de -Dprefix=/home/ryan/perl5/perlbrew/perls/perl-blead -Dusedevel -Aeval:scriptdir=/home/ryan/perl5/perlbrew/perls/perl-blead/bin
  Compiled at: Mar 30 2017 03:10:09

perlbrew:
  version: 0.78
  ENV:
    PERLBREW_ROOT: /home/ryan/perl5/perlbrew
    PERLBREW_HOME: /home/ryan/.perlbrew
    PERLBREW_PATH: /home/ryan/perl5/perlbrew/bin:/home/ryan/perl5/perlbrew/perls/perl-blead/bin
    PERLBREW_MANPATH: /home/ryan/perl5/perlbrew/perls/perl-blead/man