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:whale: Genomics Research Container Architecture
http://www.bcgsc.ca/services/orca
GNU General Public License v3.0
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BioPerl: FAIL Installing Bio::Root::Version failed #17

Closed tmozgach closed 7 years ago

tmozgach commented 7 years ago

One month ago it worked.

on docker2, run docker run -ti 24b21f10017c then cpanm -i Bio::Root::Version

The following log:

cpanm (App::cpanminus) 1.7043 on perl 5.026000 built for x86_64-linux-thread-multi
Work directory is /home/linuxbrew/.cpanm/work/1502408933.12319
You have make /usr/bin/make
You have /usr/bin/curl
You have /bin/tar: tar (GNU tar) 1.27.1
Copyright (C) 2013 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.
Searching Bio::Root::Version () on cpanmetadb ...
--> Working on Bio::Root::Version
Fetching http://www.cpan.org/authors/id/C/CJ/CJFIELDS/BioPerl-1.007001.tar.gz
-> OK
Unpacking BioPerl-1.007001.tar.gz
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 (0.4224)
Configuring BioPerl-1.007001
Running Build.PL
Checking prerequisites...
  recommends:
    *  Algorithm::Munkres is not installed
    *  Array::Compare is not installed
    *  Bio::Phylo is not installed
    *  CGI is not installed
    *  Clone is not installed
    *  Convert::Binary::C is not installed
    *  Error is not installed
    *  GD is not installed
    *  Graph is not installed
    *  GraphViz is not installed
    *  HTML::TableExtract is not installed
    *  IO::Scalar is not installed
    *  Inline::C is not installed
    *  LWP::UserAgent is not installed
    *  PostScript::TextBlock is not installed
    *  SVG is not installed
    *  SVG::Graph is not installed
    *  Set::Scalar is not installed
    *  Sort::Naturally is not installed
    *  Spreadsheet::ParseExcel is not installed
    *  XML::DOM is not installed
    *  XML::DOM::XPath is not installed
    *  XML::LibXML is not installed
    *  XML::Parser is not installed
    *  XML::Parser::PerlSAX is not installed
    *  XML::SAX::Writer is not installed
    *  XML::Simple is not installed
    *  XML::Twig is not installed
    *  XML::Writer is not installed
    *  YAML is not installed

Checking optional features...
EntrezGene............disabled
  requires:
    ! Bio::ASN1::EntrezGene is not installed
Network Tests.........disabled
  requires:
    ! LWP::UserAgent is not installed
Pg Tests..............disabled
  requires:
    ! DBD::Pg is not installed
SQLite Tests..........disabled
  requires:
    ! DBD::SQLite 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

Created MYMETA.yml and MYMETA.json
Creating new 'Build' script for 'BioPerl' version '1.007001'
-> OK
Checking dependencies from MYMETA.json ...
Checking if you have Module::Build 0.42 ... Yes (0.4224)
Checking if you have CPAN 1.81 ... Yes (2.18)
Checking if you have Scalar::Util 0 ... Yes (1.46_02)
Checking if you have URI::Escape 0 ... Yes (3.31)
Checking if you have Test::Harness 2.62 ... Yes (3.38)
Checking if you have ExtUtils::Manifest 1.52 ... Yes (1.70)
Checking if you have Test::Most 0 ... Yes (0.35)
Checking if you have Data::Stag 0.11 ... Yes (0.14)
Checking if you have IO::String 0 ... Yes (1.08)
Building and testing BioPerl-1.007001
Building BioPerl
t/Align/AlignStats.t ................... ok
t/Align/AlignUtil.t .................... ok
t/Align/Graphics.t ..................... skipped: The optional module GD (or dependencies thereof) was not installed
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
t/AlignIO/nexml.t ...................... skipped: The optional module Bio::Phylo (or dependencies thereof) was not installed
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
t/Assembly/ContigSpectrum.t ............ ok
t/Assembly/IO/bowtie.t ................. skipped: The optional module Bio::DB::Sam (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/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 ..................... skipped: The optional module SVG (or dependencies thereof) was not installed
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
BDB1557 library build did not include support for cryptography
: No such file or directory

------------- EXCEPTION -------------
MSG: Could not open index file /tmp/NsAzDID6hk/dbfa/directory.index: No such file or directory
STACK Bio::DB::IndexedBase::_open_index Bio/DB/IndexedBase.pm:712
STACK Bio::DB::IndexedBase::_index_files Bio/DB/IndexedBase.pm:689
STACK Bio::DB::IndexedBase::index_dir Bio/DB/IndexedBase.pm:487
STACK Bio::DB::IndexedBase::new Bio/DB/IndexedBase.pm:402
STACK toplevel t/LocalDB/Fasta.t:27
-------------------------------------

# Looks like your test exited with 2 before it could output anything.
t/LocalDB/Fasta.t ...................... 
Dubious, test returned 2 (wstat 512, 0x200)
Failed 109/109 subtests 
BDB1557 library build did not include support for cryptography
: No such file or directory

------------- EXCEPTION -------------
MSG: Could not open primary index file: No such file or directory (did you remember to use -write_flag=>1?)
STACK Bio::DB::Flat::BDB::_open_bdb Bio/DB/Flat/BDB.pm:435
STACK Bio::DB::Flat::BDB::primary_db Bio/DB/Flat/BDB.pm:417
STACK Bio::DB::Flat::BDB::_store_primary Bio/DB/Flat/BDB.pm:352
STACK Bio::DB::Flat::BDB::_store_index Bio/DB/Flat/BDB.pm:338
STACK Bio::DB::Flat::BDB::_index_file Bio/DB/Flat/BDB.pm:249
STACK Bio::DB::Flat::BDB::build_index Bio/DB/Flat/BDB.pm:228
STACK toplevel t/LocalDB/Flat.t:30
-------------------------------------

# Looks like your test exited with 2 just after 2.
t/LocalDB/Flat.t ....................... 
Dubious, test returned 2 (wstat 512, 0x200)
Failed 23/25 subtests 
BDB1557 library build did not include support for cryptography
: No such file or directory

------------- EXCEPTION -------------
MSG: Can't open 'DB_File' dbm file 'Wibbl' : No such file or directory
STACK Bio::Index::Abstract::open_dbm Bio/Index/Abstract.pm:398
STACK Bio::Index::Abstract::new Bio/Index/Abstract.pm:162
STACK Bio::Index::Blast::new Bio/Index/Blast.pm:143
STACK toplevel t/LocalDB/Index/Blast.t:20
-------------------------------------

# Looks like your test exited with 2 just after 3.
t/LocalDB/Index/Blast.t ................ 
Dubious, test returned 2 (wstat 512, 0x200)
Failed 23/26 subtests 
BDB1557 library build did not include support for cryptography
: No such file or directory

------------- EXCEPTION -------------
MSG: Can't open 'DB_File' dbm file 'Wibbl' : No such file or directory
STACK Bio::Index::Abstract::open_dbm Bio/Index/Abstract.pm:398
STACK Bio::Index::Abstract::new Bio/Index/Abstract.pm:162
STACK Bio::Index::BlastTable::new Bio/Index/BlastTable.pm:141
STACK toplevel t/LocalDB/Index/BlastTable.t:22
-------------------------------------

# Looks like your test exited with 2 just after 3.
t/LocalDB/Index/BlastTable.t ........... 
Dubious, test returned 2 (wstat 512, 0x200)
Failed 24/27 subtests 
BDB1557 library build did not include support for cryptography
: No such file or directory

------------- EXCEPTION -------------
MSG: Can't open 'DB_File' dbm file 'Wibbl' : No such file or directory
STACK Bio::Index::Abstract::open_dbm Bio/Index/Abstract.pm:398
STACK Bio::Index::Abstract::new Bio/Index/Abstract.pm:162
STACK Bio::Index::AbstractSeq::new Bio/Index/AbstractSeq.pm:93
STACK toplevel t/LocalDB/Index/Index.t:27
-------------------------------------

# Looks like your test exited with 2 just after 10.
t/LocalDB/Index/Index.t ................ 
Dubious, test returned 2 (wstat 512, 0x200)
Failed 63/73 subtests 
BDB1557 library build did not include support for cryptography
: No such file or directory

------------- EXCEPTION -------------
MSG: Could not open index file /tmp/S_u_Aa_yVq/dbqual/directory.index: No such file or directory
STACK Bio::DB::IndexedBase::_open_index Bio/DB/IndexedBase.pm:712
STACK Bio::DB::IndexedBase::_index_files Bio/DB/IndexedBase.pm:689
STACK Bio::DB::IndexedBase::index_dir Bio/DB/IndexedBase.pm:487
STACK Bio::DB::IndexedBase::new Bio/DB/IndexedBase.pm:402
STACK toplevel t/LocalDB/Qual.t:19
-------------------------------------

# Looks like your test exited with 2 just after 2.
t/LocalDB/Qual.t ....................... 
Dubious, test returned 2 (wstat 512, 0x200)
Failed 54/56 subtests 
BDB1557 library build did not include support for cryptography
: No such file or directory

------------- EXCEPTION -------------
MSG: Could not open primary index file: No such file or directory (did you remember to use -write_flag=>1?)
STACK Bio::DB::Flat::BDB::_open_bdb Bio/DB/Flat/BDB.pm:435
STACK Bio::DB::Flat::BDB::primary_db Bio/DB/Flat/BDB.pm:417
STACK Bio::DB::Flat::BDB::_store_primary Bio/DB/Flat/BDB.pm:352
STACK Bio::DB::Flat::BDB::_store_index Bio/DB/Flat/BDB.pm:338
STACK Bio::DB::Flat::BDB::_index_file Bio/DB/Flat/BDB.pm:249
STACK Bio::DB::Flat::BDB::build_index Bio/DB/Flat/BDB.pm:228
STACK toplevel t/LocalDB/Registry.t:42
-------------------------------------

# Looks like your test exited with 2 just after 4.
t/LocalDB/Registry.t ................... 
Dubious, test returned 2 (wstat 512, 0x200)
Failed 10/14 subtests 
BDB1557 library build did not include support for cryptography
: No such file or directory
BDB1557 library build did not include support for cryptography
: No such file or directory
BDB1557 library build did not include support for cryptography
: No such file or directory
BDB1557 library build did not include support for cryptography
: No such file or directory
Can't call method "seq" on an undefined value at Bio/DB/SeqFeature/Store/LoadHelper.pm line 173, <GEN0> line 1341.
# Looks like your test exited with 255 just after 36.
t/LocalDB/SeqFeature.t ................. 
Dubious, test returned 255 (wstat 65280, 0xff00)
Failed 80/116 subtests 
t/LocalDB/Taxonomy/greengenes.t ........ ok
t/LocalDB/Taxonomy/silva.t ............. ok
t/LocalDB/Taxonomy/sqlite.t ............ skipped: The optional module DBD::SQLite (or dependencies thereof) was not installed
BDB1557 library build did not include support for cryptography
: No such file or directory

------------- EXCEPTION -------------
MSG: Cannot open file '/tmp/FOfpff7voo/nodes': No such file or directory
STACK Bio::DB::Taxonomy::flatfile::_build_index Bio/DB/Taxonomy/flatfile.pm:373
STACK Bio::DB::Taxonomy::flatfile::new Bio/DB/Taxonomy/flatfile.pm:141
STACK Bio::DB::Taxonomy::new Bio/DB/Taxonomy.pm:119
STACK toplevel t/LocalDB/transfac_pro.t:19
-------------------------------------

# Looks like your test exited with 2 just after 3.
t/LocalDB/transfac_pro.t ............... 
Dubious, test returned 2 (wstat 512, 0x200)
Failed 112/115 subtests 
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 .................... skipped: The optional module Graph::Directed (or dependencies thereof) was not installed
t/Ontology/GraphAdaptor.t .............. skipped: The optional module Graph (or dependencies thereof) was not installed
t/Ontology/IO/go.t ..................... skipped: The optional module Graph (or dependencies thereof) was not installed
t/Ontology/IO/interpro.t ............... skipped: The optional module XML::Parser::PerlSAX (or dependencies thereof) was not installed
t/Ontology/IO/obo.t .................... skipped: The optional module Graph (or dependencies thereof) was not installed
t/Ontology/Ontology.t .................. skipped: The optional module Graph (or dependencies thereof) was not installed
t/Ontology/OntologyEngine.t ............ skipped: The optional module Graph::Directed (or dependencies thereof) was not installed
t/Ontology/OntologyStore.t ............. skipped: The optional module Graph (or dependencies thereof) was not installed
t/Ontology/Relationship.t .............. skipped: The optional module Graph::Directed (or dependencies thereof) was not installed
t/Ontology/RelationshipType.t .......... skipped: The optional module Graph::Directed (or dependencies thereof) was not installed
t/Ontology/Term.t ...................... skipped: The optional module Graph::Directed (or dependencies thereof) was not installed
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 .......................... skipped: Test::Pod 1.00 required for testing POD
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: The optional module LWP::UserAgent (or dependencies thereof) was not installed
t/RemoteDB/CUTG.t ...................... skipped: The optional module LWP::UserAgent (or dependencies thereof) was not installed
t/RemoteDB/EMBL.t ...................... skipped: The optional module LWP::UserAgent (or dependencies thereof) was not installed
t/RemoteDB/EntrezGene.t ................ skipped: The optional module LWP::UserAgent (or dependencies thereof) was not installed
t/RemoteDB/GenBank.t ................... skipped: The optional module LWP::UserAgent (or dependencies thereof) was not installed
t/RemoteDB/GenPept.t ................... skipped: The optional module LWP::UserAgent (or dependencies thereof) was not installed
t/RemoteDB/HIV/HIV.t ................... skipped: The optional module LWP::UserAgent (or dependencies thereof) was not installed
t/RemoteDB/HIV/HIVAnnotProcessor.t ..... ok
t/RemoteDB/HIV/HIVQuery.t .............. skipped: The optional module CGI (or dependencies thereof) was not installed
t/RemoteDB/HIV/HIVQueryHelper.t ........ skipped: The optional module XML::Simple (or dependencies thereof) was not installed
t/RemoteDB/MeSH.t ...................... skipped: The optional module LWP::UserAgent (or dependencies thereof) was not installed
t/RemoteDB/Query/GenBank.t ............. skipped: The optional module LWP::UserAgent (or dependencies thereof) was not installed
t/RemoteDB/RefSeq.t .................... skipped: The optional module LWP::UserAgent (or dependencies thereof) was not installed
t/RemoteDB/SeqRead_fail.t .............. skipped: The optional module LWP::UserAgent (or dependencies thereof) was not installed
t/RemoteDB/SeqVersion.t ................ skipped: The optional module LWP::UserAgent (or dependencies thereof) was not installed
t/RemoteDB/SwissProt.t ................. skipped: The optional module LWP::UserAgent (or dependencies thereof) was not installed
t/RemoteDB/Taxonomy.t .................. skipped: The optional module LWP::UserAgent (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
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
BDB1557 library build did not include support for cryptography
BDB0055 illegal flag specified to DB->set_ext_file_threshold
: No such file or directory

------------- EXCEPTION -------------
MSG: Unable to tie DB_File handle
STACK Bio::SeqFeature::Collection::new Bio/SeqFeature/Collection.pm:207
STACK toplevel t/SeqFeature/Collection.t:34
-------------------------------------

# Looks like your test exited with 2 just after 5.
t/SeqFeature/Collection.t .............. 
Dubious, test returned 2 (wstat 512, 0x200)
Failed 19/24 subtests 
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 ........................ skipped: The optional module XML::Writer (or dependencies thereof) was not installed
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 ......................... skipped: The optional module XML::DOM (or dependencies thereof) was not installed
t/SeqIO/bsml_sax.t ..................... skipped: The optional module XML::SAX::Writer (or dependencies thereof) was not installed
t/SeqIO/chadoxml.t ..................... skipped: The optional module XML::Writer (or dependencies thereof) was not installed
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 ................... skipped: The optional module Bio::ASN1::EntrezGene (or dependencies thereof) was not installed
t/SeqIO/excel.t ........................ skipped: The optional module Spreadsheet::ParseExcel (or dependencies thereof) was not installed
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 ............. skipped: The optional module XML::Writer (or dependencies thereof) was not installed
t/SeqIO/game.t ......................... skipped: The optional module XML::Parser::PerlSAX (or dependencies thereof) was not installed
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 .................... skipped: The optional module Graph::Directed (or dependencies thereof) was not installed
t/SeqIO/mbsout.t ....................... ok
t/SeqIO/metafasta.t .................... ok
t/SeqIO/msout.t ........................ ok
t/SeqIO/nexml.t ........................ skipped: The optional module Bio::Phylo (or dependencies thereof) was not installed
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 ....................... skipped: The optional module XML::LibXML (or dependencies thereof) was not installed
t/SeqIO/strider.t ...................... skipped: The optional module Convert::Binary::C (or dependencies thereof) was not installed
t/SeqIO/swiss.t ........................ ok
t/SeqIO/tab.t .......................... ok
t/SeqIO/table.t ........................ skipped: The optional module IO::Scalar (or dependencies thereof) was not installed
t/SeqIO/tigr.t ......................... skipped: The optional module Error (or dependencies thereof) was not installed
t/SeqIO/tigrxml.t ...................... skipped: The optional module XML::SAX::Writer (or dependencies thereof) was not installed
t/SeqIO/tinyseq.t ...................... skipped: The optional module XML::Parser::PerlSAX (or dependencies thereof) was not installed
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: The optional module LWP::UserAgent (or dependencies thereof) was not installed
t/Tools/Analysis/Protein/Domcut.t ...... skipped: The optional module LWP::UserAgent (or dependencies thereof) was not installed
t/Tools/Analysis/Protein/ELM.t ......... skipped: The optional module LWP::UserAgent (or dependencies thereof) was not installed
t/Tools/Analysis/Protein/GOR4.t ........ skipped: The optional module LWP::UserAgent (or dependencies thereof) was not installed
t/Tools/Analysis/Protein/HNN.t ......... skipped: The optional module LWP::UserAgent (or dependencies thereof) was not installed
t/Tools/Analysis/Protein/NetPhos.t ..... skipped: The optional module LWP::UserAgent (or dependencies thereof) was not installed
t/Tools/Analysis/Protein/Scansite.t .... skipped: The optional module LWP::UserAgent (or dependencies thereof) was not installed
t/Tools/Analysis/Protein/Sopma.t ....... skipped: The optional module LWP::UserAgent (or dependencies thereof) was not installed
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: The optional module LWP::UserAgent (or dependencies thereof) was not installed
t/Tools/Run/RemoteBlast_rpsblast.t ..... skipped: The optional module LWP::UserAgent (or dependencies thereof) was not installed
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 .................... skipped: The optional module Set::Scalar (or dependencies thereof) was not installed
t/Tree/Node.t .......................... ok
t/Tree/PhyloNetwork/Factory.t .......... skipped: The optional module Bio::PhyloNetwork (or dependencies thereof) was not installed
t/Tree/PhyloNetwork/GraphViz.t ......... skipped: The optional module Bio::PhyloNetwork (or dependencies thereof) was not installed
t/Tree/PhyloNetwork/MuVector.t ......... ok
t/Tree/PhyloNetwork/PhyloNetwork.t ..... skipped: The optional module Graph::Directed (or dependencies thereof) was not installed
t/Tree/PhyloNetwork/RandomFactory.t .... skipped: The optional module Bio::PhyloNetwork (or dependencies thereof) was not installed
t/Tree/PhyloNetwork/TreeFactory.t ...... skipped: The optional module Bio::PhyloNetwork (or dependencies thereof) was not installed
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
t/Tree/TreeIO/nexml.t .................. skipped: The optional module Bio::Phylo (or dependencies thereof) was not installed
t/Tree/TreeIO/nexus.t .................. ok
t/Tree/TreeIO/nhx.t .................... ok
t/Tree/TreeIO/phyloxml.t ............... skipped: The optional module XML::LibXML (or dependencies thereof) was not installed
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 ............. skipped: The optional module XML::Writer (or dependencies thereof) was not installed
t/nexml.t .............................. skipped: The optional module Bio::Phylo (or dependencies thereof) was not installed

Test Summary Report
-------------------
t/LocalDB/Fasta.t                    (Wstat: 512 Tests: 0 Failed: 0)
  Non-zero exit status: 2
  Parse errors: Bad plan.  You planned 109 tests but ran 0.
t/LocalDB/Flat.t                     (Wstat: 512 Tests: 2 Failed: 0)
  Non-zero exit status: 2
  Parse errors: Bad plan.  You planned 25 tests but ran 2.
t/LocalDB/Index/Blast.t              (Wstat: 512 Tests: 3 Failed: 0)
  Non-zero exit status: 2
  Parse errors: Bad plan.  You planned 26 tests but ran 3.
t/LocalDB/Index/BlastTable.t         (Wstat: 512 Tests: 3 Failed: 0)
  Non-zero exit status: 2
  Parse errors: Bad plan.  You planned 27 tests but ran 3.
t/LocalDB/Index/Index.t              (Wstat: 512 Tests: 10 Failed: 0)
  Non-zero exit status: 2
  Parse errors: Bad plan.  You planned 73 tests but ran 10.
t/LocalDB/Qual.t                     (Wstat: 512 Tests: 2 Failed: 0)
  Non-zero exit status: 2
  Parse errors: Bad plan.  You planned 56 tests but ran 2.
t/LocalDB/Registry.t                 (Wstat: 512 Tests: 4 Failed: 0)
  Non-zero exit status: 2
  Parse errors: Bad plan.  You planned 14 tests but ran 4.
t/LocalDB/SeqFeature.t               (Wstat: 65280 Tests: 36 Failed: 0)
  Non-zero exit status: 255
  Parse errors: Bad plan.  You planned 116 tests but ran 36.
t/LocalDB/transfac_pro.t             (Wstat: 512 Tests: 3 Failed: 0)
  Non-zero exit status: 2
  Parse errors: Bad plan.  You planned 115 tests but ran 3.
t/SeqFeature/Collection.t            (Wstat: 512 Tests: 5 Failed: 0)
  Non-zero exit status: 2
  Parse errors: Bad plan.  You planned 24 tests but ran 5.
Files=325, Tests=17866, 133 wallclock secs ( 4.47 usr  3.61 sys + 110.58 cusr 17.87 csys = 136.53 CPU)
Result: FAIL
Failed 10/325 test programs. 0/17866 subtests failed.
-> FAIL Installing Bio::Root::Version failed. See /home/linuxbrew/.cpanm/work/1502408933.12319/build.log for details. Retry with --force to force install it.
tmozgach commented 7 years ago

@sjackman could you please look at? 1 month ago it worked. May be it is really better to use structure of the following image? https://hub.docker.com/r/bioperl/bioperl-deps/~/dockerfile/

sjackman commented 7 years ago 
Failed 10/325 test programs. 0/17866 subtests failed.

Looks like the first failed test is t/LocalDB/Fasta.t:27

------------- EXCEPTION -------------
MSG: Could not open index file /tmp/NsAzDID6hk/dbfa/directory.index: No such file or directory
STACK Bio::DB::IndexedBase::_open_index Bio/DB/IndexedBase.pm:712
STACK Bio::DB::IndexedBase::_index_files Bio/DB/IndexedBase.pm:689
STACK Bio::DB::IndexedBase::index_dir Bio/DB/IndexedBase.pm:487
STACK Bio::DB::IndexedBase::new Bio/DB/IndexedBase.pm:402
STACK toplevel t/LocalDB/Fasta.t:27
-------------------------------------

# Looks like your test exited with 2 before it could output anything.
t/LocalDB/Fasta.t ...................... 
Dubious, test returned 2 (wstat 512, 0x200)
Failed 109/109 subtests 
BDB1557 library build did not include support for cryptography
: No such file or directory

Start an interactive container from the Docker image right before this failure, and confirm that you can reproduce the failure interactively.

Google the above error message, and see what you can find.

tmozgach commented 7 years ago

@sjackman That error was produced interactively. I didn't find anything in Google except that 

Sometimes you may see a failed test. Remember that there are over 900 modules in BioPerl and the test suite is running more than 12000 individual tests, a failed test may not affect your usage of BioPerl.

If there’s a failed test and you think that the failed test will not affect how you intend to use BioPerl then do
`cpan>force install C/CJ/CJFIELDS/BioPerl-1.007001.tar.gz`

http://bioperl.org/INSTALL.html

sjackman commented 7 years ago

I wouldn't be very comfortable with force installing, since we don't yet know whether it affects the functionality of BioPerl. There should hopefully be a more detailed log giving a more informative error message. Perhaps the failure is related to this message:

BDB1557 library build did not include support for cryptography

Googling "library build did not include support for cryptography" (with quotes) suggests that it may be a problem with berkeley-db, which I'm guessing is a dependency of t/LocalDB/Fasta.t.

sjackman commented 7 years ago

That's a berkeley-db error message: https://github.com/berkeleydb/libdb/blob/master/src/env/env_method.c#L816

The berkeley-db bottle does not appear to have cryptography support. I tried brew install -s berkeley-db The problem is…

checking if --with-cryptography option specified... no

https://gist.github.com/anonymous/db85021ee01c0daff2849620709b3a8c#file-01-configure-L66

@tmozgach Can you see if adding configure --with-cryptography to the berkeley-db formula helps?

sjackman commented 7 years ago

If it does, please open a PR against berkeley-db adding --with-cryptography and bump the revision.

tmozgach commented 7 years ago

Install perl from the source, install Bio::Perl => succeed Install perl from the bottle, install Bio::Perl => failed Install previous version berkley-db, Install perl from the bottle, install Bio::Perl => succeed

Rebuild bottle of perl fixes the problem.