BioPerl v1.7.6 Perl 5 v5.16.3 x86_64-linux-thread-multi
- Status
- Fail
- From
- David Cantrell (DCANTRELL)
- Dist
-
BioPerl v1.7.6
- Platform
- Perl 5 v5.16.3 x86_64-linux-thread-multi
- Date
- 2019-11-07 14:37:55
- ID
- 2f64ee9c-016c-11ea-8d8b-1d35052d0de1
This distribution has been tested as part of the CPAN Testers
project, supporting the Perl programming language. See
http://wiki.cpantesters.org/ for more information or email
questions to cpan-testers-discuss@perl.org
--
Dear carandraug,
This is a computer-generated report for BioPerl-1.7.6
on perl 5.16.3, created by CPAN-Reporter-1.2018.
Thank you for uploading your work to CPAN. However, there was a problem
testing your distribution.
If you think this report is invalid, please consult the CPAN Testers Wiki
for suggestions on how to avoid getting FAIL reports for missing library
or binary dependencies, unsupported operating systems, and so on:
http://wiki.cpantesters.org/wiki/CPANAuthorNotes
Sections of this report:
* Tester comments
* Program output
* Prerequisites
* Environment and other context
------------------------------
TESTER COMMENTS
------------------------------
Additional comments from tester:
this report is from an automated smoke testing program
and was not reviewed by a human for accuracy
------------------------------
PROGRAM OUTPUT
------------------------------
Output from '/usr/bin/make test':
PERL_DL_NONLAZY=1 "/home/david/cpantesting/perl-5.16.3/bin/perl" "-MExtUtils::Command::MM" "-MTest::Harness" "-e" "undef *Test::Harness::Switches; test_harness(0, 'blib/lib', 'blib/arch')" t/*.t t/Align/*.t t/AlignIO/*.t t/Annotation/*.t t/LocalDB/*.t t/LocalDB/Index/*.t t/LocalDB/Taxonomy/*.t t/Matrix/*.t t/Matrix/IO/*.t t/Ontology/*.t t/Ontology/IO/*.t t/RemoteDB/*.t t/Root/*.t t/SearchIO/*.t t/SearchIO/Writer/*.t t/Seq/*.t t/SeqFeature/*.t t/SeqIO/*.t t/SeqTools/*.t t/Tools/*.t t/Tools/Alignment/*.t t/Tools/EMBOSS/*.t t/Tools/Phylo/*.t t/Tools/Phylo/Phylip/*.t t/Tools/Signalp/*.t t/Tools/Spidey/*.t t/Tree/*.t t/Tree/TreeIO/*.t
# Failed test 'bin/bp_chaos_plot compiled ok'
# at t/00-compile.t line 589.
# got: '512'
# expected: '0'
Can't locate GD.pm in @INC (@INC contains: /home/david/cpantesting/perl-5.16.3/.cpan/build/BioPerl-1.7.6-NMHM5z/blib/arch /home/david/cpantesting/perl-5.16.3/.cpan/build/BioPerl-1.7.6-NMHM5z/blib/lib /home/david/cpantesting/perl-5.16.3/.cpan/build/BioPerl-1.7.6-NMHM5z/blib/lib /home/david/cpantesting/perl-5.16.3/.cpan/build/BioPerl-1.7.6-NMHM5z/blib/arch /home/david/cpantesting/perl-5.16.3/lib/site_perl/5.16.3/x86_64-linux-thread-multi /home/david/cpantesting/perl-5.16.3/lib/site_perl/5.16.3 /home/david/cpantesting/perl-5.16.3/lib/5.16.3/x86_64-linux-thread-multi /home/david/cpantesting/perl-5.16.3/lib/5.16.3 .) at bin/bp_chaos_plot line 8.BEGIN failed--compilation aborted at bin/bp_chaos_plot line 8. at t/00-compile.t line 598, <GEN1900> line 2.
# Looks like you failed 1 test of 513.
t/00-compile.t ......................
Dubious, test returned 1 (wstat 256, 0x100)
Failed 1/513 subtests
t/Align/AlignStats.t ................ ok
t/Align/AlignUtil.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
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/xmfa.t .................... ok
t/Annotation/Annotation.t ........... ok
t/Annotation/AnnotationAdaptor.t .... ok
t/author-mojibake.t ................. skipped: these tests are for testing by the author
t/author-pod-syntax.t ............... skipped: these tests are for testing by the author
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
--------------------- WARNING ---------------------
MSG: Couldn't load Bio::DB::BioFetch
---------------------------------------------------
--------------------- WARNING ---------------------
MSG: Couldn't load Bio::DB::BioFetch
---------------------------------------------------
t/LocalDB/Registry.t ................ ok
t/LocalDB/Taxonomy/greengenes.t ..... ok
t/LocalDB/Taxonomy/silva.t .......... ok
t/Matrix/InstanceSite.t ............. ok
t/Matrix/IO/masta.t ................. ok
t/Matrix/IO/psm.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 .......... ok
t/Ontology/Relationship.t ........... ok
t/Ontology/RelationshipType.t ....... ok
t/Ontology/Term.t ................... ok
t/RemoteDB/SeqRead_fail.t ........... ok
t/RemoteDB/Taxonomy.t ............... ok
t/Root/Exception.t .................. ok
t/Root/HTTPget.t .................... ok
t/Root/IO.t ......................... ok
t/Root/RootI.t ...................... ok
t/Root/RootIO.t ..................... ok
t/Root/Storable.t ................... ok
t/Root/Utilities.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/CigarString.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/infernal.t ............... ok
t/SearchIO/megablast.t .............. ok
t/SearchIO/psl.t .................... ok
t/SearchIO/rnamotif.t ............... ok
t/SearchIO/SearchIO.t ............... ok
t/SearchIO/sim4.t ................... ok
t/SearchIO/SimilarityPair.t ......... ok
t/SearchIO/Tiling.t ................. ok
t/SearchIO/waba.t ................... ok
t/SearchIO/wise.t ................... ok
t/SearchIO/Writer/GbrowseGFF.t ...... ok
t/SearchIO/Writer/HitTableWriter.t .. ok
t/SearchIO/Writer/HSPTableWriter.t .. ok
t/SearchIO/Writer/HTMLWriter.t ...... ok
t/SearchIO/Writer/TextWriter.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/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/ace.t ....................... ok
t/SeqIO/asciitree.t ................. ok
t/SeqIO/bsml.t ...................... ok
t/SeqIO/bsml_sax.t .................. ok
t/SeqIO/embl.t ...................... ok
t/SeqIO/fasta.t ..................... ok
t/SeqIO/fastq.t ..................... ok
t/SeqIO/game.t ...................... ok
t/SeqIO/gbxml.t ..................... ok
t/SeqIO/gcg.t ....................... ok
t/SeqIO/genbank.t ................... ok
t/SeqIO/Handler.t ................... ok
t/SeqIO/interpro.t .................. ok
t/SeqIO/kegg.t ...................... ok
t/SeqIO/largefasta.t ................ ok
t/SeqIO/locuslink.t ................. ok
t/SeqIO/mbsout.t .................... ok
t/SeqIO/metafasta.t ................. ok
t/SeqIO/msout.t ..................... ok
t/SeqIO/MultiFile.t ................. ok
t/SeqIO/Multiple_fasta.t ............ ok
t/SeqIO/phd.t ....................... ok
t/SeqIO/pir.t ....................... ok
t/SeqIO/qual.t ...................... ok
t/SeqIO/raw.t ....................... ok
t/SeqIO/scf.t ....................... ok
t/SeqIO/SeqBuilder.t ................ ok
t/SeqIO/SeqIO.t ..................... ok
t/SeqIO/seqxml.t .................... ok
t/SeqIO/Splicedseq.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/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/Tools/Alignment/Consed.t .......... ok
t/Tools/AmpliconSearch.t ............ ok
t/Tools/EMBOSS/Palindrome.t ......... ok
t/Tools/ePCR.t ...................... ok
t/Tools/Est2Genome.t ................ ok
t/Tools/FootPrinter.t ............... ok
t/Tools/Geneid.t .................... ok
t/Tools/Genewise.t .................. ok
t/Tools/Genomewise.t ................ ok
t/Tools/Genpred.t ................... ok
t/Tools/GFF.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/Phylip/ProtDist.t ..... ok
t/Tools/pICalculator.t .............. ok
t/Tools/Primer3.t ................... ok
t/Tools/Promoterwise.t .............. ok
t/Tools/PrositeScan.t ............... ok
t/Tools/Pseudowise.t ................ ok
t/Tools/QRNA.t ...................... ok
t/Tools/RandDistFunctions.t ......... ok
t/Tools/RepeatMasker.t .............. ok
t/Tools/Seg.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/tRNAscanSE.t ................ ok
t/Tree/Compatible.t ................. ok
t/Tree/Node.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
t/Tree/TreeIO/nexus.t ............... ok
t/Tree/TreeIO/nhx.t ................. ok
t/Tree/TreeIO/phyloxml.t ............ ok
t/Tree/TreeIO/tabtree.t ............. ok
t/Tree/TreeStatistics.t ............. ok
Test Summary Report
-------------------
t/00-compile.t (Wstat: 256 Tests: 513 Failed: 1)
Failed test: 476
Non-zero exit status: 1
Files=212, Tests=14858, 834 wallclock secs ( 2.22 usr 0.37 sys + 86.57 cusr 7.18 csys = 96.34 CPU)
Result: FAIL
Failed 1/212 test programs. 1/14858 subtests failed.
Makefile:3304: recipe for target 'test_dynamic' failed
make: *** [test_dynamic] Error 255
------------------------------
PREREQUISITES
------------------------------
Prerequisite modules loaded:
requires:
Module Need Have
---------------------- ----- ----------
AnyDBM_File 0 1.01
base 0 2.18
Carp 0 1.26
constant 0 1.23
Cwd 0 3.39_02
Data::Dumper 0 2.135_06
Data::Stag 0 0.14
DB_File 0 1.826
Digest::MD5 0 2.51
Dumpvalue 0 1.17
Error 0 0.17028
Exporter 0 5.73
Fcntl 0 1.11
File::Basename 0 2.84
File::Copy 0 2.23
File::Path 0 2.08_01
File::Spec 0 3.39_02
File::Spec::Functions 0 3.39_02
File::Temp 0 0.2309
FileHandle 0 2.02
Getopt::Long 0 2.51
Graph::Directed 0 0
HTTP::Request::Common 0 6.18
HTTP::Response 0 6.18
integer 0 1.00
IO::File 0 1.16
IO::Handle 0 1.33
IO::Pipe 0 1.15
IO::Scalar 0 2.111
IO::Socket 0 1.34
IO::String 0 1.08
IPC::Run 0 20180523.0
List::MoreUtils 0 0.428
List::Util 0 1.53
LWP::UserAgent 0 6.41
Math::BigFloat 0 1.997
Module::Build 0 0.4229
overload 0 1.18
parent 0 0.237
perl 5.006 5.016003
Pod::Usage 0 1.69
POSIX 0 1.30
Scalar::Util 0 1.53
Set::Scalar 0 1.29
Storable 0 2.34
strict 0 1.07
Symbol 0 1.07
Test::Builder 0 1.302162
Test::Builder::Module 0 1.302162
Test::Most 0 0.35
Test::RequiresInternet 0 0.05
Text::Balanced 0 2.02
Text::Wrap 0 2009.0305
Tie::Handle 0 4.2
Tie::RefHash 0 1.39
Time::HiRes 0 1.9725
UNIVERSAL 0 1.11
URI 0 1.76
utf8 0 1.09
vars 0 1.02
version 0 0.99
warnings 0 1.13
XML::DOM 0 1.46
XML::DOM::XPath 0 0.14
XML::LibXML 0 2.0201
XML::LibXML::Reader 0 2.0201
XML::Parser::PerlSAX 0 0.08
XML::SAX 0 1.02
XML::SAX::Base 0 1.09
XML::SAX::Writer 0 0.57
XML::Twig 0 3.52
XML::Writer 0 0.625
YAML 0 1.29
build_requires:
Module Need Have
---------------------- ----- ----------
ExtUtils::MakeMaker 0 7.34
File::Spec 0 3.39_02
FindBin 0 1.51
IO::Handle 0 1.33
IPC::Open3 0 1.12
lib 0 0.63
Test::Memory::Cycle 0 1.06
Test::More 0 1.302162
Test::Weaken 0 3.022000
configure_requires:
Module Need Have
---------------------- ----- ----------
ExtUtils::MakeMaker 0 7.34
------------------------------
ENVIRONMENT AND OTHER CONTEXT
------------------------------
Environment variables:
AUTOMATED_TESTING = 1
LANG = en_US.UTF-8
NONINTERACTIVE_TESTING = 1
PATH = /usr/local/bin:/usr/bin:/bin:/usr/local/games:/usr/games
PERL = 5.16.3
PERL5LIB =
PERL5OPT =
PERL5_CPANPLUS_IS_RUNNING = 12642
PERL5_CPAN_IS_RUNNING = 12642
PERLVER = 5.16.3
PERL_INLINE_DIRECTORY = /home/david/.Inline-5.16.3
PERL_MM_USE_DEFAULT = 1
PERL_USE_UNSAFE_INC = 0
SHELL = /bin/bash
TERM = screen
Perl special variables (and OS-specific diagnostics, for MSWin32):
$^X = /home/david/cpantesting/perl-5.16.3/bin/perl
$UID/$EUID = 1000 / 1000
$GID = 1000 27 1000
$EGID = 1000 27 1000
Perl module toolchain versions installed:
Module Have
------------------- --------
CPAN 1.9800
CPAN::Meta 2.143240
Cwd 3.39_02
ExtUtils::CBuilder 0.280206
ExtUtils::Command 7.34
ExtUtils::Install 2.06
ExtUtils::MakeMaker 7.34
ExtUtils::Manifest 1.70
ExtUtils::ParseXS 3.35
File::Spec 3.39_02
JSON 4.02
JSON::PP 4.02
Module::Build 0.4229
Module::Signature n/a
Parse::CPAN::Meta 1.4414
Test::Harness 3.42
Test::More 1.302162
YAML 1.29
YAML::Syck 1.31
version 0.99
--
Summary of my perl5 (revision 5 version 16 subversion 3) configuration:
Platform:
osname=linux, osvers=4.9.0-8-amd64, archname=x86_64-linux-thread-multi
uname='linux pigsty 4.9.0-8-amd64 #1 smp debian 4.9.144-3 (2019-02-02) x86_64 gnulinux '
config_args='-de -Duse64bitall -Dusethreads -Dprefix=/home/david/cpantesting/perl-5.16.3 -A ccflags=-fwrapv'
hint=previous, useposix=true, d_sigaction=define
useithreads=define, usemultiplicity=define
useperlio=define, d_sfio=undef, uselargefiles=define, usesocks=undef
use64bitint=define, use64bitall=define, uselongdouble=undef
usemymalloc=n, bincompat5005=undef
Compiler:
cc='cc', ccflags ='-D_REENTRANT -D_GNU_SOURCE -fwrapv -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fwrapv -fwrapv',
optimize='-O2',
cppflags='-D_REENTRANT -D_GNU_SOURCE -fwrapv -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_REENTRANT -D_GNU_SOURCE -fwrapv -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fwrapv -D_REENTRANT -D_GNU_SOURCE -fwrapv -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fwrapv -fwrapv'
ccversion='', gccversion='6.3.0 20170516', gccosandvers=''
intsize=4, longsize=8, ptrsize=8, doublesize=8, byteorder=12345678
d_longlong=define, longlongsize=8, d_longdbl=define, longdblsize=16
ivtype='long', ivsize=8, nvtype='double', nvsize=8, Off_t='off_t', lseeksize=8
alignbytes=8, prototype=define
Linker and Libraries:
ld='cc', ldflags =' -fstack-protector -L/usr/local/lib'
libpth=/usr/local/lib /lib/x86_64-linux-gnu /lib/../lib /usr/lib/x86_64-linux-gnu /usr/lib/../lib /lib /usr/lib
libs=-lnsl -ldb -ldl -lm -lcrypt -lutil -lpthread -lc
perllibs=-lnsl -ldl -lm -lcrypt -lutil -lpthread -lc
libc=libc-2.24.so, so=so, useshrplib=false, libperl=libperl.a
gnulibc_version='2.24'
Dynamic Linking:
dlsrc=dl_dlopen.xs, dlext=so, d_dlsymun=undef, ccdlflags='-Wl,-E'
cccdlflags='-fPIC', lddlflags='-shared -O2 -L/usr/local/lib -fstack-protector'
Characteristics of this binary (from libperl):
Compile-time options: HAS_TIMES MULTIPLICITY PERLIO_LAYERS
PERL_DONT_CREATE_GVSV PERL_IMPLICIT_CONTEXT
PERL_MALLOC_WRAP PERL_PRESERVE_IVUV USE_64_BIT_ALL
USE_64_BIT_INT USE_ITHREADS USE_LARGE_FILES
USE_LOCALE USE_LOCALE_COLLATE USE_LOCALE_CTYPE
USE_LOCALE_NUMERIC USE_PERLIO USE_PERL_ATOF
USE_REENTRANT_API
Locally applied patches:
Devel::PatchPerl 1.56
Built under linux
Compiled at Apr 25 2019 22:17:10
%ENV:
PERL="5.16.3"
PERL5LIB=""
PERL5OPT=""
PERL5_CPANPLUS_IS_RUNNING="12642"
PERL5_CPAN_IS_RUNNING="12642"
PERLVER="5.16.3"
PERL_INLINE_DIRECTORY="/home/david/.Inline-5.16.3"
PERL_MM_USE_DEFAULT="1"
PERL_USE_UNSAFE_INC="0"
@INC:
/home/david/cpantesting/perl-5.16.3/lib/site_perl/5.16.3/x86_64-linux-thread-multi
/home/david/cpantesting/perl-5.16.3/lib/site_perl/5.16.3
/home/david/cpantesting/perl-5.16.3/lib/5.16.3/x86_64-linux-thread-multi
/home/david/cpantesting/perl-5.16.3/lib/5.16.3
.