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FAIL bioperl-1.4 IP35-irix-64int 6.5
From:
david
Date:
July 27, 2008 04:16
Subject:
FAIL bioperl-1.4 IP35-irix-64int 6.5
This distribution has been tested as part of the cpan-testers
effort to test as many new uploads to CPAN as possible. See
http://testers.cpan.org/
--
Dear Ewan Birney,
This is a computer-generated report for bioperl-1.4
on perl 5.8.8, created by CPAN-Reporter-1.15.
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://cpantest.grango.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 '/sbin/make test':
PERL_DL_NONLAZY=1 /usr/people/drc/cpantesting/perl-5.8.8/bin/perl "-MExtUtils::Command::MM" "-e" "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t
t/AAChange.....................ok
t/AAReverseMutate..............ok
t/AlignIO......................ok
t/AlignStats...................ok
t/Allele.......................ok
t/Alphabet.....................ok
t/Annotation...................ok
t/AnnotationAdaptor............ok
t/Assembly.....................ok
t/Biblio.......................SOAP::Lite not installed. Skipping some tests.
XML::Parser not installed. Skipping some tests.
ok
t/Biblio_biofetch..............ok
t/BiblioReferences.............ok
t/BioDBGFF.....................ok
t/BioFetch_DB.................. Failed 4/27 subtests
t/BioGraphics..................GD or Text::Shellwords modules are not installed. This means that Bio::Graphics module is unusable. Skipping tests.
ok
t/BlastIndex...................ok
t/BPbl2seq.....................ok
t/BPlite.......................ok
t/BPpsilite....................ok
t/Chain........................ok
t/cigarstring..................ok
t/ClusterIO....................XML::Parser::PerlSAX not loaded. This means ClusterIO::dbsnp test cannot be executed. Skipping
ok
t/Coalescent...................ok
t/CodonTable...................ok
t/consed.......................ok
t/CoordinateGraph..............ok
t/CoordinateMapper.............ok
t/Correlate....................ok
t/CytoMap......................ok
t/DB........................... Failed 2/78 subtests
(less 1 skipped subtest: 75 okay)
t/DBCUTG.......................ok
t/DBFasta......................ok
t/DNAMutation..................ok
t/Domcut.......................ok
t/ECnumber.....................ok
t/ELM..........................
-------------------- WARNING ---------------------
MSG: Bio::Tools::Analysis::Protein::ELM Request Error:
400 URL must be absolute
Content-Type: text/plain
Client-Date: Sun, 27 Jul 2008 11:06:52 GMT
Client-Warning: Internal response
400 URL must be absolute
---------------------------------------------------
ok
t/EMBL_DB...................... Failed 3/15 subtests
t/EMBOSS_Tools.................ok
t/EncodedSeq...................ok
t/ePCR.........................ok
t/ESEfinder....................ok
t/est2genome...................ok
t/Exception....................ok
t/Exonerate....................ok
t/flat.........................ok
t/FootPrinter..................ok
t/game.........................XML::Parser::PerlSAX not loaded. This means game test cannot be executed. Skipping
ok
t/GDB..........................ok
t/GeneCoordinateMapper.........
-------------------- WARNING ---------------------
MSG: sorted sublocation array requested but root location doesn't define seq_id (at least one sublocation does!)
---------------------------------------------------
-------------------- WARNING ---------------------
MSG: sorted sublocation array requested but root location doesn't define seq_id (at least one sublocation does!)
---------------------------------------------------
Use of uninitialized value in concatenation (.) or string at /usr/people/drc/cpantesting/perl-5.8.8/.cpan/build/bioperl-1.4-nJ1PWz/blib/lib/Bio/Coordinate/GeneMapper.pm line 814.
ok
t/Geneid.......................ok
t/Genewise.....................ok
t/Genomewise...................ok
t/Genpred......................ok
t/GFF..........................Filehandle GEN0 opened only for output at /usr/people/drc/cpantesting/perl-5.8.8/.cpan/build/bioperl-1.4-nJ1PWz/blib/lib/Bio/Root/IO.pm line 440.
Filehandle GEN1 opened only for output at /usr/people/drc/cpantesting/perl-5.8.8/.cpan/build/bioperl-1.4-nJ1PWz/blib/lib/Bio/Root/IO.pm line 440.
ok
t/GOR4.........................ok
t/GOterm.......................ok
t/GuessSeqFormat...............Bio::SeqIO: game cannot be found
Exception
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Failed to load module Bio::SeqIO::game. Can't locate XML/Parser/PerlSAX.pm in @INC (@INC contains: t .. /usr/people/drc/cpantesting/perl-5.8.8/.cpan/build/bioperl-1.4-nJ1PWz/blib/lib /usr/people/drc/cpantesting/perl-5.8.8/.cpan/build/bioperl-1.4-nJ1PWz/blib/arch /usr/people/drc/cpantesting/perl-5.8.8/lib/5.8.8/IP35-irix-64int /usr/people/drc/cpantesting/perl-5.8.8/lib/5.8.8 /usr/people/drc/cpantesting/perl-5.8.8/lib/site_perl/5.8.8/IP35-irix-64int /usr/people/drc/cpantesting/perl-5.8.8/lib/site_perl/5.8.8 /usr/people/drc/cpantesting/perl-5.8.8/lib/site_perl .) at /usr/people/drc/cpantesting/perl-5.8.8/.cpan/build/bioperl-1.4-nJ1PWz/blib/lib/Bio/SeqIO/game/gameSubs.pm line 70.
BEGIN failed--compilation aborted at /usr/people/drc/cpantesting/perl-5.8.8/.cpan/build/bioperl-1.4-nJ1PWz/blib/lib/Bio/SeqIO/game/gameSubs.pm line 70.
Compilation failed in require at /usr/people/drc/cpantesting/perl-5.8.8/.cpan/build/bioperl-1.4-nJ1PWz/blib/lib/Bio/SeqIO/game/gameHandler.pm line 62.
BEGIN failed--compilation aborted at /usr/people/drc/cpantesting/perl-5.8.8/.cpan/build/bioperl-1.4-nJ1PWz/blib/lib/Bio/SeqIO/game/gameHandler.pm line 62.
Compilation failed in require at /usr/people/drc/cpantesting/perl-5.8.8/.cpan/build/bioperl-1.4-nJ1PWz/blib/lib/Bio/SeqIO/game.pm line 76.
BEGIN failed--compilation aborted at /usr/people/drc/cpantesting/perl-5.8.8/.cpan/build/bioperl-1.4-nJ1PWz/blib/lib/Bio/SeqIO/game.pm line 76.
Compilation failed in require at /usr/people/drc/cpantesting/perl-5.8.8/.cpan/build/bioperl-1.4-nJ1PWz/blib/lib/Bio/Root/Root.pm line 394.
STACK: Error::throw
STACK: Bio::Root::Root::throw /usr/people/drc/cpantesting/perl-5.8.8/.cpan/build/bioperl-1.4-nJ1PWz/blib/lib/Bio/Root/Root.pm:328
STACK: Bio::Root::Root::_load_module /usr/people/drc/cpantesting/perl-5.8.8/.cpan/build/bioperl-1.4-nJ1PWz/blib/lib/Bio/Root/Root.pm:396
STACK: Bio::SeqIO::_load_format_module /usr/people/drc/cpantesting/perl-5.8.8/.cpan/build/bioperl-1.4-nJ1PWz/blib/lib/Bio/SeqIO.pm:549
STACK: Bio::SeqIO::new /usr/people/drc/cpantesting/perl-5.8.8/.cpan/build/bioperl-1.4-nJ1PWz/blib/lib/Bio/SeqIO.pm:377
STACK: t/GuessSeqFormat.t:61
-----------------------------------------------------------
For more information about the SeqIO system please see the SeqIO docs.
This includes ways of checking for formats at compile time, not run time
Failed 1/46 subtests
t/hmmer........................ok
t/HNN..........................ok
t/Index........................ok
t/InstanceSite.................ok
t/InterProParser...............XML::Parser not installed. This means that InterPro Ontology Parsing module is not usable. Skipping tests.
ok
t/IUPAC........................ok
t/largefasta...................ok
t/largepseq....................ok
t/LinkageMap...................ok
t/LiveSeq......................ok
t/LocatableSeq.................ok
t/Location.....................ok
t/LocationFactory..............ok
t/LocusLink....................ok
t/lucy.........................ok
t/Map..........................ok
t/MapIO........................ok
t/Matrix.......................ok
t/Measure......................ok
t/MeSH.........................ok
t/MetaSeq......................ok
t/MicrosatelliteMarker.........ok
t/MiniMIMentry.................ok
t/MitoProt.....................ok
t/Molphy.......................ok
t/multiple_fasta...............ok
t/Mutation.....................ok
t/Mutator......................ok
t/NetPhos......................ok
t/Node.........................ok
t/OddCodes.....................ok
t/OMIMentry....................ok
t/OMIMentryAllelicVariant......ok
t/OMIMparser...................ok
t/Ontology.....................
Graph.pm doesn't seem to be installed on this system -- the GO Parser needs it...
ok
t/OntologyEngine...............ok
t/PAML.........................ok
t/Perl.........................Use of uninitialized value in substitution (s///) at /usr/people/drc/cpantesting/perl-5.8.8/.cpan/build/bioperl-1.4-nJ1PWz/blib/lib/Bio/SeqIO/swiss.pm line 855, <STREAM> line 45.
ok
t/phd..........................ok
t/Phenotype....................ok
t/PhylipDist...................ok
t/pICalculator.................ok
t/Pictogram....................SVG not installed, skipping tests at t/Pictogram.t line 29.
ok
t/PopGen.......................ok
t/PopGenSims...................ok
t/primaryqual..................ok
t/PrimarySeq...................ok
t/primedseq....................ok
t/Primer.......................ok
t/primer3......................ok
t/Promoterwise.................ok
t/ProtDist.....................ok
t/psm..........................ok
t/QRNA.........................ok
t/qual.........................ok
t/RandDistFunctions............ok
t/RandomTreeFactory............ok
t/Range........................ok
t/RangeI.......................ok
t/RefSeq.......................ok
t/Registry.....................DB_File and BerkeleyDB not found. Skipping DB_File tests
ok
t/Relationship.................ok
t/RelationshipType.............ok
t/RemoteBlast..................ok
t/RepeatMasker.................ok
t/RestrictionAnalysis..........ok
t/RestrictionEnzyme............ok
t/RestrictionIO................ok
t/RNAChange....................ok
t/RootI........................ok
t/RootIO.......................ok
t/RootStorable.................ok
t/Scansite.....................ok
t/scf..........................ok
t/SearchDist...................ok
t/SearchIO.....................XML::Parser::PerlSAX or HTML::Entities not loaded. This means SearchIO::blastxml test cannot be executed. Skipping
ok
t/Seq..........................ok
t/SeqAnalysisParser............ok
t/SeqBuilder...................ok
t/SeqDiff......................ok
t/SeqFeatCollection............ok
t/SeqFeature...................ok
t/seqfeaturePrimer.............ok
t/SeqIO........................ok
t/SeqPattern...................ok
t/SeqStats.....................ok
t/SequenceFamily...............ok
t/sequencetrace................ok
t/SeqUtils.....................ok
t/seqwithquality...............ok
t/SeqWords.....................ok
t/Sigcleave....................ok
t/Sim4.........................ok
t/SimilarityPair...............ok
t/SimpleAlign..................ok
t/simpleGOparser...............
Graph.pm doesn't seem to be installed on this system -- the GO Parser needs it...
ok
t/sirna........................ok
t/SiteMatrix...................ok
t/SNP..........................ok
t/Sopma........................ok
t/Species......................ok
t/splicedseq...................ok
t/StandAloneBlast..............ok
t/StructIO.....................ok
t/Structure....................ok
t/Swiss........................ok
t/Symbol.......................ok
t/Taxonomy.....................ok
t/Tempfile.....................ok
t/Term.........................ok
t/Tools........................ok
t/Tree.........................ok
t/TreeIO.......................ok
t/trim.........................ok
t/tutorial.....................Use of uninitialized value in substitution (s///) at Bio/SeqIO/swiss.pm line 855, <STREAM> line 45.
Cannot run demo_xml
Problem parsing GAME format or missing necessary installed modules XML::Parser XML::Parser::PerlSAX
ok
t/UCSCParsers..................ok
t/Unflattener..................ok
t/Unflattener2.................ok
t/UniGene......................ok
t/Variation_IO.................
The XML-format conversion requires the CPAN modules XML::Twig, XML::Writer, and IO::String to be installed on your system, which they probably aren't. Skipping these tests.
ok
t/WABA.........................ok
t/XEMBL_DB.....................SOAP::Lite and/or XML::DOM not installed. This means that Bio::DB::XEMBL module is not usable. Skipping tests.
ok
Test Summary Report
-------------------
t/BioFetch_DB.t (Wstat: 0 Tests: 27 Failed: 4)
Failed tests: 8, 20-21, 27
t/DB.t (Wstat: 0 Tests: 78 Failed: 2)
Failed tests: 30-31
t/EMBL_DB.t (Wstat: 0 Tests: 15 Failed: 3)
Failed tests: 6, 13-14
t/GuessSeqFormat.t (Wstat: 0 Tests: 46 Failed: 1)
Failed test: 11
Files=179, Tests=8122, 287 wallclock secs ( 6.59 usr 1.17 sys + 218.66 cusr 17.66 csys = 244.08 CPU)
Result: FAIL
Failed 4/179 test programs. 10/8122 subtests failed.
*** Error code 255 (bu21)
------------------------------
PREREQUISITES
------------------------------
Prerequisite modules loaded:
requires:
Module Need Have
-------------- ---- ------
DB_File 0 1.814
File::Spec 0 3.2701
File::Temp 0 0.16
HTML::Entities 0 1.35
IO::Scalar 0 2.110
IO::String 0 1.08
------------------------------
ENVIRONMENT AND OTHER CONTEXT
------------------------------
Environment variables:
AUTOMATED_TESTING = 1
LC_ALL = en
PATH = /usr/people/drc/bin:/sbin:/usr/sbin:/usr/nekoware/sbin:/usr/nekoware/bin:/usr/bsd:/usr/bin:/etc:/usr/sysadm/privbin:/usr/etc:/usr/bin/X11:/usr/gfx:/usr/nekoware/mysql4/bin:/usr/nekoware/qt4/bin:/usr/nekoware/kde/bin:/usr/nekoware/php5/bin
PERL = /usr/nekoware/bin/perl
PERL5LIB =
PERL5_CPANPLUS_IS_RUNNING = 9621851
PERL5_CPAN_IS_RUNNING = 9621851
SHELL = /usr/nekoware/bin/bash
TERM = vt100
Perl special variables (and OS-specific diagnostics, for MSWin32):
$^X = /usr/people/drc/cpantesting/perl-5.8.8/bin/perl
$UID/$EUID = 25020 / 25020
$GID = 20 20
$EGID = 20 20
Perl module toolchain versions installed:
Module Have
------------------- ------
CPAN 1.9205
Cwd 3.2701
ExtUtils::CBuilder n/a
ExtUtils::Command 1.13
ExtUtils::Install 1.45
ExtUtils::MakeMaker 6.44
ExtUtils::Manifest 1.51
ExtUtils::ParseXS n/a
File::Spec 3.2701
Module::Build 0.2808
Module::Signature n/a
Test::Harness 3.10
Test::More 0.80
YAML 0.66
YAML::Syck 1.05
version 0.76
--
Summary of my perl5 (revision 5 version 8 subversion 8) configuration:
Platform:
osname=irix, osvers=6.5, archname=IP35-irix-64int
uname='irix64 o3k 6.5 07202013 ip35 '
config_args='-de -Dprefix=/usr/people/drc/cpantesting/perl-5.8.8 -Duse64bitint'
hint=recommended, useposix=true, d_sigaction=define
usethreads=undef use5005threads=undef useithreads=undef usemultiplicity=undef
useperlio=define d_sfio=undef uselargefiles=define usesocks=undef
use64bitint=define use64bitall=undef uselongdouble=undef
usemymalloc=n, bincompat5005=undef
Compiler:
cc='cc -n32', ccflags ='-D_BSD_TYPES -D_BSD_TIME -woff 1184,1552 -I/usr/local/include -DLANGUAGE_C',
optimize='-O3 -OPT:Olimit=0:space=ON',
cppflags='-D_BSD_TYPES -D_BSD_TIME -woff 1184,1552 -I/usr/local/include -DLANGUAGE_C'
ccversion='MIPSpro Compilers: Version 7.4.4m', gccversion='', gccosandvers=''
intsize=4, longsize=4, ptrsize=4, doublesize=8, byteorder=87654321
d_longlong=define, longlongsize=8, d_longdbl=define, longdblsize=16
ivtype='long long', ivsize=8, nvtype='double', nvsize=8, Off_t='off_t', lseeksize=8
alignbytes=8, prototype=define
Linker and Libraries:
ld='cc -n32', ldflags =' -Wl,-woff,84 -L/usr/local/lib'
libpth=/usr/local/lib /usr/lib32 /lib32 /lib /usr/lib
libs=-ldb -lm -lc
perllibs=-lm -lc
libc=/usr/lib32/libc.so, so=so, useshrplib=false, libperl=libperl.a
gnulibc_version=''
Dynamic Linking:
dlsrc=dl_dlopen.xs, dlext=so, d_dlsymun=undef, ccdlflags=' '
cccdlflags=' ', lddlflags='-n32 -shared -L/usr/local/lib'
-
FAIL bioperl-1.4 IP35-irix-64int 6.5
by david