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FAIL bioperl-1.4 i386-freebsd 6.2-release
From:
david
Date:
August 22, 2007 10:41
Subject:
FAIL bioperl-1.4 i386-freebsd 6.2-release
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/
Please cc any replies to cpan-testers@perl.org to keep other
test volunteers informed and to prevent any duplicate effort.
--
Dear Ewan Birney,
This is a computer-generated test report for bioperl-1.4, created
automatically by CPAN::Reporter, version 0.48, and sent to the CPAN
Testers mailing list. If you have received this email directly, it is
because the person testing your distribution chose to send a copy to your
CPAN email address; there may be a delay before the official report is
received and processed by CPAN Testers.
Thank you for uploading your work to CPAN. However, it appears that
there were some problems testing your distribution.
Sections of this report:
* Tester comments
* Prerequisites
* Environment and other context
* Test output
------------------------------
TESTER COMMENTS
------------------------------
Additional comments from tester:
[none provided]
------------------------------
PREREQUISITES
------------------------------
Prerequisite modules loaded:
requires:
Module Need Have
-------------- ---- -----
DB_File 0 1.815
File::Spec 0 3.25
File::Temp 0 0.18
HTML::Entities 0 1.35
IO::Scalar 0 2.110
IO::String 0 1.08
------------------------------
ENVIRONMENT AND OTHER CONTEXT
------------------------------
Environment variables:
PATH = /sbin:/bin:/usr/sbin:/usr/bin:/usr/games:/usr/local/sbin:/usr/local/bin:/usr/X11R6/bin:/home/david/bin
PERL5LIB =
PERL5_CPANPLUS_IS_RUNNING = 1
PERL5_CPAN_IS_RUNNING = 1
SHELL = /usr/local/bin/bash
TERM = screen
Perl special variables (and OS-specific diagnostics, for MSWin32):
Perl: $^X = /home/david/cpantesting/perl-5.9.5/bin/perl5.9.5
UID: $< = 1001
EUID: $> = 1001
GID: $( = 1001 1001 1001 0
EGID: $) = 1001 1001 1001 0
Perl module toolchain versions installed:
Module Have
------------------- -------
CPAN 1.9102
Cwd 3.25
ExtUtils::CBuilder 0.19
ExtUtils::Command 1.13
ExtUtils::Install 1.41_01
ExtUtils::MakeMaker 6.36
ExtUtils::Manifest 1.51_01
ExtUtils::ParseXS 2.18
File::Spec 3.25
Module::Build 0.2808
Module::Signature n/a
Test::Harness 2.64
Test::More 0.70
version 0.7203
------------------------------
TEST OUTPUT
------------------------------
Output from '/usr/bin/make test':
PERL_DL_NONLAZY=1 /home/david/cpantesting/perl-5.9.5/bin/perl5.9.5 "-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.................Useless localization of scalar assignment at /usr/home/david/cpantesting/perl-5.9.5/.cpan/build/bioperl-1.4-2y1QED/blib/lib/Bio/Root/Object.pm line 699.
ok
t/AnnotationAdaptor..........ok
t/Assembly...................ok
t/Biblio.....................SOAP::Lite not installed. Skipping some tests.
XML::Parser not installed. Skipping some tests.
ok
22/24 skipped: various reasons
t/Biblio_biofetch............ok
t/BiblioReferences...........ok
t/BioDBGFF...................ok
t/BioFetch_DB................FAILED test 8
Failed 1/27 tests, 96.30% okay
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..................Useless localization of scalar assignment at /usr/home/david/cpantesting/perl-5.9.5/.cpan/build/bioperl-1.4-2y1QED/blib/lib/Bio/Root/Object.pm line 699.
ok
t/CytoMap....................ok
t/DB.........................ok
t/DBCUTG.....................ok
t/DBFasta....................ok
t/DNAMutation................ok
t/Domcut.....................ok
t/ECnumber...................Useless localization of scalar assignment at /usr/home/david/cpantesting/perl-5.9.5/.cpan/build/bioperl-1.4-2y1QED/blib/lib/Bio/Root/Object.pm line 699.
ok
t/ELM........................
-------------------- WARNING ---------------------
MSG: Bio::Tools::Analysis::Protein::ELM Request Error:
400 URL must be absolute
Content-Type: text/plain
Client-Date: Wed, 22 Aug 2007 17:24:06 GMT
Client-Warning: Internal response
400 URL must be absolute
---------------------------------------------------
ok
t/EMBL_DB....................FAILED tests 6, 13-14
Failed 3/15 tests, 80.00% okay
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/home/david/cpantesting/perl-5.9.5/.cpan/build/bioperl-1.4-2y1QED/blib/lib/Bio/Coordinate/GeneMapper.pm line 814.
ok
t/Geneid.....................ok
t/Genewise...................ok
2/51 skipped: various reasons
t/Genomewise.................ok
t/Genpred....................ok
t/GFF........................Filehandle GEN0 opened only for output at /usr/home/david/cpantesting/perl-5.9.5/.cpan/build/bioperl-1.4-2y1QED/blib/lib/Bio/Root/IO.pm line 440.
Filehandle GEN1 opened only for output at /usr/home/david/cpantesting/perl-5.9.5/.cpan/build/bioperl-1.4-2y1QED/blib/lib/Bio/Root/IO.pm line 440.
ok
t/GOR4.......................ok
t/GOterm.....................Useless localization of scalar assignment at /usr/home/david/cpantesting/perl-5.9.5/.cpan/build/bioperl-1.4-2y1QED/blib/lib/Bio/Root/Object.pm line 699.
ok
t/GuessSeqFormat.............Bio::SeqIO: game cannot be found
Exception
------------- EXCEPTION -------------
MSG: Failed to load module Bio::SeqIO::game. Can't locate XML/Parser/PerlSAX.pm in @INC (@INC contains: t .. /usr/home/david/cpantesting/perl-5.9.5/.cpan/build/bioperl-1.4-2y1QED/blib/lib /usr/home/david/cpantesting/perl-5.9.5/.cpan/build/bioperl-1.4-2y1QED/blib/arch /home/david/cpantesting/perl-5.9.5/lib/5.9.5/i386-freebsd /home/david/cpantesting/perl-5.9.5/lib/5.9.5 /home/david/cpantesting/perl-5.9.5/lib/site_perl/5.9.5/i386-freebsd /home/david/cpantesting/perl-5.9.5/lib/site_perl/5.9.5 .) at /usr/home/david/cpantesting/perl-5.9.5/.cpan/build/bioperl-1.4-2y1QED/blib/lib/Bio/SeqIO/game/gameSubs.pm line 70.
BEGIN failed--compilation aborted at /usr/home/david/cpantesting/perl-5.9.5/.cpan/build/bioperl-1.4-2y1QED/blib/lib/Bio/SeqIO/game/gameSubs.pm line 70.
Compilation failed in require at /usr/home/david/cpantesting/perl-5.9.5/.cpan/build/bioperl-1.4-2y1QED/blib/lib/Bio/SeqIO/game/gameHandler.pm line 62.
BEGIN failed--compilation aborted at /usr/home/david/cpantesting/perl-5.9.5/.cpan/build/bioperl-1.4-2y1QED/blib/lib/Bio/SeqIO/game/gameHandler.pm line 62.
Compilation failed in require at /usr/home/david/cpantesting/perl-5.9.5/.cpan/build/bioperl-1.4-2y1QED/blib/lib/Bio/SeqIO/game.pm line 76.
BEGIN failed--compilation aborted at /usr/home/david/cpantesting/perl-5.9.5/.cpan/build/bioperl-1.4-2y1QED/blib/lib/Bio/SeqIO/game.pm line 76.
Compilation failed in require at /usr/home/david/cpantesting/perl-5.9.5/.cpan/build/bioperl-1.4-2y1QED/blib/lib/Bio/Root/Root.pm line 394.
STACK Bio::Root::Root::_load_module /usr/home/david/cpantesting/perl-5.9.5/.cpan/build/bioperl-1.4-2y1QED/blib/lib/Bio/Root/Root.pm:396
STACK (eval) /usr/home/david/cpantesting/perl-5.9.5/.cpan/build/bioperl-1.4-2y1QED/blib/lib/Bio/SeqIO.pm:549
STACK Bio::SeqIO::_load_format_module /usr/home/david/cpantesting/perl-5.9.5/.cpan/build/bioperl-1.4-2y1QED/blib/lib/Bio/SeqIO.pm:548
STACK Bio::SeqIO::new /usr/home/david/cpantesting/perl-5.9.5/.cpan/build/bioperl-1.4-2y1QED/blib/lib/Bio/SeqIO.pm:377
STACK (eval) t/GuessSeqFormat.t:61
STACK toplevel t/GuessSeqFormat.t:60
--------------------------------------
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 test 11
Failed 1/46 tests, 97.83% okay
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..................Useless localization of scalar assignment at /usr/home/david/cpantesting/perl-5.9.5/.cpan/build/bioperl-1.4-2y1QED/blib/lib/Bio/Root/Object.pm line 699.
ok
t/lucy.......................ok
t/Map........................ok
t/MapIO......................ok
t/Matrix.....................ok
t/Measure....................Useless localization of scalar assignment at /usr/home/david/cpantesting/perl-5.9.5/.cpan/build/bioperl-1.4-2y1QED/blib/lib/Bio/Root/Object.pm line 699.
ok
t/MeSH.......................ok
t/MetaSeq....................ok
t/MicrosatelliteMarker.......ok
t/MiniMIMentry...............Useless localization of scalar assignment at /usr/home/david/cpantesting/perl-5.9.5/.cpan/build/bioperl-1.4-2y1QED/blib/lib/Bio/Root/Object.pm line 699.
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..................Useless localization of scalar assignment at /usr/home/david/cpantesting/perl-5.9.5/.cpan/build/bioperl-1.4-2y1QED/blib/lib/Bio/Root/Object.pm line 699.
ok
t/OMIMentryAllelicVariant....Useless localization of scalar assignment at /usr/home/david/cpantesting/perl-5.9.5/.cpan/build/bioperl-1.4-2y1QED/blib/lib/Bio/Root/Object.pm line 699.
ok
t/OMIMparser.................Useless localization of scalar assignment at /usr/home/david/cpantesting/perl-5.9.5/.cpan/build/bioperl-1.4-2y1QED/blib/lib/Bio/Root/Object.pm line 699.
ok
t/Ontology...................
Graph.pm doesn't seem to be installed on this system -- the GO Parser needs it...
ok
t/OntologyEngine.............Useless localization of scalar assignment at /usr/home/david/cpantesting/perl-5.9.5/.cpan/build/bioperl-1.4-2y1QED/blib/lib/Bio/Root/Object.pm line 699.
ok
t/PAML.......................ok
t/Perl.......................ok
t/phd........................ok
t/Phenotype..................Useless localization of scalar assignment at /usr/home/david/cpantesting/perl-5.9.5/.cpan/build/bioperl-1.4-2y1QED/blib/lib/Bio/Root/Object.pm line 699.
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...............Useless localization of scalar assignment at /usr/home/david/cpantesting/perl-5.9.5/.cpan/build/bioperl-1.4-2y1QED/blib/lib/Bio/Root/Object.pm line 699.
ok
t/RelationshipType...........Useless localization of scalar assignment at /usr/home/david/cpantesting/perl-5.9.5/.cpan/build/bioperl-1.4-2y1QED/blib/lib/Bio/Root/Object.pm line 699.
ok
t/RemoteBlast................ok
4/6 skipped: various reasons
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.................Useless localization of scalar assignment at /usr/home/david/cpantesting/perl-5.9.5/.cpan/build/bioperl-1.4-2y1QED/blib/lib/Bio/Root/Object.pm line 699.
ok
t/seqfeaturePrimer...........ok
t/SeqIO......................ok
3/235 skipped: various reasons
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.......................Useless localization of scalar assignment at /usr/home/david/cpantesting/perl-5.9.5/.cpan/build/bioperl-1.4-2y1QED/blib/lib/Bio/Root/Object.pm line 699.
ok
t/Tools......................ok
t/Tree.......................ok
t/TreeIO.....................ok
t/trim.......................ok
t/tutorial...................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
Failed Test Stat Wstat Total Fail List of Failed
-------------------------------------------------------------------------------
t/BioFetch_DB.t 27 1 8
t/EMBL_DB.t 15 3 6 13-14
t/GuessSeqFormat.t 46 1 11
31 subtests skipped.
Failed 3/179 test scripts. 5/8122 subtests failed.
Files=179, Tests=8122, 141 wallclock secs (44.27 cusr + 42.28 csys = 86.55 CPU)
Failed 3/179 test programs. 5/8122 subtests failed.
*** Error code 255
Stop in /usr/home/david/cpantesting/perl-5.9.5/.cpan/build/bioperl-1.4-2y1QED.
--
Summary of my perl5 (revision 5 version 9 subversion 5) configuration:
Platform:
osname=freebsd, osvers=6.2-release, archname=i386-freebsd
uname='freebsd poacher.barnyard.co.uk 6.2-release freebsd 6.2-release #0: fri jan 12 10:40:27 utc 2007 root@dessler.cse.buffalo.edu:usrobjusrsrcsysgeneric i386 '
config_args='-Dprefix=/home/david/cpantesting/perl-5.9.5 -de -Dusedevel'
hint=recommended, useposix=true, d_sigaction=define
useithreads=undef, usemultiplicity=undef
useperlio=define, d_sfio=undef, uselargefiles=define, usesocks=undef
use64bitint=undef, use64bitall=undef, uselongdouble=undef
usemymalloc=n, bincompat5005=undef
Compiler:
cc='cc', ccflags ='-DHAS_FPSETMASK -DHAS_FLOATINGPOINT_H -fno-strict-aliasing -pipe -I/usr/local/include',
optimize='-O',
cppflags='-DHAS_FPSETMASK -DHAS_FLOATINGPOINT_H -fno-strict-aliasing -pipe -I/usr/local/include'
ccversion='', gccversion='3.4.6 [FreeBSD] 20060305', gccosandvers=''
intsize=4, longsize=4, ptrsize=4, doublesize=8, byteorder=1234
d_longlong=define, longlongsize=8, d_longdbl=define, longdblsize=12
ivtype='long', ivsize=4, nvtype='double', nvsize=8, Off_t='off_t', lseeksize=8
alignbytes=4, prototype=define
Linker and Libraries:
ld='cc', ldflags ='-Wl,-E -L/usr/local/lib'
libpth=/usr/lib /usr/local/lib
libs=-lgdbm -lm -lcrypt -lutil -lc
perllibs=-lm -lcrypt -lutil -lc
libc=, so=so, useshrplib=false, libperl=libperl.a
gnulibc_version=''
Dynamic Linking:
dlsrc=dl_dlopen.xs, dlext=so, d_dlsymun=undef, ccdlflags=' '
cccdlflags='-DPIC -fPIC', lddlflags='-shared -L/usr/local/lib'
-
FAIL bioperl-1.4 i386-freebsd 6.2-release
by david