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 [email protected] 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 [EMAIL PROTECTED]: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'
