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-1.2.3, 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: No requirements found ------------------------------ ENVIRONMENT AND OTHER CONTEXT ------------------------------ Environment variables: PATH = /usr/bin:/bin:/usr/sbin:/sbin PERL5LIB = PERL5_CPANPLUS_IS_RUNNING = 1 PERL5_CPAN_IS_RUNNING = 1 SHELL = /bin/bash TERM = screen Perl special variables (and OS-specific diagnostics, for MSWin32): Perl: $^X = /Users/david/cpantesting/perl-5.9.5/bin/perl5.9.5 UID: $< = 501 EUID: $> = 501 GID: $( = 501 501 81 79 80 EGID: $) = 501 501 81 79 80 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 'make test': PERL_DL_NONLAZY=1 /Users/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 /Users/david/cpantesting/perl-5.9.5/.cpan/build/bioperl-1.2.3-7x9sH3/blib/lib/Bio/Root/Object.pm line 700. 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................Can't locate LWP/UserAgent.pm in @INC (@INC contains: t . ./blib/lib /Users/david/cpantesting/perl-5.9.5/.cpan/build/bioperl-1.2.3-7x9sH3/blib/lib /Users/david/cpantesting/perl-5.9.5/.cpan/build/bioperl-1.2.3-7x9sH3/blib/arch /Users/david/cpantesting/perl-5.9.5/lib/5.9.5/darwin-2level /Users/david/cpantesting/perl-5.9.5/lib/5.9.5 /Users/david/cpantesting/perl-5.9.5/lib/site_perl/5.9.5/darwin-2level /Users/david/cpantesting/perl-5.9.5/lib/site_perl/5.9.5) at Bio/DB/WebDBSeqI.pm line 86. BEGIN failed--compilation aborted at Bio/DB/WebDBSeqI.pm line 86. Compilation failed in require at Bio/DB/BioFetch.pm line 16. BEGIN failed--compilation aborted at Bio/DB/BioFetch.pm line 16. Compilation failed in require at t/BioFetch_DB.t line 51. dubious Test returned status 2 (wstat 512, 0x200) after all the subtests completed successfully 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/ClusterIO..................XML::Parser::PerlSAX not loaded. This means ClusterIO::dbsnp test cannot be executed. Skipping ok t/CodonTable.................ok t/consed.....................ok t/CoordinateGraph............ok t/CoordinateMapper...........ok t/Correlate..................Useless localization of scalar assignment at /Users/david/cpantesting/perl-5.9.5/.cpan/build/bioperl-1.2.3-7x9sH3/blib/lib/Bio/Root/Object.pm line 700. ok t/CytoMap....................ok t/DB.........................Can't locate LWP/UserAgent.pm in @INC (@INC contains: t .. . ./blib/lib /Users/david/cpantesting/perl-5.9.5/.cpan/build/bioperl-1.2.3-7x9sH3/blib/lib /Users/david/cpantesting/perl-5.9.5/.cpan/build/bioperl-1.2.3-7x9sH3/blib/arch /Users/david/cpantesting/perl-5.9.5/lib/5.9.5/darwin-2level /Users/david/cpantesting/perl-5.9.5/lib/5.9.5 /Users/david/cpantesting/perl-5.9.5/lib/site_perl/5.9.5/darwin-2level /Users/david/cpantesting/perl-5.9.5/lib/site_perl/5.9.5) at Bio/DB/WebDBSeqI.pm line 86. BEGIN failed--compilation aborted at Bio/DB/WebDBSeqI.pm line 86. Compilation failed in require at Bio/DB/NCBIHelper.pm line 82. BEGIN failed--compilation aborted at Bio/DB/NCBIHelper.pm line 82. Compilation failed in require at Bio/DB/GenBank.pm line 124. BEGIN failed--compilation aborted at Bio/DB/GenBank.pm line 124. Compilation failed in require at t/DB.t line 48. dubious Test returned status 2 (wstat 512, 0x200) after all the subtests completed successfully t/DBFasta....................ok t/DNAMutation................ok t/ECnumber...................Useless localization of scalar assignment at /Users/david/cpantesting/perl-5.9.5/.cpan/build/bioperl-1.2.3-7x9sH3/blib/lib/Bio/Root/Object.pm line 700. ok t/EMBL_DB....................Can't locate HTTP/Request/Common.pm in @INC (@INC contains: t /Users/david/cpantesting/perl-5.9.5/.cpan/build/bioperl-1.2.3-7x9sH3/blib/lib /Users/david/cpantesting/perl-5.9.5/.cpan/build/bioperl-1.2.3-7x9sH3/blib/arch /Users/david/cpantesting/perl-5.9.5/lib/5.9.5/darwin-2level /Users/david/cpantesting/perl-5.9.5/lib/5.9.5 /Users/david/cpantesting/perl-5.9.5/lib/site_perl/5.9.5/darwin-2level /Users/david/cpantesting/perl-5.9.5/lib/site_perl/5.9.5 .) at /Users/david/cpantesting/perl-5.9.5/.cpan/build/bioperl-1.2.3-7x9sH3/blib/lib/Bio/DB/DBFetch.pm line 74. BEGIN failed--compilation aborted at /Users/david/cpantesting/perl-5.9.5/.cpan/build/bioperl-1.2.3-7x9sH3/blib/lib/Bio/DB/DBFetch.pm line 74. Compilation failed in require at /Users/david/cpantesting/perl-5.9.5/.cpan/build/bioperl-1.2.3-7x9sH3/blib/lib/Bio/DB/EMBL.pm line 103. BEGIN failed--compilation aborted at /Users/david/cpantesting/perl-5.9.5/.cpan/build/bioperl-1.2.3-7x9sH3/blib/lib/Bio/DB/EMBL.pm line 103. Compilation failed in require at t/EMBL_DB.t line 46. dubious Test returned status 2 (wstat 512, 0x200) after all the subtests completed successfully t/EncodedSeq.................ok t/ePCR.......................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........................Cannot load LWP::UserAgent or HTML::Parser, skipping tests ok t/GeneCoordinateMapper.......ok t/Genewise...................ok t/Genomewise.................ok t/Genpred....................ok t/GFF........................ok t/GOterm.....................Useless localization of scalar assignment at /Users/david/cpantesting/perl-5.9.5/.cpan/build/bioperl-1.2.3-7x9sH3/blib/lib/Bio/Root/Object.pm line 700. ok t/hmmer......................ok t/Index......................ok t/IUPAC......................ok t/largefasta.................ok t/largepseq..................ok t/LinkageMap.................ok t/LiveSeq....................Can't locate HTTP/Request/Common.pm in @INC (@INC contains: t /Users/david/cpantesting/perl-5.9.5/.cpan/build/bioperl-1.2.3-7x9sH3/blib/lib /Users/david/cpantesting/perl-5.9.5/.cpan/build/bioperl-1.2.3-7x9sH3/blib/arch /Users/david/cpantesting/perl-5.9.5/lib/5.9.5/darwin-2level /Users/david/cpantesting/perl-5.9.5/lib/5.9.5 /Users/david/cpantesting/perl-5.9.5/lib/site_perl/5.9.5/darwin-2level /Users/david/cpantesting/perl-5.9.5/lib/site_perl/5.9.5 .) at /Users/david/cpantesting/perl-5.9.5/.cpan/build/bioperl-1.2.3-7x9sH3/blib/lib/Bio/DB/DBFetch.pm line 74. BEGIN failed--compilation aborted at /Users/david/cpantesting/perl-5.9.5/.cpan/build/bioperl-1.2.3-7x9sH3/blib/lib/Bio/DB/DBFetch.pm line 74. Compilation failed in require at /Users/david/cpantesting/perl-5.9.5/.cpan/build/bioperl-1.2.3-7x9sH3/blib/lib/Bio/DB/EMBL.pm line 103. BEGIN failed--compilation aborted at /Users/david/cpantesting/perl-5.9.5/.cpan/build/bioperl-1.2.3-7x9sH3/blib/lib/Bio/DB/EMBL.pm line 103. Compilation failed in require at /Users/david/cpantesting/perl-5.9.5/.cpan/build/bioperl-1.2.3-7x9sH3/blib/lib/Bio/LiveSeq/IO/BioPerl.pm line 110. BEGIN failed--compilation aborted at /Users/david/cpantesting/perl-5.9.5/.cpan/build/bioperl-1.2.3-7x9sH3/blib/lib/Bio/LiveSeq/IO/BioPerl.pm line 110. Compilation failed in require at t/LiveSeq.t line 39. dubious Test returned status 2 (wstat 512, 0x200) DIED. FAILED tests 1-48 Failed 48/48 tests, 0.00% okay t/LocatableSeq...............ok t/Location...................ok t/LocationFactory............ok t/LocusLink..................Useless localization of scalar assignment at /Users/david/cpantesting/perl-5.9.5/.cpan/build/bioperl-1.2.3-7x9sH3/blib/lib/Bio/Root/Object.pm line 700. ok t/lucy.......................ok t/Map........................ok t/MapIO......................ok t/Measure....................Useless localization of scalar assignment at /Users/david/cpantesting/perl-5.9.5/.cpan/build/bioperl-1.2.3-7x9sH3/blib/lib/Bio/Root/Object.pm line 700. ok t/MicrosatelliteMarker.......ok t/MiniMIMentry...............Useless localization of scalar assignment at /Users/david/cpantesting/perl-5.9.5/.cpan/build/bioperl-1.2.3-7x9sH3/blib/lib/Bio/Root/Object.pm line 700. ok t/Molphy.....................ok t/multiple_fasta.............ok t/Mutation...................ok t/Mutator....................Can't locate HTTP/Request/Common.pm in @INC (@INC contains: t /Users/david/cpantesting/perl-5.9.5/.cpan/build/bioperl-1.2.3-7x9sH3/blib/lib /Users/david/cpantesting/perl-5.9.5/.cpan/build/bioperl-1.2.3-7x9sH3/blib/arch /Users/david/cpantesting/perl-5.9.5/lib/5.9.5/darwin-2level /Users/david/cpantesting/perl-5.9.5/lib/5.9.5 /Users/david/cpantesting/perl-5.9.5/lib/site_perl/5.9.5/darwin-2level /Users/david/cpantesting/perl-5.9.5/lib/site_perl/5.9.5 .) at /Users/david/cpantesting/perl-5.9.5/.cpan/build/bioperl-1.2.3-7x9sH3/blib/lib/Bio/DB/DBFetch.pm line 74. BEGIN failed--compilation aborted at /Users/david/cpantesting/perl-5.9.5/.cpan/build/bioperl-1.2.3-7x9sH3/blib/lib/Bio/DB/DBFetch.pm line 74. Compilation failed in require at /Users/david/cpantesting/perl-5.9.5/.cpan/build/bioperl-1.2.3-7x9sH3/blib/lib/Bio/DB/EMBL.pm line 103. BEGIN failed--compilation aborted at /Users/david/cpantesting/perl-5.9.5/.cpan/build/bioperl-1.2.3-7x9sH3/blib/lib/Bio/DB/EMBL.pm line 103. Compilation failed in require at /Users/david/cpantesting/perl-5.9.5/.cpan/build/bioperl-1.2.3-7x9sH3/blib/lib/Bio/LiveSeq/IO/BioPerl.pm line 110. BEGIN failed--compilation aborted at /Users/david/cpantesting/perl-5.9.5/.cpan/build/bioperl-1.2.3-7x9sH3/blib/lib/Bio/LiveSeq/IO/BioPerl.pm line 110. Compilation failed in require at t/Mutator.t line 36. dubious Test returned status 2 (wstat 512, 0x200) DIED. FAILED tests 1-13 Failed 13/13 tests, 0.00% okay t/Node.......................ok t/OddCodes...................ok t/OMIMentry..................Useless localization of scalar assignment at /Users/david/cpantesting/perl-5.9.5/.cpan/build/bioperl-1.2.3-7x9sH3/blib/lib/Bio/Root/Object.pm line 700. ok t/OMIMentryAllelicVariant....Useless localization of scalar assignment at /Users/david/cpantesting/perl-5.9.5/.cpan/build/bioperl-1.2.3-7x9sH3/blib/lib/Bio/Root/Object.pm line 700. ok t/OMIMparser.................Useless localization of scalar assignment at /Users/david/cpantesting/perl-5.9.5/.cpan/build/bioperl-1.2.3-7x9sH3/blib/lib/Bio/Root/Object.pm line 700. ok t/Ontology...................Useless localization of scalar assignment at /Users/david/cpantesting/perl-5.9.5/.cpan/build/bioperl-1.2.3-7x9sH3/blib/lib/Bio/Root/Object.pm line 700. set_attribute: not a compat02 graph at /Users/david/cpantesting/perl-5.9.5/lib/site_perl/5.9.5/Graph.pm line 2394, <GEN0> line 10. dubious Test returned status 9 (wstat 2304, 0x900) DIED. FAILED tests 1-50 Failed 50/50 tests, 0.00% okay t/OntologyEngine.............Useless localization of scalar assignment at /Users/david/cpantesting/perl-5.9.5/.cpan/build/bioperl-1.2.3-7x9sH3/blib/lib/Bio/Root/Object.pm line 700. ok t/PAML.......................ok t/Perl.......................ok t/phd........................ok t/Phenotype..................Useless localization of scalar assignment at /Users/david/cpantesting/perl-5.9.5/.cpan/build/bioperl-1.2.3-7x9sH3/blib/lib/Bio/Root/Object.pm line 700. ok t/PhylipDist.................ok t/primaryqual................ok t/PrimarySeq.................ok t/primedseq..................ok t/primer3....................ok t/ProtDist...................ok t/qual.......................ok t/RandomTreeFactory..........ok t/Range......................ok t/RangeI.....................ok t/RefSeq.....................Can't locate HTTP/Request/Common.pm in @INC (@INC contains: t /Users/david/cpantesting/perl-5.9.5/.cpan/build/bioperl-1.2.3-7x9sH3/blib/lib /Users/david/cpantesting/perl-5.9.5/.cpan/build/bioperl-1.2.3-7x9sH3/blib/arch /Users/david/cpantesting/perl-5.9.5/lib/5.9.5/darwin-2level /Users/david/cpantesting/perl-5.9.5/lib/5.9.5 /Users/david/cpantesting/perl-5.9.5/lib/site_perl/5.9.5/darwin-2level /Users/david/cpantesting/perl-5.9.5/lib/site_perl/5.9.5 .) at /Users/david/cpantesting/perl-5.9.5/.cpan/build/bioperl-1.2.3-7x9sH3/blib/lib/Bio/DB/DBFetch.pm line 74. BEGIN failed--compilation aborted at /Users/david/cpantesting/perl-5.9.5/.cpan/build/bioperl-1.2.3-7x9sH3/blib/lib/Bio/DB/DBFetch.pm line 74. Compilation failed in require at /Users/david/cpantesting/perl-5.9.5/.cpan/build/bioperl-1.2.3-7x9sH3/blib/lib/Bio/DB/RefSeq.pm line 107. BEGIN failed--compilation aborted at /Users/david/cpantesting/perl-5.9.5/.cpan/build/bioperl-1.2.3-7x9sH3/blib/lib/Bio/DB/RefSeq.pm line 107. Compilation failed in require at t/RefSeq.t line 46. dubious Test returned status 2 (wstat 512, 0x200) after all the subtests completed successfully t/Relationship...............Useless localization of scalar assignment at /Users/david/cpantesting/perl-5.9.5/.cpan/build/bioperl-1.2.3-7x9sH3/blib/lib/Bio/Root/Object.pm line 700. ok t/RelationshipType...........Useless localization of scalar assignment at /Users/david/cpantesting/perl-5.9.5/.cpan/build/bioperl-1.2.3-7x9sH3/blib/lib/Bio/Root/Object.pm line 700. ok t/RepeatMasker...............ok t/RestrictionEnzyme..........ok t/RNAChange..................ok t/RootI......................ok t/RootIO.....................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 /Users/david/cpantesting/perl-5.9.5/.cpan/build/bioperl-1.2.3-7x9sH3/blib/lib/Bio/Root/Object.pm line 700. ok t/seqfeaturePrimer...........ok t/SeqIO......................ok 3/184 skipped: various reasons t/SeqPattern.................ok t/SeqStats...................ok t/SequenceFamily.............ok t/sequencetrace..............ok t/SeqUtils...................ok t/seqwithquality.............ok t/Sigcleave..................ok t/Sim4.......................ok t/SimilarityPair.............ok t/SimpleAlign................ok t/simpleGOparser.............Useless localization of scalar assignment at /Users/david/cpantesting/perl-5.9.5/.cpan/build/bioperl-1.2.3-7x9sH3/blib/lib/Bio/Root/Object.pm line 700. set_attribute: not a compat02 graph at /Users/david/cpantesting/perl-5.9.5/lib/site_perl/5.9.5/Graph.pm line 2394, <GEN1> line 14. dubious Test returned status 9 (wstat 2304, 0x900) DIED. FAILED tests 1-88 Failed 88/88 tests, 0.00% okay t/Species....................ok t/splicedseq.................Skipping remote location tests ok t/StandAloneBlast............ok t/StateMachine...............ok t/StructIO...................ok t/Structure..................ok t/Swiss......................ok t/Symbol.....................ok t/Tempfile...................ok t/Term.......................Useless localization of scalar assignment at /Users/david/cpantesting/perl-5.9.5/.cpan/build/bioperl-1.2.3-7x9sH3/blib/lib/Bio/Root/Object.pm line 700. ok t/Tools......................ok t/Tree.......................ok t/TreeIO.....................ok t/trim.......................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 2 512 27 0 ?? t/DB.t 2 512 78 0 ?? t/EMBL_DB.t 2 512 15 0 ?? t/LiveSeq.t 2 512 48 96 1-48 t/Mutator.t 2 512 13 26 1-13 t/Ontology.t 9 2304 50 100 1-50 t/RefSeq.t 2 512 13 0 ?? t/simpleGOparser.t 9 2304 88 176 1-88 25 subtests skipped. Failed 8/137 test scripts. 199/6319 subtests failed. Files=137, Tests=6319, 42 wallclock secs (27.70 cusr + 3.29 csys = 30.99 CPU) Failed 8/137 test programs. 199/6319 subtests failed. make: *** [test_dynamic] Error 255 -- Summary of my perl5 (revision 5 version 9 subversion 5) configuration: Platform: osname=darwin, osvers=8.10.1, archname=darwin-2level uname='darwin cowshed-door.barnyard.co.uk 8.10.1 darwin kernel version 8.10.1: wed may 23 16:33:00 pdt 2007; root:xnu-792.22.5~1release_i386 i386 i386 ' config_args='-de -Dprefix=/Users/david/cpantesting/perl-5.9.5 -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 ='-fno-common -DPERL_DARWIN -no-cpp-precomp -fno-strict-aliasing -pipe', optimize='-O3', cppflags='-no-cpp-precomp -fno-common -DPERL_DARWIN -no-cpp-precomp -fno-strict-aliasing -pipe' ccversion='', gccversion='4.0.1 (Apple Computer, Inc. build 5367)', gccosandvers='' intsize=4, longsize=4, ptrsize=4, doublesize=8, byteorder=1234 d_longlong=define, longlongsize=8, d_longdbl=define, longdblsize=16 ivtype='long', ivsize=4, nvtype='double', nvsize=8, Off_t='off_t', lseeksize=8 alignbytes=8, prototype=define Linker and Libraries: ld='env MACOSX_DEPLOYMENT_TARGET=10.3 cc', ldflags ='' libpth=/usr/lib libs=-ldbm -ldl -lm -lc perllibs=-ldl -lm -lc libc=/usr/lib/libc.dylib, so=dylib, useshrplib=false, libperl=libperl.a gnulibc_version='' Dynamic Linking: dlsrc=dl_dlopen.xs, dlext=bundle, d_dlsymun=undef, ccdlflags=' ' cccdlflags=' ', lddlflags=' -bundle -undefined dynamic_lookup'
