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 report for bioperl-1.2.3 on perl-5.10.0 patch 31856, created automatically by CPAN-Reporter-1.06 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. Congratulations! All tests were successful. Sections of this report: * Tester comments * Program output * Prerequisites * Environment and other context ------------------------------ TESTER COMMENTS ------------------------------ Additional comments from tester: [none provided] ------------------------------ PROGRAM OUTPUT ------------------------------ Output from 'make test': PERL_DL_NONLAZY=1 /arpa/af/d/drhyde/perl-5.10.0/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.................Useless localization of scalar assignment at /tmp/drhyde/build/bioperl-1.2.3-Gym3Ik/blib/lib/Bio/Root/Object.pm line 700. ok t/AnnotationAdaptor..........ok t/Assembly...................ok t/Biblio.....................SOAP::Lite not installed. Skipping some tests. IO::String 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................ok 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 /tmp/drhyde/build/bioperl-1.2.3-Gym3Ik/blib/lib/Bio/Root/Object.pm line 700. ok t/CytoMap....................ok t/DB.........................IO::String not installed. This means the Bio::DB::* modules are not usable. Skipping tests. ok t/DBFasta....................ok t/DNAMutation................ok t/ECnumber...................Useless localization of scalar assignment at /tmp/drhyde/build/bioperl-1.2.3-Gym3Ik/blib/lib/Bio/Root/Object.pm line 700. ok t/EMBL_DB....................ok 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 /tmp/drhyde/build/bioperl-1.2.3-Gym3Ik/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....................IO::String not installed. This means the Bio::DB::* modules are not usable. Skipping tests. ok t/LocatableSeq...............ok t/Location...................ok t/LocationFactory............ok t/LocusLink..................Useless localization of scalar assignment at /tmp/drhyde/build/bioperl-1.2.3-Gym3Ik/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 /tmp/drhyde/build/bioperl-1.2.3-Gym3Ik/blib/lib/Bio/Root/Object.pm line 700. ok t/MicrosatelliteMarker.......ok t/MiniMIMentry...............Useless localization of scalar assignment at /tmp/drhyde/build/bioperl-1.2.3-Gym3Ik/blib/lib/Bio/Root/Object.pm line 700. ok t/Molphy.....................no IO string installed ok t/multiple_fasta.............ok t/Mutation...................ok t/Mutator....................IO::String not installed. This means the Bio::DB::* modules are not usable. Skipping tests. ok t/Node.......................ok t/OddCodes...................ok t/OMIMentry..................Useless localization of scalar assignment at /tmp/drhyde/build/bioperl-1.2.3-Gym3Ik/blib/lib/Bio/Root/Object.pm line 700. ok t/OMIMentryAllelicVariant....Useless localization of scalar assignment at /tmp/drhyde/build/bioperl-1.2.3-Gym3Ik/blib/lib/Bio/Root/Object.pm line 700. ok t/OMIMparser.................Useless localization of scalar assignment at /tmp/drhyde/build/bioperl-1.2.3-Gym3Ik/blib/lib/Bio/Root/Object.pm line 700. 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 /tmp/drhyde/build/bioperl-1.2.3-Gym3Ik/blib/lib/Bio/Root/Object.pm line 700. ok t/PAML.......................no IO string installed ok t/Perl.......................IO::String not installed. This means the Bio::DB::* modules are not usable. Skipping some tests. ok t/phd........................ok t/Phenotype..................Useless localization of scalar assignment at /tmp/drhyde/build/bioperl-1.2.3-Gym3Ik/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.....................ok t/Relationship...............Useless localization of scalar assignment at /tmp/drhyde/build/bioperl-1.2.3-Gym3Ik/blib/lib/Bio/Root/Object.pm line 700. ok t/RelationshipType...........Useless localization of scalar assignment at /tmp/drhyde/build/bioperl-1.2.3-Gym3Ik/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 /tmp/drhyde/build/bioperl-1.2.3-Gym3Ik/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................IO::String not installed. Skipping tests. ok t/simpleGOparser............. Graph.pm doesn't seem to be installed on this system -- the GO Parser needs it... ok 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 /tmp/drhyde/build/bioperl-1.2.3-Gym3Ik/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 All tests successful, 25 subtests skipped. Files=137, Tests=6183, 169 wallclock secs (129.67 cusr + 9.63 csys = 139.30 CPU) ------------------------------ PREREQUISITES ------------------------------ Prerequisite modules loaded: No requirements found ------------------------------ ENVIRONMENT AND OTHER CONTEXT ------------------------------ Environment variables: PATH = /usr/bin:/bin:/usr/pkg/bin:/usr/local/bin PERL5LIB = PERL5_CPANPLUS_IS_RUNNING = 11850 PERL5_CPAN_IS_RUNNING = 11850 SHELL = /usr/pkg/bin/bash TERM = screen Perl special variables (and OS-specific diagnostics, for MSWin32): $^X = /arpa/af/d/drhyde/perl-5.10.0/bin/perl $UID/$EUID = 40631 / 40631 $GID = 500 500 $EGID = 500 500 Perl module toolchain versions installed: Module Have ------------------- --------- CPAN 1.9205 Cwd 3.25 ExtUtils::CBuilder 0.19 ExtUtils::Command 1.13 ExtUtils::Install 1.44 ExtUtils::MakeMaker 6.36_01 ExtUtils::Manifest 1.51_01 ExtUtils::ParseXS 2.18 File::Spec 3.25 Module::Build 0.2808_01 Module::Signature n/a Test::Harness 2.64 Test::More 0.70 YAML n/a YAML::Syck n/a version 0.7203 -- Summary of my perl5 (revision 5 version 10 subversion 0 patch 31856) configuration: Platform: osname=netbsd, osvers=2.1.0_stable, archname=alpha-netbsd uname='netbsd sdf 2.1.0_stable netbsd 2.1.0_stable (sdf) #0: fri mar 30 02:24:32 utc 2007 [EMAIL PROTECTED]:varsysarchalphacompilesdf alpha ' config_args='-de -Dprefix=/arpa/af/d/drhyde/perl-5.10.0 -Duse64bitall' hint=recommended, useposix=true, d_sigaction=define useithreads=undef, usemultiplicity=undef useperlio=define, d_sfio=undef, uselargefiles=define, usesocks=undef use64bitint=define, use64bitall=define, uselongdouble=undef usemymalloc=n, bincompat5005=undef Compiler: cc='cc', ccflags ='-fno-strict-aliasing -pipe -I/usr/pkg/include', optimize='-O', cppflags='-fno-strict-aliasing -pipe -I/usr/pkg/include' ccversion='', gccversion='3.3.3 (NetBSD nb3 20040520)', gccosandvers='' intsize=4, longsize=8, ptrsize=8, doublesize=8, byteorder=12345678 d_longlong=define, longlongsize=8, d_longdbl=define, longdblsize=8 ivtype='long', ivsize=8, nvtype='double', nvsize=8, Off_t='off_t', lseeksize=8 alignbytes=8, prototype=define Linker and Libraries: ld='cc', ldflags =' -Wl,-rpath,/usr/pkg/lib -Wl,-rpath,/usr/local/lib -L/usr/pkg/lib' libpth=/usr/pkg/lib /lib /usr/lib libs=-lbind -lgdbm -lm -lcrypt -lutil -lc -lposix perllibs=-lbind -lm -lcrypt -lutil -lc -lposix libc=/lib/libc.so, so=so, useshrplib=false, libperl=libperl.a gnulibc_version='' Dynamic Linking: dlsrc=dl_dlopen.xs, dlext=so, d_dlsymun=undef, ccdlflags='-Wl,-E ' cccdlflags='-DPIC -fPIC ', lddlflags='--whole-archive -shared -L/usr/pkg/lib'
