BioPerl v1.7.8 Perl 5 v5.32.1 amd64-openbsd

Status
Pass
From
Alceu Rodrigues de Freitas Junior
Dist
BioPerl v1.7.8
Platform
Perl 5 v5.32.1 amd64-openbsd
Date
2022-05-09 13:27:45
ID
cfb31568-cf9b-11ec-b737-db65ffa5fe2c
This distribution has been tested as part of the CPAN Testers
project, supporting the Perl programming language.  See
http://wiki.cpantesters.org/ for more information or email
questions to cpan-testers-discuss@perl.org


--
Dear Christopher Fields,

This is a computer-generated report for BioPerl-1.7.8
on perl 5.32.1, created by CPAN-Reporter-1.2018.

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:

this report is from an automated smoke testing program
and was not reviewed by a human for accuracy

------------------------------
PROGRAM OUTPUT
------------------------------

Output from '/usr/bin/make test':

PERL_DL_NONLAZY=1 "/usr/bin/perl" "-MExtUtils::Command::MM" "-MTest::Harness" "-e" "undef *Test::Harness::Switches; test_harness(0, 'blib/lib', 'blib/arch')" t/*.t t/Align/*.t t/AlignIO/*.t t/Annotation/*.t t/LocalDB/*.t t/LocalDB/Index/*.t t/LocalDB/Taxonomy/*.t t/Matrix/*.t t/Matrix/IO/*.t t/Ontology/*.t t/Ontology/IO/*.t t/RemoteDB/*.t t/Root/*.t t/SearchIO/*.t t/SearchIO/Writer/*.t t/Seq/*.t t/SeqFeature/*.t t/SeqIO/*.t t/SeqTools/*.t t/Tools/*.t t/Tools/Alignment/*.t t/Tools/EMBOSS/*.t t/Tools/Phylo/*.t t/Tools/Phylo/Phylip/*.t t/Tools/Signalp/*.t t/Tools/Spidey/*.t t/Tree/*.t t/Tree/TreeIO/*.t
t/00-compile.t ...................... ok
t/Align/AlignStats.t ................ ok
t/Align/AlignUtil.t ................. ok
t/Align/SimpleAlign.t ............... ok
t/Align/TreeBuild.t ................. ok
t/Align/Utilities.t ................. ok
t/AlignIO/AlignIO.t ................. ok
t/AlignIO/arp.t ..................... ok
t/AlignIO/bl2seq.t .................. ok
t/AlignIO/clustalw.t ................ ok
t/AlignIO/emboss.t .................. ok
t/AlignIO/fasta.t ................... ok
t/AlignIO/largemultifasta.t ......... ok
t/AlignIO/maf.t ..................... ok
t/AlignIO/mase.t .................... ok
t/AlignIO/mega.t .................... ok
t/AlignIO/meme.t .................... ok
t/AlignIO/metafasta.t ............... ok
t/AlignIO/msf.t ..................... ok
t/AlignIO/nexus.t ................... ok
t/AlignIO/pfam.t .................... ok
t/AlignIO/phylip.t .................. ok
t/AlignIO/po.t ...................... ok
t/AlignIO/prodom.t .................. ok
t/AlignIO/psi.t ..................... ok
t/AlignIO/selex.t ................... ok
t/AlignIO/xmfa.t .................... ok
t/Annotation/Annotation.t ........... ok
t/Annotation/AnnotationAdaptor.t .... ok
t/author-mojibake.t ................. skipped: these tests are for testing by the author
t/author-pod-syntax.t ............... skipped: these tests are for testing by the author
Subroutine new redefined at /mnt/cpan_build_dir/goku/BioPerl-1.7.8-0/blib/lib/Bio/DB/IndexedBase.pm line 1121.
Subroutine next_seq redefined at /mnt/cpan_build_dir/goku/BioPerl-1.7.8-0/blib/lib/Bio/DB/IndexedBase.pm line 1130.
Subroutine TIEHANDLE redefined at /mnt/cpan_build_dir/goku/BioPerl-1.7.8-0/blib/lib/Bio/DB/IndexedBase.pm line 1139.
Subroutine READLINE redefined at /mnt/cpan_build_dir/goku/BioPerl-1.7.8-0/blib/lib/Bio/DB/IndexedBase.pm line 1144.
t/LocalDB/Fasta.t ................... ok
t/LocalDB/Flat.t .................... ok
t/LocalDB/Index/Blast.t ............. ok
t/LocalDB/Index/BlastTable.t ........ ok
t/LocalDB/Index/Index.t ............. ok
t/LocalDB/Qual.t .................... ok

--------------------- WARNING ---------------------
MSG: Couldn't load Bio::DB::BioFetch
---------------------------------------------------

--------------------- WARNING ---------------------
MSG: Couldn't load Bio::DB::BioFetch
---------------------------------------------------
t/LocalDB/Registry.t ................ ok
t/LocalDB/Taxonomy/greengenes.t ..... ok
t/LocalDB/Taxonomy/silva.t .......... ok
t/Matrix/InstanceSite.t ............. ok
t/Matrix/IO/masta.t ................. ok
t/Matrix/IO/psm.t ................... ok
t/Matrix/Matrix.t ................... ok
t/Matrix/ProtMatrix.t ............... ok
t/Matrix/ProtPsm.t .................. ok
t/Matrix/SiteMatrix.t ............... ok
t/Ontology/GOterm.t ................. ok
t/Ontology/GraphAdaptor.t ........... ok
t/Ontology/IO/go.t .................. ok
t/Ontology/IO/interpro.t ............ ok
t/Ontology/IO/obo.t ................. ok
t/Ontology/Ontology.t ............... ok
t/Ontology/OntologyEngine.t ......... ok
t/Ontology/OntologyStore.t .......... ok
t/Ontology/Relationship.t ........... ok
t/Ontology/RelationshipType.t ....... ok
t/Ontology/Term.t ................... ok
t/RemoteDB/SeqRead_fail.t ........... ok
t/RemoteDB/Taxonomy.t ............... ok
t/Root/Exception.t .................. ok
t/Root/HTTPget.t .................... ok
t/Root/IO.t ......................... ok
t/Root/RootI.t ...................... ok
t/Root/RootIO.t ..................... ok
t/Root/Storable.t ................... ok
t/Root/Utilities.t .................. ok
t/SearchIO/axt.t .................... ok
t/SearchIO/blast.t .................. ok
t/SearchIO/blast_pull.t ............. ok
t/SearchIO/blasttable.t ............. ok
t/SearchIO/CigarString.t ............ ok
t/SearchIO/cross_match.t ............ ok
t/SearchIO/erpin.t .................. ok
t/SearchIO/exonerate.t .............. ok
t/SearchIO/fasta.t .................. ok
t/SearchIO/gmap_f9.t ................ ok
t/SearchIO/infernal.t ............... ok
t/SearchIO/megablast.t .............. ok
t/SearchIO/psl.t .................... ok
t/SearchIO/rnamotif.t ............... ok
t/SearchIO/SearchIO.t ............... ok
t/SearchIO/sim4.t ................... ok
t/SearchIO/SimilarityPair.t ......... ok
t/SearchIO/Tiling.t ................. ok
t/SearchIO/waba.t ................... ok
t/SearchIO/wise.t ................... ok
t/SearchIO/Writer/GbrowseGFF.t ...... ok
t/SearchIO/Writer/HitTableWriter.t .. ok
t/SearchIO/Writer/HSPTableWriter.t .. ok
t/SearchIO/Writer/HTMLWriter.t ...... ok
t/SearchIO/Writer/TextWriter.t ...... ok
t/Seq/DBLink.t ...................... ok
t/Seq/EncodedSeq.t .................. ok
t/Seq/LargeLocatableSeq.t ........... ok
t/Seq/LargePSeq.t ................... ok
t/Seq/LocatableSeq.t ................ ok
t/Seq/MetaSeq.t ..................... ok
t/Seq/PrimaryQual.t ................. ok
t/Seq/PrimarySeq.t .................. ok
t/Seq/PrimedSeq.t ................... ok
t/Seq/Quality.t ..................... ok
t/Seq/Seq.t ......................... ok
t/Seq/SimulatedRead.t ............... ok
t/SeqFeature/Amplicon.t ............. ok
t/SeqFeature/Clone.t ................ ok
t/SeqFeature/Collection.t ........... ok
t/SeqFeature/Computation.t .......... ok
t/SeqFeature/FeaturePair.t .......... ok
t/SeqFeature/Gene.t ................. ok
t/SeqFeature/Generic.t .............. ok
t/SeqFeature/Location.t ............. ok
t/SeqFeature/LocationFactory.t ...... ok
t/SeqFeature/Primer.t ............... ok
t/SeqFeature/Range.t ................ ok
t/SeqFeature/RangeI.t ............... ok
t/SeqFeature/SeqAnalysisParser.t .... ok
t/SeqFeature/SubSeq.t ............... ok
t/SeqFeature/Unflattener.t .......... ok
t/SeqIO/ace.t ....................... ok
t/SeqIO/asciitree.t ................. ok
t/SeqIO/bsml.t ...................... ok
t/SeqIO/bsml_sax.t .................. ok
t/SeqIO/embl.t ...................... ok
t/SeqIO/fasta.t ..................... ok
t/SeqIO/fastq.t ..................... ok
t/SeqIO/game.t ...................... ok
t/SeqIO/gbxml.t ..................... ok
t/SeqIO/gcg.t ....................... ok
t/SeqIO/genbank.t ................... ok
t/SeqIO/Handler.t ................... ok
t/SeqIO/kegg.t ...................... ok
t/SeqIO/largefasta.t ................ ok
t/SeqIO/locuslink.t ................. ok
t/SeqIO/mbsout.t .................... ok
t/SeqIO/metafasta.t ................. ok
t/SeqIO/msout.t ..................... ok
t/SeqIO/MultiFile.t ................. ok
t/SeqIO/Multiple_fasta.t ............ ok
t/SeqIO/phd.t ....................... ok
t/SeqIO/pir.t ....................... ok
t/SeqIO/qual.t ...................... ok
t/SeqIO/raw.t ....................... ok
t/SeqIO/scf.t ....................... ok
t/SeqIO/SeqBuilder.t ................ ok
t/SeqIO/SeqIO.t ..................... ok
t/SeqIO/seqxml.t .................... ok
t/SeqIO/Splicedseq.t ................ ok
t/SeqIO/swiss.t ..................... ok
t/SeqIO/tab.t ....................... ok
t/SeqIO/table.t ..................... ok
t/SeqIO/tigr.t ...................... ok
t/SeqIO/tigrxml.t ................... ok
t/SeqIO/tinyseq.t ................... ok
t/SeqTools/Backtranslate.t .......... ok
t/SeqTools/CodonTable.t ............. ok
t/SeqTools/ECnumber.t ............... ok
t/SeqTools/GuessSeqFormat.t ......... ok
t/SeqTools/OddCodes.t ............... ok
t/SeqTools/SeqPattern.t ............. ok
t/SeqTools/SeqStats.t ............... ok
t/SeqTools/SeqUtils.t ............... ok
t/SeqTools/SeqWords.t ............... ok
t/Species.t ......................... ok
t/Tools/Alignment/Consed.t .......... ok
t/Tools/AmpliconSearch.t ............ ok
t/Tools/EMBOSS/Palindrome.t ......... ok
t/Tools/ePCR.t ...................... ok
t/Tools/Est2Genome.t ................ ok
t/Tools/FootPrinter.t ............... ok
t/Tools/Geneid.t .................... ok
t/Tools/Genewise.t .................. ok
t/Tools/Genomewise.t ................ ok
t/Tools/Genpred.t ................... ok
t/Tools/GFF.t ....................... ok
t/Tools/IUPAC.t ..................... ok
t/Tools/Lucy.t ...................... ok
t/Tools/Match.t ..................... ok
t/Tools/Phylo/Gerp.t ................ ok
t/Tools/Phylo/Molphy.t .............. ok
t/Tools/Phylo/Phylip/ProtDist.t ..... ok
t/Tools/pICalculator.t .............. ok
t/Tools/Primer3.t ................... ok
t/Tools/Promoterwise.t .............. ok
t/Tools/PrositeScan.t ............... ok
t/Tools/Pseudowise.t ................ ok
t/Tools/QRNA.t ...................... ok
t/Tools/RandDistFunctions.t ......... ok
t/Tools/RepeatMasker.t .............. ok
t/Tools/Seg.t ....................... ok
t/Tools/Sigcleave.t ................. ok
t/Tools/Signalp.t ................... ok
t/Tools/Signalp/ExtendedSignalp.t ... ok
t/Tools/Sim4.t ...................... ok
t/Tools/Spidey/Spidey.t ............. ok
t/Tools/TandemRepeatsFinder.t ....... ok
t/Tools/TargetP.t ................... ok
t/Tools/Tmhmm.t ..................... ok
t/Tools/tRNAscanSE.t ................ ok
t/Tree/Compatible.t ................. ok
t/Tree/Node.t ....................... ok
t/Tree/RandomTreeFactory.t .......... ok
t/Tree/Tree.t ....................... ok
t/Tree/TreeIO.t ..................... ok
t/Tree/TreeIO/lintree.t ............. ok
t/Tree/TreeIO/newick.t .............. ok
t/Tree/TreeIO/nexus.t ............... ok
t/Tree/TreeIO/nhx.t ................. ok
t/Tree/TreeIO/phyloxml.t ............ ok
t/Tree/TreeIO/tabtree.t ............. ok
t/Tree/TreeStatistics.t ............. ok
All tests successful.
Files=211, Tests=14841, 192 wallclock secs ( 2.20 usr  1.17 sys + 141.37 cusr 44.40 csys = 189.14 CPU)
Result: PASS

------------------------------
PREREQUISITES
------------------------------

Prerequisite modules loaded:

requires:

    Module                 Need  Have      
    ---------------------- ----- ----------
    AnyDBM_File            0     1.01      
    base                   0     2.27      
    Carp                   0     1.50      
    constant               0     1.33      
    Cwd                    0     3.78      
    Data::Dumper           0     2.183     
    Data::Stag             0     0.14      
    DB_File                0     1.857     
    Digest::MD5            0     2.58      
    Dumpvalue              0     1.21      
    Error                  0     0.17029   
    Exporter               0     5.74      
    Fcntl                  0     1.13      
    File::Basename         0     2.85      
    File::Copy             0     2.34      
    File::Path             0     2.18      
    File::Spec             0     3.78      
    File::Spec::Functions  0     3.78      
    File::Temp             0     0.2311    
    FileHandle             0     2.03      
    Getopt::Long           0     2.52      
    Graph::Directed        0     0         
    HTTP::Request::Common  0     6.36      
    HTTP::Response         0     6.36      
    integer                0     1.01      
    IO::File               0     1.48      
    IO::Handle             0     1.48      
    IO::Pipe               0     1.49      
    IO::Scalar             0     2.113     
    IO::Socket             0     1.49      
    IO::String             0     1.08      
    IPC::Run               0     20200505.0
    List::MoreUtils        0     0.430     
    List::Util             0     1.62      
    LWP::UserAgent         0     6.64      
    Math::BigFloat         0     1.999830  
    Module::Build          0     0.4231    
    overload               0     1.31      
    parent                 0     0.238     
    perl                   5.006 5.032001  
    Pod::Usage             0     2.01      
    POSIX                  0     1.94      
    Scalar::Util           0     1.62      
    Set::Scalar            0     1.29      
    Storable               0     3.25      
    strict                 0     1.11      
    Symbol                 0     1.08      
    Test::Builder          0     1.302190  
    Test::Builder::Module  0     1.302190  
    Test::Most             0     0.37      
    Test::RequiresInternet 0     0.05      
    Text::Balanced         0     2.04_02   
    Text::Wrap             0     2021.0814 
    Tie::Handle            0     4.2       
    Tie::RefHash           0     1.40      
    Time::HiRes            0     1.9764_02 
    UNIVERSAL              0     1.13      
    URI                    0     5.10      
    utf8                   0     1.22      
    vars                   0     1.05      
    version                0     0.9929    
    warnings               0     1.47      
    XML::DOM               0     1.46      
    XML::LibXML            0     2.0207    
    XML::LibXML::Reader    0     2.0207    
    XML::Parser::PerlSAX   0     0.08      
    XML::SAX               0     1.02      
    XML::SAX::Base         0     1.09      
    XML::SAX::Writer       0     0.57      
    XML::Twig              0     3.52      
    XML::Writer            0     0.900     
    YAML                   0     1.30      

build_requires:

    Module                 Need  Have      
    ---------------------- ----- ----------
    ExtUtils::MakeMaker    0     7.64      
    File::Spec             0     3.78      
    FindBin                0     1.52      
    IO::Handle             0     1.48      
    IPC::Open3             0     1.21      
    lib                    0     0.65      
    Test::Memory::Cycle    0     1.06      
    Test::More             0     1.302190  
    Test::Weaken           0     3.022000  

configure_requires:

    Module                 Need  Have      
    ---------------------- ----- ----------
    ExtUtils::MakeMaker    0     7.64      


------------------------------
ENVIRONMENT AND OTHER CONTEXT
------------------------------

Environment variables:

    AUTOMATED_TESTING = 1
    PATH = /home/goku/perl5/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/X11R6/bin:/usr/local/bin:/usr/local/sbin
    PERL5LIB = /home/goku/perl5/lib/perl5
    PERL5OPT = 
    PERL5_CPANPLUS_IS_RUNNING = 14236
    PERL5_CPAN_IS_RUNNING = 14236
    PERL5_CPAN_IS_RUNNING_IN_RECURSION = 64178,14236
    PERL_CR_SMOKER_CURRENT = Bio-DB-NCBIHelper-1.7.7
    PERL_EXTUTILS_AUTOINSTALL = --defaultdeps
    PERL_LOCAL_LIB_ROOT = /home/goku/perl5
    PERL_MB_OPT = --install_base "/home/goku/perl5"
    PERL_MM_OPT = INSTALL_BASE=/home/goku/perl5
    PERL_MM_USE_DEFAULT = 1
    PERL_USE_UNSAFE_INC = 1
    SHELL = /bin/ksh
    TERM = xterm-256color

Perl special variables (and OS-specific diagnostics, for MSWin32):

    $^X = /usr/bin/perl
    $UID/$EUID = 1001 / 1001
    $GID = 1002 1002 1001
    $EGID = 1002 1002 1001

Perl module toolchain versions installed:

    Module              Have    
    ------------------- --------
    CPAN                2.33    
    CPAN::Meta          2.150010
    Cwd                 3.78    
    ExtUtils::CBuilder  0.280236
    ExtUtils::Command   7.64    
    ExtUtils::Install   2.20    
    ExtUtils::MakeMaker 7.64    
    ExtUtils::Manifest  1.73    
    ExtUtils::ParseXS   3.44    
    File::Spec          3.78    
    JSON                4.05    
    JSON::PP            4.08    
    Module::Build       0.4231  
    Module::Signature   0.88    
    Parse::CPAN::Meta   2.150010
    Test::Harness       3.44    
    Test::More          1.302190
    YAML                1.30    
    YAML::Syck          1.34    
    version             0.9929  


--

Summary of my perl5 (revision 5 version 32 subversion 1) configuration:
   
  Platform:
    osname=openbsd
    osvers=7.0
    archname=amd64-openbsd
    uname='openbsd'
    config_args='-dse -Dopenbsd_distribution=defined -Dmksymlinks'
    hint=recommended
    useposix=true
    d_sigaction=define
    useithreads=undef
    usemultiplicity=undef
    use64bitint=define
    use64bitall=define
    uselongdouble=undef
    usemymalloc=n
    default_inc_excludes_dot=define
    bincompat5005=undef
  Compiler:
    cc='cc'
    ccflags ='-DNO_LOCALE_NUMERIC -DNO_LOCALE_COLLATE -fno-strict-aliasing -fno-delete-null-pointer-checks -pipe -fstack-protector-strong -I/usr/local/include'
    optimize='-O2'
    cppflags='-DBIG_TIME -DNO_LOCALE_NUMERIC -DNO_LOCALE_COLLATE -fno-strict-aliasing -fno-delete-null-pointer-checks -pipe -fstack-protector-strong -I/usr/local/include'
    ccversion=''
    gccversion='OpenBSD Clang 11.1.0'
    gccosandvers=''
    intsize=4
    longsize=8
    ptrsize=8
    doublesize=8
    byteorder=12345678
    doublekind=3
    d_longlong=define
    longlongsize=8
    d_longdbl=define
    longdblsize=16
    longdblkind=3
    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,-E  -fstack-protector-strong -L/usr/local/lib'
    libpth=/usr/lib /usr/local/lib
    libs=-lm -lc
    perllibs=-lm -lc
    libc=/usr/lib/libc.so.96.1
    so=so
    useshrplib=true
    libperl=libperl.so.22.0
    gnulibc_version=''
  Dynamic Linking:
    dlsrc=dl_dlopen.xs
    dlext=so
    d_dlsymun=undef
    ccdlflags='-Wl,-R/usr/libdata/perl5/amd64-openbsd/CORE'
    cccdlflags='-DPIC -fpic '
    lddlflags='-shared -fpic  -fstack-protector-strong -L/usr/local/lib'


Characteristics of this binary (from libperl): 
  Compile-time options:
    HAS_TIMES
    PERLIO_LAYERS
    PERL_COPY_ON_WRITE
    PERL_DONT_CREATE_GVSV
    PERL_MALLOC_WRAP
    PERL_OP_PARENT
    PERL_PRESERVE_IVUV
    USE_64_BIT_ALL
    USE_64_BIT_INT
    USE_LARGE_FILES
    USE_LOCALE
    USE_LOCALE_CTYPE
    USE_LOCALE_TIME
    USE_PERLIO
    USE_PERL_ATOF
  Built under openbsd
  %ENV:
    PERL5LIB="/home/goku/perl5/lib/perl5"
    PERL5OPT=""
    PERL5_CPANPLUS_IS_RUNNING="14236"
    PERL5_CPAN_IS_RUNNING="14236"
    PERL5_CPAN_IS_RUNNING_IN_RECURSION="64178,14236"
    PERL_CR_SMOKER_CURRENT="Bio-DB-NCBIHelper-1.7.7"
    PERL_EXTUTILS_AUTOINSTALL="--defaultdeps"
    PERL_LOCAL_LIB_ROOT="/home/goku/perl5"
    PERL_MB_OPT="--install_base "/home/goku/perl5""
    PERL_MM_OPT="INSTALL_BASE=/home/goku/perl5"
    PERL_MM_USE_DEFAULT="1"
    PERL_USE_UNSAFE_INC="1"
  @INC:
    /home/goku/perl5/lib/perl5/5.32.1/amd64-openbsd
    /home/goku/perl5/lib/perl5/5.32.1
    /home/goku/perl5/lib/perl5/amd64-openbsd
    /home/goku/perl5/lib/perl5
    /usr/local/libdata/perl5/site_perl/amd64-openbsd
    /usr/local/libdata/perl5/site_perl
    /usr/libdata/perl5/amd64-openbsd
    /usr/libdata/perl5
    .