BioPerl v1.7.8 Perl 5 v5.14.4 MSWin32-x64-multi-thread
- Status
- Pass
- From
- LNATION
- Dist
-
BioPerl v1.7.8
- Platform
- Perl 5 v5.14.4 MSWin32-x64-multi-thread
- Date
- 2025-05-19 08:58:40
- ID
- 78f45dda-6ed0-1014-9b9f-d047e16f9b49
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 5.14.4, created by CPAN-Reporter-1.2020.
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 'C:\strawberry\c\bin\dmake.exe test':
"C:\strawberry\perl\bin\perl.exe" "-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 C:\strawberry\cpan\build\BioPerl-1.7.8-gH7syU\blib\lib/Bio/DB/IndexedBase.pm line 1121.
Subroutine next_seq redefined at C:\strawberry\cpan\build\BioPerl-1.7.8-gH7syU\blib\lib/Bio/DB/IndexedBase.pm line 1130.
Subroutine TIEHANDLE redefined at C:\strawberry\cpan\build\BioPerl-1.7.8-gH7syU\blib\lib/Bio/DB/IndexedBase.pm line 1139.
Subroutine READLINE redefined at C:\strawberry\cpan\build\BioPerl-1.7.8-gH7syU\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
Subroutine _initialize redefined at C:\strawberry\cpan\build\BioPerl-1.7.8-gH7syU\blib\lib/Bio\SeqIO\fasta.pm line 86.
Subroutine next_seq redefined at C:\strawberry\cpan\build\BioPerl-1.7.8-gH7syU\blib\lib/Bio\SeqIO\fasta.pm line 120.
Subroutine next_seq_fast redefined at C:\strawberry\cpan\build\BioPerl-1.7.8-gH7syU\blib\lib/Bio\SeqIO\fasta.pm line 200.
Subroutine write_seq redefined at C:\strawberry\cpan\build\BioPerl-1.7.8-gH7syU\blib\lib/Bio\SeqIO\fasta.pm line 264.
Subroutine width redefined at C:\strawberry\cpan\build\BioPerl-1.7.8-gH7syU\blib\lib/Bio\SeqIO\fasta.pm line 354.
Subroutine block redefined at C:\strawberry\cpan\build\BioPerl-1.7.8-gH7syU\blib\lib/Bio\SeqIO\fasta.pm line 375.
Subroutine preferred_id_type redefined at C:\strawberry\cpan\build\BioPerl-1.7.8-gH7syU\blib\lib/Bio\SeqIO\fasta.pm line 400.
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.
Test Summary Report
-------------------
t/Root/IO.t (Wstat: 0 Tests: 154 Failed: 0)
TODO passed: 109, 112, 115, 118
Files=211, Tests=14841, 258 wallclock secs ( 2.64 usr + 0.67 sys = 3.31 CPU)
Result: PASS
------------------------------
PREREQUISITES
------------------------------
Prerequisite modules loaded:
requires:
Module Need Have
---------------------- ----- ---------
AnyDBM_File 0 1.00
base 0 2.18
Carp 0 1.50
constant 0 1.33
Cwd 0 3.75
Data::Dumper 0 2.143
Data::Stag 0 0.14
DB_File 0 1.827
Digest::MD5 0 2.59
Dumpvalue 0 1.17
Error 0 0.17030
Exporter 0 5.78
Fcntl 0 1.11
File::Basename 0 2.82
File::Copy 0 2.21
File::Path 0 2.09
File::Spec 0 3.75
File::Spec::Functions 0 3.75
File::Temp 0 0.2311
FileHandle 0 2.02
Getopt::Long 0 2.58
Graph::Directed 0 0
HTTP::Request::Common 0 7.00
HTTP::Response 0 7.00
integer 0 1.00
IO::File 0 1.15
IO::Handle 0 1.31
IO::Pipe 0 1.14
IO::Scalar 0 2.113
IO::Socket 0 1.32
IO::String 0 1.08
IPC::Run 0 0.92
List::MoreUtils 0 0.430
List::Util 0 1.69
LWP::UserAgent 0 6.04
Math::BigFloat 0 2.005003
Module::Build 0 0.4234
overload 0 1.13
parent 0 0.225
perl 5.006 5.014004
Pod::Usage 0 1.61
POSIX 0 1.24
Scalar::Util 0 1.69
Set::Scalar 0 1.29
Storable 0 3.25
strict 0 1.04
Symbol 0 1.07
Test::Builder 0 1.302213
Test::Builder::Module 0 1.302213
Test::Most 0 0.38
Test::RequiresInternet 0 0.05
Text::Balanced 0 2.02
Text::Wrap 0 2012.0818
Tie::Handle 0 4.2
Tie::RefHash 0 1.39
Time::HiRes 0 1.9764
UNIVERSAL 0 1.08
URI 0 5.32
utf8 0 1.09
vars 0 1.02
version 0 0.9933
warnings 0 1.12
Win32 0 0.47
XML::DOM 0 1.46
XML::LibXML 0 2.0014
XML::LibXML::Reader 0 2.0014
XML::Parser::PerlSAX 0 0.08
XML::SAX 0 0.99
XML::SAX::Base 0 1.08
XML::SAX::Writer 0 0.57
XML::Twig 0 3.53
XML::Writer 0 0.900
YAML 0 1.31
build_requires:
Module Need Have
---------------------- ----- ---------
ExtUtils::MakeMaker 0 7.74
File::Spec 0 3.75
FindBin 0 1.50
IO::Handle 0 1.31
IPC::Open3 0 1.0901
lib 0 0.63
Test::Memory::Cycle 0 1.06
Test::More 0 1.302213
Test::Weaken 0 3.022000
configure_requires:
Module Need Have
---------------------- ----- ---------
ExtUtils::MakeMaker 0 7.74
------------------------------
ENVIRONMENT AND OTHER CONTEXT
------------------------------
Environment variables:
AUTOMATED_TESTING = 1
COMSPEC = C:\Windows\system32\cmd.exe
NUMBER_OF_PROCESSORS = 2
PATH = C:\Windows\system32;C:\Windows;C:\Windows\System32\Wbem;C:\Windows\System32\WindowsPowerShell\v1.0\;C:\Windows\System32\OpenSSH\;C:\Program Files\Amazon\cfn-bootstrap\;C:\strawberry\c\bin;C:\strawberry\perl\site\bin;C:\strawberry\perl\bin;C:\Users\Administrator\AppData\Local\Microsoft\WindowsApps;C:\Users\Administrator\AppData\Local\Microsoft\WinGet\Links;
PERL5LIB =
PERL5OPT =
PERL5_CPANPLUS_IS_RUNNING = 8856
PERL5_CPAN_IS_RUNNING = 8856
PERL5_CPAN_IS_RUNNING_IN_RECURSION = 10804,8856
PERL_CR_SMOKER_CURRENT = Bio-Community-0.001008
PERL_EXTUTILS_AUTOINSTALL = --defaultdeps
PERL_MM_USE_DEFAULT = 1
PROCESSOR_IDENTIFIER = Intel64 Family 6 Model 85 Stepping 7, GenuineIntel
TEMP = C:\Users\ADMINI~1\AppData\Local\Temp\2
TERM = dumb
Perl special variables (and OS-specific diagnostics, for MSWin32):
$^X = C:\strawberry\perl\bin\perl.exe
$UID/$EUID = 0 / 0
$GID = 0
$EGID = 0
Win32::GetOSName = Win2012
Win32::GetOSVersion = , 6, 2, 9200, 2, 0, 0, 400, 3
Win32::FsType = NTFS
Win32::IsAdminUser = 1
Perl module toolchain versions installed:
Module Have
------------------- --------
CPAN 1.9800
CPAN::Meta 2.150010
Cwd 3.75
ExtUtils::CBuilder 0.280236
ExtUtils::Command 7.74
ExtUtils::Install 2.06
ExtUtils::MakeMaker 7.74
ExtUtils::Manifest 1.75
ExtUtils::ParseXS 3.57
File::Spec 3.75
JSON 4.10
JSON::PP 4.16
Module::Build 0.4234
Module::Signature n/a
Parse::CPAN::Meta 2.150010
Test2 1.302213
Test::Harness 3.52
Test::More 1.302213
YAML 1.31
YAML::Syck 1.23
version 0.9933
--
Summary of my perl5 (revision 5 version 14 subversion 4) configuration:
Platform:
osname=MSWin32, osvers=4.0, archname=MSWin32-x64-multi-thread
uname='Win32 strawberry-perl 5.14.4.1 #1 Mon Mar 11 18:06:54 2013 x64'
config_args='undef'
hint=recommended, useposix=true, d_sigaction=undef
useithreads=define, usemultiplicity=define
useperlio=define, d_sfio=undef, uselargefiles=define, usesocks=undef
use64bitint=define, use64bitall=undef, uselongdouble=undef
usemymalloc=n, bincompat5005=undef
Compiler:
cc='gcc', ccflags =' -s -O2 -DWIN32 -DWIN64 -DCONSERVATIVE -DPERL_TEXTMODE_SCRIPTS -DPERL_IMPLICIT_CONTEXT -DPERL_IMPLICIT_SYS -fno-strict-aliasing -mms-bitfields',
optimize='-s -O2',
cppflags='-DWIN32'
ccversion='', gccversion='4.6.3', gccosandvers=''
intsize=4, longsize=4, ptrsize=8, doublesize=8, byteorder=12345678
d_longlong=define, longlongsize=8, d_longdbl=define, longdblsize=12
ivtype='long long', ivsize=8, nvtype='double', nvsize=8, Off_t='long long', lseeksize=8
alignbytes=8, prototype=define
Linker and Libraries:
ld='g++', ldflags ='-s -L"C:\strawberry\perl\lib\CORE" -L"C:\strawberry\c\lib"'
libpth=C:\strawberry\c\lib C:\strawberry\c\x86_64-w64-mingw32\lib
libs=-lmoldname -lkernel32 -luser32 -lgdi32 -lwinspool -lcomdlg32 -ladvapi32 -lshell32 -lole32 -loleaut32 -lnetapi32 -luuid -lws2_32 -lmpr -lwinmm -lversion -lodbc32 -lodbccp32 -lcomctl32
perllibs=-lmoldname -lkernel32 -luser32 -lgdi32 -lwinspool -lcomdlg32 -ladvapi32 -lshell32 -lole32 -loleaut32 -lnetapi32 -luuid -lws2_32 -lmpr -lwinmm -lversion -lodbc32 -lodbccp32 -lcomctl32
libc=, so=dll, useshrplib=true, libperl=libperl514.a
gnulibc_version=''
Dynamic Linking:
dlsrc=dl_win32.xs, dlext=dll, d_dlsymun=undef, ccdlflags=' '
cccdlflags=' ', lddlflags='-mdll -s -L"C:\strawberry\perl\lib\CORE" -L"C:\strawberry\c\lib"'
Characteristics of this binary (from libperl):
Compile-time options: MULTIPLICITY PERL_DONT_CREATE_GVSV
PERL_IMPLICIT_CONTEXT PERL_IMPLICIT_SYS
PERL_MALLOC_WRAP PERL_PRESERVE_IVUV PL_OP_SLAB_ALLOC
USE_64_BIT_INT USE_ITHREADS USE_LARGE_FILES
USE_PERLIO USE_PERL_ATOF
Built under MSWin32
Compiled at Mar 11 2013 18:11:21
%ENV:
PERL5_CPANPLUS_IS_RUNNING="8856"
PERL5_CPAN_IS_RUNNING="8856"
PERL5_CPAN_IS_RUNNING_IN_RECURSION="10804,8856"
PERL_CR_SMOKER_CURRENT="Bio-Community-0.001008"
PERL_EXTUTILS_AUTOINSTALL="--defaultdeps"
PERL_MM_USE_DEFAULT="1"
@INC:
C:/strawberry/perl/site/lib
C:/strawberry/perl/vendor/lib
C:/strawberry/perl/lib
.