BioPerl v1.7.8 Perl 5 v5.37.3 x86_64-linux-thread-multi
- Status
- Pass
- From
- Andreas J. König (ANDK)
- Dist
-
BioPerl v1.7.8
- Platform
- Perl 5 v5.37.3 x86_64-linux-thread-multi
- Date
- 2022-09-19T00:21:36
- ID
- 061dc238-37b1-11ed-87e9-119f2e66c2cc
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 5.37.3, 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 "/tmp/basesmoker-reloperl-XsdS/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 /tmp/loop_over_bdir-955171-ImLVhl/BioPerl-1.7.8-0/blib/lib/Bio/DB/IndexedBase.pm line 1121.
Subroutine next_seq redefined at /tmp/loop_over_bdir-955171-ImLVhl/BioPerl-1.7.8-0/blib/lib/Bio/DB/IndexedBase.pm line 1130.
Subroutine TIEHANDLE redefined at /tmp/loop_over_bdir-955171-ImLVhl/BioPerl-1.7.8-0/blib/lib/Bio/DB/IndexedBase.pm line 1139.
Subroutine READLINE redefined at /tmp/loop_over_bdir-955171-ImLVhl/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
--------------------- WARNING ---------------------
MSG: find_exe: Multiple paths to 'gzip' found. Using /usr/bin/gzip.
---------------------------------------------------
--------------------- WARNING ---------------------
MSG: find_exe: Multiple paths to 'gzip' found. Using /usr/bin/gzip.
---------------------------------------------------
--------------------- WARNING ---------------------
MSG: find_exe: Multiple paths to 'gunzip' found. Using /usr/bin/gunzip.
---------------------------------------------------
--------------------- WARNING ---------------------
MSG: find_exe: Multiple paths to 'gzip' found. Using /usr/bin/gzip.
---------------------------------------------------
--------------------- WARNING ---------------------
MSG: find_exe: Multiple paths to 'gunzip' found. Using /usr/bin/gunzip.
---------------------------------------------------
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, 106 wallclock secs ( 1.73 usr 0.30 sys + 92.25 cusr 9.63 csys = 103.91 CPU)
Result: PASS
------------------------------
PREREQUISITES
------------------------------
Prerequisite modules loaded:
requires:
Module Need Have
---------------------- ----- ----------
AnyDBM_File 0 1.01
base 0 2.27
Carp 0 1.53
constant 0 1.33
Cwd 0 3.86
Data::Dumper 0 2.186
Data::Stag 0 0.14
DB_File 0 1.858
Digest::MD5 0 2.58
Dumpvalue 0 1.21
Error 0 0.17029
Exporter 0 5.77
Fcntl 0 1.15
File::Basename 0 2.85
File::Copy 0 2.39
File::Path 0 2.18
File::Spec 0 3.86
File::Spec::Functions 0 3.86
File::Temp 0 0.2311
FileHandle 0 2.04
Getopt::Long 0 2.52
Graph::Directed 0 0
HTTP::Request::Common 0 6.37
HTTP::Response 0 6.37
integer 0 1.01
IO::File 0 1.48
IO::Handle 0 1.49
IO::Pipe 0 1.50
IO::Scalar 0 2.113
IO::Socket 0 1.49
IO::String 0 1.08
IPC::Run 0 20220807.0
List::MoreUtils 0 0.430
List::Util 0 1.63
LWP::UserAgent 0 6.67
Math::BigFloat 0 1.999837
Module::Build 0 0.4231
overload 0 1.35
parent 0 0.238
perl 5.006 5.037003
Pod::Usage 0 2.03
POSIX 0 2.04
Scalar::Util 0 1.63
Set::Scalar 0 1.29
Storable 0 3.27
strict 0 1.12
Symbol 0 1.09
Test::Builder 0 1.302191
Test::Builder::Module 0 1.302191
Test::Most 0 0.37
Test::RequiresInternet 0 0.05
Text::Balanced 0 2.06
Text::Wrap 0 2021.0814
Tie::Handle 0 4.3
Tie::RefHash 0 1.40
Time::HiRes 0 1.9770
UNIVERSAL 0 1.14
URI 0 5.12
utf8 0 1.24
vars 0 1.05
version 0 0.9929
warnings 0 1.58
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 3.86
FindBin 0 1.53
IO::Handle 0 1.49
IPC::Open3 0 1.22
lib 0 0.65
Test::Memory::Cycle 0 1.06
Test::More 0 1.302191
! Test::Weaken 0 n/a
configure_requires:
Module Need Have
---------------------- ----- ----------
ExtUtils::MakeMaker 0 7.64
------------------------------
ENVIRONMENT AND OTHER CONTEXT
------------------------------
Environment variables:
AUTOMATED_TESTING = 1
LANG = en_US.UTF-8
PATH = /home/sand/bin:/usr/local/bin:/usr/local/sbin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/usr/local/perl/bin:/usr/X11/bin
PERL5LIB = /tmp/loop_over_bdir-955171-ImLVhl/Devel-Required-0.16-0/blib/arch:/tmp/loop_over_bdir-955171-ImLVhl/Devel-Required-0.16-0/blib/lib
PERL5OPT =
PERL5_CPANPLUS_IS_RUNNING = 955179
PERL5_CPAN_IS_RUNNING = 955179
PERL_CANARY_STABILITY_NOPROMPT = 1
PERL_MM_USE_DEFAULT = 1
PERL_USE_UNSAFE_INC = 1
SHELL = /usr/bin/zsh
TERM = screen
Perl special variables (and OS-specific diagnostics, for MSWin32):
$^X = /tmp/basesmoker-reloperl-XsdS/bin/perl
$UID/$EUID = 1005 / 1005
$GID = 1005 1005
$EGID = 1005 1005
Perl module toolchain versions installed:
Module Have
------------------- --------
CPAN 2.34
CPAN::Meta 2.150010
Cwd 3.86
ExtUtils::CBuilder 0.280237
ExtUtils::Command 7.64
ExtUtils::Install 2.20
ExtUtils::MakeMaker 7.64
ExtUtils::Manifest 1.73
ExtUtils::ParseXS 3.45
File::Spec 3.86
JSON 4.09
JSON::PP 4.11
Module::Build 0.4231
Module::Signature 0.88
Parse::CPAN::Meta 2.150010
Test::Harness 3.44
Test::More 1.302191
YAML 1.30
YAML::Syck 1.34
version 0.9929
--
Summary of my perl5 (revision 5 version 37 subversion 3) configuration:
Commit id: 29b290ccaa79f40de7d941c9a79810119f5c6363
Platform:
osname=linux
osvers=5.4.0-125-generic
archname=x86_64-linux-thread-multi
uname='linux k93focal 5.4.0-125-generic #141-ubuntu smp wed aug 10 13:42:03 utc 2022 x86_64 x86_64 x86_64 gnulinux '
config_args='-Dprefix=/home/sand/src/perl/repoperls/installed-perls/host/k93focal/v5.37.2-224-g29b290ccaa/d119 -Dmyhostname=k93focal -Dinstallusrbinperl=n -Uversiononly -Dusedevel -des -Ui_db -Dlibswanted=cl pthread socket inet nsl gdbm dbm malloc dl ld sun m crypt sec util c cposix posix ucb BSD gdbm_compat -Duseithreads -Uuselongdouble -DEBUGGING=both'
hint=recommended
useposix=true
d_sigaction=define
useithreads=define
usemultiplicity=define
use64bitint=define
use64bitall=define
uselongdouble=undef
usemymalloc=n
default_inc_excludes_dot=define
Compiler:
cc='cc'
ccflags ='-D_REENTRANT -D_GNU_SOURCE -fwrapv -DDEBUGGING -fno-strict-aliasing -pipe -fstack-protector-strong -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64'
optimize='-O2 -g'
cppflags='-D_REENTRANT -D_GNU_SOURCE -fwrapv -DDEBUGGING -fno-strict-aliasing -pipe -fstack-protector-strong -I/usr/local/include'
ccversion=''
gccversion='9.4.0'
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 =' -fstack-protector-strong -L/usr/local/lib'
libpth=/usr/local/lib /usr/lib/x86_64-linux-gnu /usr/lib /usr/lib64
libs=-lpthread -lnsl -ldl -lm -lcrypt -lutil -lc
perllibs=-lpthread -lnsl -ldl -lm -lcrypt -lutil -lc
libc=libc-2.31.so
so=so
useshrplib=false
libperl=libperl.a
gnulibc_version='2.31'
Dynamic Linking:
dlsrc=dl_dlopen.xs
dlext=so
d_dlsymun=undef
ccdlflags='-Wl,-E'
cccdlflags='-fPIC'
lddlflags='-shared -O2 -g -L/usr/local/lib -fstack-protector-strong'
Characteristics of this binary (from libperl):
Compile-time options:
DEBUGGING
HAS_TIMES
MULTIPLICITY
PERLIO_LAYERS
PERL_COPY_ON_WRITE
PERL_DONT_CREATE_GVSV
PERL_HASH_FUNC_SIPHASH13
PERL_HASH_USE_SBOX32
PERL_MALLOC_WRAP
PERL_OP_PARENT
PERL_PRESERVE_IVUV
PERL_TRACK_MEMPOOL
PERL_USE_DEVEL
PERL_USE_SAFE_PUTENV
USE_64_BIT_ALL
USE_64_BIT_INT
USE_ITHREADS
USE_LARGE_FILES
USE_LOCALE
USE_LOCALE_COLLATE
USE_LOCALE_CTYPE
USE_LOCALE_NUMERIC
USE_LOCALE_TIME
USE_PERLIO
USE_PERL_ATOF
USE_REENTRANT_API
USE_THREAD_SAFE_LOCALE
Built under linux
Compiled at Sep 17 2022 07:57:23
%ENV:
PERL5LIB="/tmp/loop_over_bdir-955171-ImLVhl/Devel-Required-0.16-0/blib/arch:/tmp/loop_over_bdir-955171-ImLVhl/Devel-Required-0.16-0/blib/lib"
PERL5OPT=""
PERL5_CPANPLUS_IS_RUNNING="955179"
PERL5_CPAN_IS_RUNNING="955179"
PERL_CANARY_STABILITY_NOPROMPT="1"
PERL_MM_USE_DEFAULT="1"
PERL_USE_UNSAFE_INC="1"
@INC:
/tmp/loop_over_bdir-955171-ImLVhl/Devel-Required-0.16-0/blib/arch
/tmp/loop_over_bdir-955171-ImLVhl/Devel-Required-0.16-0/blib/lib
/home/sand/src/perl/repoperls/installed-perls/host/k93focal/v5.37.2-224-g29b290ccaa/d119/lib/site_perl/5.37.3/x86_64-linux-thread-multi
/home/sand/src/perl/repoperls/installed-perls/host/k93focal/v5.37.2-224-g29b290ccaa/d119/lib/site_perl/5.37.3
/home/sand/src/perl/repoperls/installed-perls/host/k93focal/v5.37.2-224-g29b290ccaa/d119/lib/5.37.3/x86_64-linux-thread-multi
/home/sand/src/perl/repoperls/installed-perls/host/k93focal/v5.37.2-224-g29b290ccaa/d119/lib/5.37.3
.