BioPerl v1.7.8 Perl 5 v5.24.4 x86_64-linux-thread-multi
- Status
- Pass
- From
- David Cantrell (DCANTRELL)
- Dist
-
BioPerl v1.7.8
- Platform
- Perl 5 v5.24.4 x86_64-linux-thread-multi
- Date
- 2022-07-03 02:12:56
- ID
- a732f25c-fa75-11ec-a1c6-9a9eb13da39e
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 5.24.4, 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 "/home/david/cpantesting/perl-5.24.4/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
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, 977 wallclock secs ( 3.73 usr 0.81 sys + 167.52 cusr 18.06 csys = 190.12 CPU)
Result: PASS
------------------------------
PREREQUISITES
------------------------------
Prerequisite modules loaded:
requires:
Module Need Have
---------------------- ----- ----------
AnyDBM_File 0 1.01
base 0 2.23_01
Carp 0 1.40
constant 0 1.33
Cwd 0 3.63_01
Data::Dumper 0 2.160
Data::Stag 0 0.14
DB_File 0 1.835
Digest::MD5 0 2.54
Dumpvalue 0 1.18
Error 0 0.17029
Exporter 0 5.74
Fcntl 0 1.13
File::Basename 0 2.85
File::Copy 0 2.31
File::Path 0 2.12_01
File::Spec 0 3.63_01
File::Spec::Functions 0 3.63_01
File::Temp 0 0.2304
FileHandle 0 2.02
Getopt::Long 0 2.48
Graph::Directed 0 0
HTTP::Request::Common 0 6.37
HTTP::Response 0 6.37
integer 0 1.01
IO::File 0 1.16
IO::Handle 0 1.36
IO::Pipe 0 1.15
IO::Scalar 0 2.113
IO::Socket 0 1.38
IO::String 0 1.08
IPC::Run 0 20200505.0
List::MoreUtils 0 0.430
List::Util 0 1.62
LWP::UserAgent 0 6.67
Math::BigFloat 0 1.999715
Module::Build 0 0.4231
overload 0 1.26
parent 0 0.234
perl 5.006 5.024004
Pod::Usage 0 2.03
POSIX 0 1.65_01
Scalar::Util 0 1.62
Set::Scalar 0 1.29
Storable 0 3.25
strict 0 1.11
Symbol 0 1.07
Test::Builder 0 1.302190
Test::Builder::Module 0 1.302190
Test::Most 0 0.37
Test::RequiresInternet 0 0.05
Text::Balanced 0 2.03
Text::Wrap 0 2013.0523
Tie::Handle 0 4.2
Tie::RefHash 0 1.39
Time::HiRes 0 1.9741
UNIVERSAL 0 1.13
URI 0 5.10
utf8 0 1.19
vars 0 1.03
version 0 0.9916
warnings 0 1.36
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 3.63_01
FindBin 0 1.51
IO::Handle 0 1.36
IPC::Open3 0 1.20
lib 0 0.63
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
LANG = en_GB.UTF-8
LANGUAGE = en_GB:en
LC_TERMINAL = iTerm2
LC_TERMINAL_VERSION = 3.4.14
NONINTERACTIVE_TESTING = 1
PATH = /home/david/perl5/perlbrew/bin:/home/david/perl5/perlbrew/perls/perl-5.30.2/bin:/home/david/bin:/usr/local/bin:/usr/bin:/bin:/usr/local/games:/usr/games
PERL = 5.24.4
PERL5LIB =
PERL5OPT =
PERL5_CPANPLUS_IS_RUNNING = 1286146
PERL5_CPAN_IS_RUNNING = 1286146
PERLBREW_HOME = /home/david/.perlbrew
PERLBREW_MANPATH = /home/david/perl5/perlbrew/perls/perl-5.30.2/man
PERLBREW_PATH = /home/david/perl5/perlbrew/bin:/home/david/perl5/perlbrew/perls/perl-5.30.2/bin
PERLBREW_PERL = perl-5.30.2
PERLBREW_ROOT = /home/david/perl5/perlbrew
PERLBREW_SHELLRC_VERSION = 0.89
PERLBREW_VERSION = 0.89
PERLVER = 5.24.4
PERL_INLINE_DIRECTORY = /home/david/.Inline-5.24.4
PERL_MM_USE_DEFAULT = 1
PERL_USE_UNSAFE_INC = 0
SHELL = /bin/bash
TERM = screen
Perl special variables (and OS-specific diagnostics, for MSWin32):
$^X = /home/david/cpantesting/perl-5.24.4/bin/perl
$UID/$EUID = 1000 / 1000
$GID = 1000 24 25 27 29 30 44 46 109 1000
$EGID = 1000 24 25 27 29 30 44 46 109 1000
Perl module toolchain versions installed:
Module Have
------------------- ----------
CPAN 2.11_01
CPAN::Meta 2.150005
Cwd 3.63_01
ExtUtils::CBuilder 0.280225
ExtUtils::Command 7.64
ExtUtils::Install 2.06
ExtUtils::MakeMaker 7.64
ExtUtils::Manifest 1.70
ExtUtils::ParseXS 3.31
File::Spec 3.63_01
JSON 4.07
JSON::PP 4.10
Module::Build 0.4231
Module::Signature n/a
Parse::CPAN::Meta 1.4417_001
Test::Harness 3.36_01
Test::More 1.302190
YAML 1.30
YAML::Syck n/a
version 0.9916
--
Summary of my perl5 (revision 5 version 24 subversion 4) configuration:
Platform:
osname=linux, osvers=5.10.0-11-amd64, archname=x86_64-linux-thread-multi
uname='linux cpantesting-linux-utm 5.10.0-11-amd64 #1 smp debian 5.10.92-1 (2022-01-18) x86_64 gnulinux '
config_args='-de -Dusethreads -Dprefix=/home/david/cpantesting/perl-5.24.4'
hint=recommended, useposix=true, d_sigaction=define
useithreads=define, usemultiplicity=define
use64bitint=define, use64bitall=define, uselongdouble=undef
usemymalloc=n, bincompat5005=undef
Compiler:
cc='cc', ccflags ='-D_REENTRANT -D_GNU_SOURCE -fwrapv -fno-strict-aliasing -pipe -fstack-protector-strong -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_FORTIFY_SOURCE=2',
optimize='-O2',
cppflags='-D_REENTRANT -D_GNU_SOURCE -fwrapv -fno-strict-aliasing -pipe -fstack-protector-strong -I/usr/local/include'
ccversion='', gccversion='10.2.1 20210110', 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/include/x86_64-linux-gnu /usr/lib /lib/x86_64-linux-gnu /lib/../lib /usr/lib/x86_64-linux-gnu /usr/lib/../lib /lib /lib64 /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 -L/usr/local/lib -fstack-protector-strong'
Characteristics of this binary (from libperl):
Compile-time options: HAS_TIMES MULTIPLICITY PERLIO_LAYERS
PERL_COPY_ON_WRITE PERL_DONT_CREATE_GVSV
PERL_HASH_FUNC_ONE_AT_A_TIME_HARD
PERL_IMPLICIT_CONTEXT PERL_MALLOC_WRAP
PERL_PRESERVE_IVUV 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
Locally applied patches:
Devel::PatchPerl 2.08
Built under linux
Compiled at Feb 5 2022 21:03:51
%ENV:
PERL="5.24.4"
PERL5LIB=""
PERL5OPT=""
PERL5_CPANPLUS_IS_RUNNING="1286146"
PERL5_CPAN_IS_RUNNING="1286146"
PERLBREW_HOME="/home/david/.perlbrew"
PERLBREW_MANPATH="/home/david/perl5/perlbrew/perls/perl-5.30.2/man"
PERLBREW_PATH="/home/david/perl5/perlbrew/bin:/home/david/perl5/perlbrew/perls/perl-5.30.2/bin"
PERLBREW_PERL="perl-5.30.2"
PERLBREW_ROOT="/home/david/perl5/perlbrew"
PERLBREW_SHELLRC_VERSION="0.89"
PERLBREW_VERSION="0.89"
PERLVER="5.24.4"
PERL_INLINE_DIRECTORY="/home/david/.Inline-5.24.4"
PERL_MM_USE_DEFAULT="1"
PERL_USE_UNSAFE_INC="0"
@INC:
/home/david/cpantesting/perl-5.24.4/lib/site_perl/5.24.4/x86_64-linux-thread-multi
/home/david/cpantesting/perl-5.24.4/lib/site_perl/5.24.4
/home/david/cpantesting/perl-5.24.4/lib/5.24.4/x86_64-linux-thread-multi
/home/david/cpantesting/perl-5.24.4/lib/5.24.4
.