BioPerl v1.7.5 Perl 5 v5.28.2 amd64-freebsd-thread-multi
- Status
- Pass
- From
- Slaven Rezić (SREZIC)
- Dist
-
BioPerl v1.7.5
- Platform
- Perl 5 v5.28.2 amd64-freebsd-thread-multi
- Date
- 2019-07-22 04:14:27
- ID
- 321bb1fa-ac37-11e9-b2db-a06a1f24ea8f
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 carandraug,
This is a computer-generated report for BioPerl-1.7.5
on perl 5.28.2, 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:
none provided
------------------------------
PROGRAM OUTPUT
------------------------------
Output from '/usr/bin/make test':
PERL_DL_NONLAZY=1 "/usr/local/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
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/interpro.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=212, Tests=14858, 961 wallclock secs ( 4.45 usr 1.53 sys + 183.19 cusr 766.77 csys = 955.94 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 3.74
Data::Dumper 0 2.170
Data::Stag 0 0.14
DB_File 0 1.840
DBI 0 1.642
Digest::MD5 0 2.55
Dumpvalue 0 1.18
Env 0 1.04
Error 0 0.17027
Exporter 0 5.73
Fcntl 0 1.13
File::Basename 0 2.85
File::Copy 0 2.33
File::Path 0 2.15
File::Spec 0 3.74
File::Spec::Functions 0 3.74
File::Temp 0 0.2309
FileHandle 0 2.03
GD 0 2.71
Getopt::Long 0 2.5
Graph::Directed 0 0
HTTP::Request::Common 0 6.18
HTTP::Response 0 6.18
integer 0 1.01
IO::File 0 1.39
IO::Handle 0 1.39
IO::Pipe 0 1.39
IO::Scalar 0 2.111
IO::Socket 0 1.39
IO::String 0 1.08
IPC::Run 0 20180523.0
List::MoreUtils 0 0.428
List::Util 0 1.50
LWP::UserAgent 0 6.39
Math::BigFloat 0 1.999811
Module::Build 0 0.4229
overload 0 1.30
parent 0 0.236
perl 5.006 5.028002
Pod::Usage 0 1.69
POSIX 0 1.84
Scalar::Util 0 1.50
Set::Scalar 0 1.29
Storable 0 3.08_01
strict 0 1.11
Symbol 0 1.08
Test::Builder 0 1.302164
Test::Builder::Module 0 1.302164
Test::Most 0 0.35
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 1.9759
UNIVERSAL 0 1.13
URI 0 1.76
utf8 0 1.21
vars 0 1.04
version 0 0.9923
warnings 0 1.42
XML::DOM 0 1.46
XML::DOM::XPath 0 0.14
XML::LibXML 0 2.0134
XML::LibXML::Reader 0 2.0134
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 0.625
YAML 0 1.29
build_requires:
Module Need Have
---------------------- ----- ----------
ExtUtils::MakeMaker 0 7.34
File::Spec 0 3.74
IO::Handle 0 1.39
IPC::Open3 0 1.20
Test::Memory::Cycle 0 1.06
Test::More 0 1.302164
Test::Weaken 0 3.022000
configure_requires:
Module Need Have
---------------------- ----- ----------
ExtUtils::MakeMaker 0 7.34
------------------------------
ENVIRONMENT AND OTHER CONTEXT
------------------------------
Environment variables:
PATH = /usr/local/bin:/usr/bin:/bin:/usr/local/sbin:/usr/sbin:/sbin:/home/cpansand/bin/sh:/home/cpansand/bin:/usr/games:/home/cpansand/devel:/usr/home/eserte/src/srezic-misc/scripts
PERL5LIB = 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PERL5OPT =
PERL5_CPANPLUS_IS_RUNNING = 82374
PERL5_CPAN_IS_RUNNING = 82374
PERL5_CPAN_IS_RUNNING_IN_RECURSION = 82343,82374
PERL_BATCH = yes
PERL_CANARY_STABILITY_NOPROMPT = 1
PERL_CPAN_REPORTER_CONFIG = /var/tmp/cpansmoker-1023/2019072202/cpanreporter_000_config.ini
PERL_EXTUTILS_AUTOINSTALL = --defaultdeps
PERL_USE_UNSAFE_INC = 1
SHELL = /bin/sh
TMPDIR = /var/tmp/cpansmoker-1023/2019072202
Perl special variables (and OS-specific diagnostics, for MSWin32):
$^X = /usr/local/bin/perl
$UID/$EUID = 1023 / 1023
$GID = 1023 1023
$EGID = 1023 1023
Perl module toolchain versions installed:
Module Have
------------------- --------
CPAN 2.20
CPAN::Meta 2.150010
Cwd 3.74
ExtUtils::CBuilder 0.280230
ExtUtils::Command 7.34
ExtUtils::Install 2.14
ExtUtils::MakeMaker 7.34
ExtUtils::Manifest 1.70
ExtUtils::ParseXS 3.39
File::Spec 3.74
JSON 4.02
JSON::PP 2.97001
Module::Build 0.4229
Module::Signature n/a
Parse::CPAN::Meta 2.150010
Test::Harness 3.42
Test::More 1.302164
YAML 1.29
YAML::Syck 1.31
version 0.9923
--
Summary of my perl5 (revision 5 version 28 subversion 2) configuration:
Platform:
osname=freebsd
osvers=12.0-release-p3
archname=amd64-freebsd-thread-multi
uname='freebsd 120amd64-default-job-01 12.0-release-p3 freebsd 12.0-release-p3 amd64 '
config_args='-sde -Dprefix=/usr/local -Dlibperl=libperl.so.5.28.2 -Darchlib=/usr/local/lib/perl5/5.28/mach -Dprivlib=/usr/local/lib/perl5/5.28 -Dman3dir=/usr/local/lib/perl5/5.28/perl/man/man3 -Dman1dir=/usr/local/lib/perl5/5.28/perl/man/man1 -Dsitearch=/usr/local/lib/perl5/site_perl/mach/5.28 -Dsitelib=/usr/local/lib/perl5/site_perl -Dscriptdir=/usr/local/bin -Dsiteman3dir=/usr/local/lib/perl5/site_perl/man/man3 -Dsiteman1dir=/usr/local/lib/perl5/site_perl/man/man1 -Ui_malloc -Ui_iconv -Uinstallusrbinperl -Dusenm=n -Dcc=cc -Duseshrplib -Dinc_version_list=none -Dcf_by=mat -Dcf_email=mat@FreeBSD.org -Dcf_time=Fri Apr 19 15:08:02 UTC 2019 -Alddlflags=-L/wrkdirs/usr/ports/lang/perl5.28/work/perl-5.28.2 -L/usr/local/lib/perl5/5.28/mach/CORE -lperl -Dshrpldflags=$(LDDLFLAGS:N-L/wrkdirs/usr/ports/lang/perl5.28/work/perl-5.28.2:N-L/usr/local/lib/perl5/5.28/mach/CORE:N-lperl) -Wl,-soname,$(LIBPERL:R) -Doptimize=-O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Dusedtrace -Ui_gdbm -Dusemultiplicity=y -Duse64bitint -Dusemymalloc=n -Dusethreads=y'
hint=recommended
useposix=true
d_sigaction=define
useithreads=define
usemultiplicity=define
use64bitint=define
use64bitall=define
uselongdouble=undef
usemymalloc=n
default_inc_excludes_dot=define
bincompat5005=undef
Compiler:
cc='cc'
ccflags ='-DHAS_FPSETMASK -DHAS_FLOATINGPOINT_H -fno-strict-aliasing -pipe -fstack-protector-strong -I/usr/local/include -D_FORTIFY_SOURCE=2'
optimize='-O2 -pipe -fstack-protector-strong -fno-strict-aliasing '
cppflags='-DHAS_FPSETMASK -DHAS_FLOATINGPOINT_H -fno-strict-aliasing -pipe -fstack-protector-strong -I/usr/local/include'
ccversion=''
gccversion='4.2.1 Compatible FreeBSD Clang 6.0.1 (tags/RELEASE_601/final 335540)'
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 ='-pthread -Wl,-E -fstack-protector-strong -L/usr/local/lib'
libpth=/usr/lib /usr/local/lib /usr/lib/clang/6.0.1/lib /usr/lib
libs=-lpthread -lm -lcrypt -lutil
perllibs=-lpthread -lm -lcrypt -lutil
libc=
so=so
useshrplib=true
libperl=libperl.so.5.28.2
gnulibc_version=''
Dynamic Linking:
dlsrc=dl_dlopen.xs
dlext=so
d_dlsymun=undef
ccdlflags=' -Wl,-R/usr/local/lib/perl5/5.28/mach/CORE'
cccdlflags='-DPIC -fPIC'
lddlflags='-shared -L/usr/local/lib/perl5/5.28/mach/CORE -lperl -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_IMPLICIT_CONTEXT
PERL_MALLOC_WRAP
PERL_OP_PARENT
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
Built under freebsd
%ENV:
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PERL5OPT=""
PERL5_CPANPLUS_IS_RUNNING="82374"
PERL5_CPAN_IS_RUNNING="82374"
PERL5_CPAN_IS_RUNNING_IN_RECURSION="82343,82374"
PERL_BATCH="yes"
PERL_CANARY_STABILITY_NOPROMPT="1"
PERL_CPAN_REPORTER_CONFIG="/var/tmp/cpansmoker-1023/2019072202/cpanreporter_000_config.ini"
PERL_EXTUTILS_AUTOINSTALL="--defaultdeps"
PERL_USE_UNSAFE_INC="1"
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