BioPerl v1.007002 Perl 5 v5.20.3 darwin-thread-multi-2level
- Status
- Fail
- From
- Nigel Horne
- Dist
- BioPerl v1.007002
- Platform
- Perl 5 v5.20.3 darwin-thread-multi-2level
- Date
- 2018-09-25 14:05:14
- ID
- 06038e3c-c0cc-11e8-92fb-f203bec0dd2b
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-1.007002
on perl 5.20.3, created by CPAN-Reporter-1.2018.
Thank you for uploading your work to CPAN. However, there was a problem
testing your distribution.
If you think this report is invalid, please consult the CPAN Testers Wiki
for suggestions on how to avoid getting FAIL reports for missing library
or binary dependencies, unsupported operating systems, and so on:
http://wiki.cpantesters.org/wiki/CPANAuthorNotes
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 './Build test':
t/Align/AlignUtil.t .................... ok
t/Align/Graphics.t ..................... ok
t/Align/AlignStats.t ................... ok
t/Align/SimpleAlign.t .................. ok
t/Align/Utilities.t .................... ok
t/Align/TreeBuild.t .................... ok
t/AlignIO/arp.t ........................ ok
t/AlignIO/bl2seq.t ..................... ok
t/AlignIO/clustalw.t ................... ok
t/AlignIO/AlignIO.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/metafasta.t .................. ok
t/AlignIO/meme.t ....................... ok
t/AlignIO/nexml.t ...................... skipped: The optional module Bio::Phylo (or dependencies thereof) was not installed
t/AlignIO/msf.t ........................ ok
t/AlignIO/pfam.t ....................... ok
t/AlignIO/phylip.t ..................... ok
t/AlignIO/nexus.t ...................... ok
t/AlignIO/po.t ......................... ok
t/AlignIO/prodom.t ..................... ok
t/AlignIO/psi.t ........................ ok
t/AlignIO/selex.t ...................... ok
t/Alphabet.t ........................... ok
t/AlignIO/xmfa.t ....................... ok
t/AlignIO/stockholm.t .................. ok
t/Annotation/AnnotationAdaptor.t ....... ok
t/Assembly/IO/bowtie.t ................. skipped: The optional module Bio::DB::Sam (or dependencies thereof) was not installed
t/Annotation/Annotation.t .............. ok
Possible precedence issue with control flow operator at Bio/DB/IndexedBase.pm line 845, <GEN0> line 20.
t/Assembly/IO/sam.t .................... skipped: The optional module Bio::DB::Sam (or dependencies thereof) was not installed
t/Assembly/ContigSpectrum.t ............ ok
t/Cluster/UniGene.t .................... ok
Possible precedence issue with control flow operator at Bio/DB/IndexedBase.pm line 845.
t/ClusterIO/ClusterIO.t ................ ok
t/ClusterIO/SequenceFamily.t ........... ok
t/ClusterIO/unigene.t .................. ok
t/Draw/Pictogram.t ..................... ok
t/LiveSeq/Chain.t ...................... ok
t/LiveSeq/Mutation.t ................... ok
You are loading a Bio::DB::GFF database with GFF3 formatted data.
While this will likely work fine, the Bio::DB::GFF schema does not
always faithfully capture the complexity represented in GFF3 files.
Unless you have a specific reason for using Bio::DB::GFF, we suggest
that you use a Bio::DB::SeqFeature::Store database and its corresponding
loader, bp_seqfeature_load.pl.
t/LocalDB/BioDBGFF.t ................... ok
t/LiveSeq/LiveSeq.t .................... ok
Possible precedence issue with control flow operator at Bio/DB/IndexedBase.pm line 845.
t/LocalDB/Flat.t ....................... ok
t/LiveSeq/Mutator.t .................... ok
t/LocalDB/Index/Blast.t ................ ok
t/Assembly/core.t ...................... ok
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Can't open 'DB_File' dbm file 'Wibbl' : Inappropriate file type or format
STACK: Error::throw
STACK: Bio::Root::Root::throw Bio/Root/Root.pm:447
STACK: Bio::Index::Abstract::open_dbm Bio/Index/Abstract.pm:398
STACK: Bio::Index::Abstract::new Bio/Index/Abstract.pm:162
STACK: Bio::Index::AbstractSeq::new Bio/Index/AbstractSeq.pm:93
STACK: t/LocalDB/Index/Index.t:27
-----------------------------------------------------------
# Looks like your test exited with 79 just after 10.
t/LocalDB/Index/Index.t ................
Dubious, test returned 79 (wstat 20224, 0x4f00)
Failed 63/73 subtests
t/LocalDB/Index/BlastTable.t ........... ok
Possible precedence issue with control flow operator at Bio/DB/IndexedBase.pm line 845.
Possible precedence issue with control flow operator at Bio/DB/IndexedBase.pm line 845.
t/LocalDB/Registry.t ................... ok
t/LocalDB/Taxonomy/greengenes.t ........ ok
# Failed test at t/LocalDB/Qual.t line 23.
# got: '9'
# expected: '15'
# Failed test at t/LocalDB/Qual.t line 25.
# got: '17601976
[Output truncated after 1000K]
------------------------------
PREREQUISITES
------------------------------
Prerequisite modules loaded:
requires:
Module Need Have
------------------ ------ --------
Data::Stag 0.11 0.14
ExtUtils::Manifest 1.52 1.70
IO::String 0 1.08
perl v5.6.1 5.020003
Scalar::Util 0 1.46
build_requires:
Module Need Have
------------------ ------ --------
CPAN 1.81 2.16
Module::Build 0.42 0.4220
Test::Harness 2.62 3.36
Test::Most 0 0.35
URI::Escape 0 3.31
configure_requires:
Module Need Have
------------------ ------ --------
Module::Build 0.42 0.4220
------------------------------
ENVIRONMENT AND OTHER CONTEXT
------------------------------
Environment variables:
AUTOMATED_TESTING = 1
HARNESS_OPTIONS = j4
LANG = en_US.UTF-8
LC_ALL = POSIX
NONINTERACTIVE_TESTING = 1
PATH = /Users/hornenj/perl5/perlbrew/bin:/Users/hornenj/perl5/perlbrew/perls/perl-5.20.3/bin:/Users/hornenj/src/njh/smoker/bin:/Users/hornenj/homebrew/bin:/Users/hornenj/bin:/usr/bin:/bin:/usr/X11R6/bin:/sw/bin
PERL5LIB = /Users/hornenj/.cpan/build/Data-Stag-0.14-15/blib/arch:/Users/hornenj/.cpan/build/Data-Stag-0.14-15/blib/lib:/Users/hornenj/.cpan/build/Net-IDN-Encode-2.499_20180924-15/blib/arch:/Users/hornenj/.cpan/build/Net-IDN-Encode-2.499_20180924-15/blib/lib
PERL5OPT =
PERL5_CPANPLUS_IS_RUNNING = 69951
PERL5_CPAN_IS_RUNNING = 69951
PERLBREW_HOME = /Users/hornenj/.perlbrew
PERLBREW_MANPATH = /Users/hornenj/perl5/perlbrew/perls/perl-5.20.3/man
PERLBREW_PATH = /Users/hornenj/perl5/perlbrew/bin:/Users/hornenj/perl5/perlbrew/perls/perl-5.20.3/bin
PERLBREW_PERL = perl-5.20.3
PERLBREW_ROOT = /Users/hornenj/perl5/perlbrew
PERLBREW_SHELLRC_VERSION = 0.84
PERLBREW_VERSION = 0.84
PERL_MM_USE_DEFAULT = 1
SHELL = /bin/bash
TERM = xterm-256color
TMPDIR = /var/folders/pz/pd7y1qjs6s3cbk170cw50fjc000c61/T//testwrapper.69936
VERSIONER_PERL_PREFER_32_BIT = no
VERSIONER_PERL_VERSION = 5.18
Perl special variables (and OS-specific diagnostics, for MSWin32):
$^X = /Users/hornenj/perl5/perlbrew/perls/perl-5.20.3/bin/perl
$UID/$EUID = 12481 / 12481
$GID = 14 14 206 5344 37191 527 12 62 98 204 399 37223 241 223 100
$EGID = 14 14 206 5344 37191 527 12 62 98 204 399 37223 241 223 100
Perl module toolchain versions installed:
Module Have
------------------- --------
CPAN 2.16
CPAN::Meta 2.150010
Cwd 3.74
ExtUtils::CBuilder 0.280224
ExtUtils::Command 7.34
ExtUtils::Install 2.06
ExtUtils::MakeMaker 7.34
ExtUtils::Manifest 1.70
ExtUtils::ParseXS 3.30
File::Spec 3.74
JSON 2.97001
JSON::PP 2.27400
Module::Build 0.4220
Module::Signature n/a
Parse::CPAN::Meta 2.150010
Test::Harness 3.36
Test::More 1.302106
YAML 1.26
YAML::Syck 1.30
version 0.9917
--
Summary of my perl5 (revision 5 version 20 subversion 3) configuration:
Platform:
osname=darwin, osvers=14.5.0, archname=darwin-thread-multi-2level
uname='darwin ncbimac2027.ncbi.nlm.nih.gov 14.5.0 darwin kernel version 14.5.0: wed jul 29 02:26:53 pdt 2015; root:xnu-2782.40.9~1release_x86_64 x86_64 '
config_args='-de -Dprefix=/Users/hornenj/perl5/perlbrew/perls/perl-5.20.3 -Duseithreads -Dusemultiplicity -Dusedevel -Accflags=-O2 -W -Wformat=2 -Wswitch -Wshadow -Wwrite-strings -Wuninitialized -Wall -pipe -mtune=native -march=native -fomit-frame-pointer -msse2 -msse -mmmx -pedantic -D_FORTIFY_SOURCE=2 -Wpointer-arith -Wstrict-prototypes -fstack-protector -Wstack-protector -Wextra -Wbad-function-cast -Wcast-align -Wcast-qual -Wdisabled-optimization -Wendif-labels -Wfloat-equal -Wformat-nonliteral -Winline -Wmissing-declarations -Wmissing-prototypes -Wnested-externs -Wpointer-arith -Wundef -Wformat-security -fassociative-math -Acc=cc -Aeval:scriptdir=/Users/hornenj/perl5/perlbrew/perls/perl-5.20.3/bin'
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 ='-fno-common -DPERL_DARWIN -O2 -W -Wformat=2 -Wswitch -Wshadow -Wwrite-strings -Wuninitialized -Wall -pipe -mtune=native -march=native -fomit-frame-pointer -msse2 -msse -mmmx -pedantic -D_FORTIFY_SOURCE=2 -Wpointer-arith -Wstrict-prototypes -fstack-protector -Wstack-protector -Wextra -Wbad-function-cast -Wcast-align -Wcast-qual -Wdisabled-optimization -Wendif-labels -Wfloat-equal -Wformat-nonliteral -Winline -Wmissing-declarations -Wmissing-prototypes -Wnested-externs -Wpointer-arith -Wundef -Wformat-security -fassociative-math -fno-strict-aliasing -I/usr/local/include',
optimize='-O3',
cppflags='-fno-common -DPERL_DARWIN -O2 -W -Wformat=2 -Wswitch -Wshadow -Wwrite-strings -Wuninitialized -Wall -pipe -mtune=native -march=native -fomit-frame-pointer -msse2 -msse -mmmx -pedantic -D_FORTIFY_SOURCE=2 -Wpointer-arith -Wstrict-prototypes -fstack-protector -Wstack-protector -Wextra -Wbad-function-cast -Wcast-align -Wcast-qual -Wdisabled-optimization -Wendif-labels -Wfloat-equal -Wformat-nonliteral -Winline -Wmissing-declarations -Wmissing-prototypes -Wnested-externs -Wpointer-arith -Wundef -Wformat-security -fassociative-math -fno-strict-aliasing -I/usr/local/include'
ccversion='', gccversion='4.2.1 Compatible Apple LLVM 6.0 (clang-600.0.56)', gccosandvers=''
intsize=4, longsize=8, ptrsize=8, doublesize=8, byteorder=12345678
d_longlong=define, longlongsize=8, d_longdbl=define, longdblsize=16
ivtype='long', ivsize=8, nvtype='double', nvsize=8, Off_t='off_t', lseeksize=8
alignbytes=8, prototype=define
Linker and Libraries:
ld='env MACOSX_DEPLOYMENT_TARGET=10.3 cc', ldflags =' -fstack-protector -L/usr/local/lib'
libpth=/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/6.0/lib /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/lib /usr/local/lib /usr/lib
libs=-lpthread -ldbm -ldl -lm -lutil -lc
perllibs=-lpthread -ldl -lm -lutil -lc
libc=, so=dylib, useshrplib=false, libperl=libperl.a
gnulibc_version=''
Dynamic Linking:
dlsrc=dl_dlopen.xs, dlext=bundle, d_dlsymun=undef, ccdlflags=' '
cccdlflags=' ', lddlflags=' -bundle -undefined dynamic_lookup -L/usr/local/lib -fstack-protector'
Characteristics of this binary (from libperl):
Compile-time options: HAS_TIMES MULTIPLICITY PERLIO_LAYERS
PERL_DONT_CREATE_GVSV
PERL_HASH_FUNC_ONE_AT_A_TIME_HARD
PERL_IMPLICIT_CONTEXT PERL_MALLOC_WRAP
PERL_NEW_COPY_ON_WRITE PERL_PRESERVE_IVUV
PERL_USE_DEVEL 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_PERLIO USE_PERL_ATOF
USE_REENTRANT_API
Locally applied patches:
Devel::PatchPerl 1.30
Built under darwin
Compiled at Sep 14 2015 07:51:22
%ENV:
PERL5LIB="/Users/hornenj/.cpan/build/Data-Stag-0.14-15/blib/arch:/Users/hornenj/.cpan/build/Data-Stag-0.14-15/blib/lib:/Users/hornenj/.cpan/build/Net-IDN-Encode-2.499_20180924-15/blib/arch:/Users/hornenj/.cpan/build/Net-IDN-Encode-2.499_20180924-15/blib/lib"
PERL5OPT=""
PERL5_CPANPLUS_IS_RUNNING="69951"
PERL5_CPAN_IS_RUNNING="69951"
PERLBREW_HOME="/Users/hornenj/.perlbrew"
PERLBREW_MANPATH="/Users/hornenj/perl5/perlbrew/perls/perl-5.20.3/man"
PERLBREW_PATH="/Users/hornenj/perl5/perlbrew/bin:/Users/hornenj/perl5/perlbrew/perls/perl-5.20.3/bin"
PERLBREW_PERL="perl-5.20.3"
PERLBREW_ROOT="/Users/hornenj/perl5/perlbrew"
PERLBREW_SHELLRC_VERSION="0.84"
PERLBREW_VERSION="0.84"
PERL_MM_USE_DEFAULT="1"
@INC:
/Users/hornenj/.cpan/build/Data-Stag-0.14-15/blib/arch
/Users/hornenj/.cpan/build/Data-Stag-0.14-15/blib/lib
/Users/hornenj/.cpan/build/Net-IDN-Encode-2.499_20180924-15/blib/arch
/Users/hornenj/.cpan/build/Net-IDN-Encode-2.499_20180924-15/blib/lib
/Users/hornenj/perl5/perlbrew/perls/perl-5.20.3/lib/site_perl/5.20.3/darwin-thread-multi-2level
/Users/hornenj/perl5/perlbrew/perls/perl-5.20.3/lib/site_perl/5.20.3
/Users/hornenj/perl5/perlbrew/perls/perl-5.20.3/lib/5.20.3/darwin-thread-multi-2level
/Users/hornenj/perl5/perlbrew/perls/perl-5.20.3/lib/5.20.3
.