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Postings from February 2007
FAIL onto-perl-0.26 alpha-freebsd 6.0-release
From:
chris
Date:
February 5, 2007 06:57
Subject:
FAIL onto-perl-0.26 alpha-freebsd 6.0-release
This distribution has been tested as part of the cpan-testers
effort to test as many new uploads to CPAN as possible. See
http://testers.cpan.org/
Please cc any replies to cpan-testers@perl.org to keep other
test volunteers informed and to prevent any duplicate effort.
--
Dear EASR,
This is a computer-generated error report created automatically by
CPANPLUS, version 0.076. Testers personal comments may appear
at the end of this report.
Thank you for uploading your work to CPAN. However, it appears that
there were some problems testing your distribution.
TEST RESULTS:
Below is the error stack from stage 'make test':
[MSG] [Mon Feb 5 14:56:33 2007] Trying to get 'http://www.cpan.org/authors/id/E/EA/EASR/onto-perl/onto-perl-0.26.tar.gz'
[MSG] [Mon Feb 5 14:56:37 2007] Trying to get 'http://www.cpan.org/authors/id/E/EA/EASR/onto-perl/CHECKSUMS'
[MSG] [Mon Feb 5 14:56:37 2007] Checksum matches for 'onto-perl-0.26.tar.gz'
[MSG] [Mon Feb 5 14:56:39 2007] Extracted 'onto-perl-latest/'
[MSG] [Mon Feb 5 14:56:39 2007] Extracted 'onto-perl-latest/t/'
[MSG] [Mon Feb 5 14:56:39 2007] Extracted 'onto-perl-latest/t/data/'
[MSG] [Mon Feb 5 14:56:39 2007] Extracted 'onto-perl-latest/t/data/cco-names.html'
[MSG] [Mon Feb 5 14:56:39 2007] Extracted 'onto-perl-latest/t/data/fake_ulo_cco.obo'
[MSG] [Mon Feb 5 14:56:39 2007] Extracted 'onto-perl-latest/t/data/pre_cco_taxa.obo'
[MSG] [Mon Feb 5 14:56:39 2007] Extracted 'onto-perl-latest/t/data/out_cco.obo'
[MSG] [Mon Feb 5 14:56:39 2007] Extracted 'onto-perl-latest/t/data/.DS_Store'
[MSG] [Mon Feb 5 14:56:39 2007] Extracted 'onto-perl-latest/t/data/goa_assoc.txt'
[MSG] [Mon Feb 5 14:56:39 2007] Extracted 'onto-perl-latest/t/data/names_dummy.dmp'
[MSG] [Mon Feb 5 14:56:39 2007] Extracted 'onto-perl-latest/t/data/nodes_dummy.dmp'
[MSG] [Mon Feb 5 14:56:39 2007] Extracted 'onto-perl-latest/t/data/pre_cco.obo'
[MSG] [Mon Feb 5 14:56:39 2007] Extracted 'onto-perl-latest/t/data/test1.obo'
[MSG] [Mon Feb 5 14:56:39 2007] Extracted 'onto-perl-latest/t/data/test1.xml'
[MSG] [Mon Feb 5 14:56:39 2007] Extracted 'onto-perl-latest/t/data/test2.dot'
[MSG] [Mon Feb 5 14:56:39 2007] Extracted 'onto-perl-latest/t/data/test2.obo'
[MSG] [Mon Feb 5 14:56:39 2007] Extracted 'onto-perl-latest/t/data/test2.owl'
[MSG] [Mon Feb 5 14:56:39 2007] Extracted 'onto-perl-latest/t/data/test2.xml'
[MSG] [Mon Feb 5 14:56:39 2007] Extracted 'onto-perl-latest/t/data/test_ulo_cco.dot'
[MSG] [Mon Feb 5 14:56:39 2007] Extracted 'onto-perl-latest/t/data/test_ulo_cco.owl'
[MSG] [Mon Feb 5 14:56:39 2007] Extracted 'onto-perl-latest/t/data/ulo_cco.obo'
[MSG] [Mon Feb 5 14:56:39 2007] Extracted 'onto-perl-latest/t/data/pre_cco_core.obo'
[MSG] [Mon Feb 5 14:56:39 2007] Extracted 'onto-perl-latest/t/data/cco_b.ids'
[MSG] [Mon Feb 5 14:56:39 2007] Extracted 'onto-perl-latest/t/data/cco_t.ids'
[MSG] [Mon Feb 5 14:56:39 2007] Extracted 'onto-perl-latest/t/GoaAssociationSet.t'
[MSG] [Mon Feb 5 14:56:39 2007] Extracted 'onto-perl-latest/t/Def.t'
[MSG] [Mon Feb 5 14:56:39 2007] Extracted 'onto-perl-latest/t/Relationship.t'
[MSG] [Mon Feb 5 14:56:39 2007] Extracted 'onto-perl-latest/t/RelationshipType.t'
[MSG] [Mon Feb 5 14:56:39 2007] Extracted 'onto-perl-latest/t/TermSet.t'
[MSG] [Mon Feb 5 14:56:39 2007] Extracted 'onto-perl-latest/t/DbxrefSet.t'
[MSG] [Mon Feb 5 14:56:39 2007] Extracted 'onto-perl-latest/t/Term.t'
[MSG] [Mon Feb 5 14:56:39 2007] Extracted 'onto-perl-latest/t/NCBIParser.t'
[MSG] [Mon Feb 5 14:56:39 2007] Extracted 'onto-perl-latest/t/SynonymSet.t'
[MSG] [Mon Feb 5 14:56:39 2007] Extracted 'onto-perl-latest/t/Dbxref.t'
[MSG] [Mon Feb 5 14:56:39 2007] Extracted 'onto-perl-latest/t/Ontology.t'
[MSG] [Mon Feb 5 14:56:39 2007] Extracted 'onto-perl-latest/t/Set.t'
[MSG] [Mon Feb 5 14:56:39 2007] Extracted 'onto-perl-latest/t/Synonym.t'
[MSG] [Mon Feb 5 14:56:39 2007] Extracted 'onto-perl-latest/t/OBOParser.t'
[MSG] [Mon Feb 5 14:56:40 2007] Extracted 'onto-perl-latest/t/GoaAssociation.t'
[MSG] [Mon Feb 5 14:56:40 2007] Extracted 'onto-perl-latest/t/GoaParser.t'
[MSG] [Mon Feb 5 14:56:40 2007] Extracted 'onto-perl-latest/CCO/'
[MSG] [Mon Feb 5 14:56:40 2007] Extracted 'onto-perl-latest/CCO/Core/'
[MSG] [Mon Feb 5 14:56:40 2007] Extracted 'onto-perl-latest/CCO/Core/Ontology.pm'
[MSG] [Mon Feb 5 14:56:40 2007] Extracted 'onto-perl-latest/CCO/Core/Term.pm'
[MSG] [Mon Feb 5 14:56:40 2007] Extracted 'onto-perl-latest/CCO/Core/Dbxref.pm'
[MSG] [Mon Feb 5 14:56:40 2007] Extracted 'onto-perl-latest/CCO/Core/GoaAssociation.pm'
[MSG] [Mon Feb 5 14:56:40 2007] Extracted 'onto-perl-latest/CCO/Core/Synonym.pm'
[MSG] [Mon Feb 5 14:56:40 2007] Extracted 'onto-perl-latest/CCO/Core/Def.pm'
[MSG] [Mon Feb 5 14:56:40 2007] Extracted 'onto-perl-latest/CCO/Core/Relationship.pm'
[MSG] [Mon Feb 5 14:56:40 2007] Extracted 'onto-perl-latest/CCO/Core/RelationshipType.pm'
[MSG] [Mon Feb 5 14:56:40 2007] Extracted 'onto-perl-latest/CCO/Parser/'
[MSG] [Mon Feb 5 14:56:40 2007] Extracted 'onto-perl-latest/CCO/Parser/OBOParser.pm'
[MSG] [Mon Feb 5 14:56:40 2007] Extracted 'onto-perl-latest/CCO/Parser/NCBIParser.pm'
[MSG] [Mon Feb 5 14:56:40 2007] Extracted 'onto-perl-latest/CCO/Parser/GoaParser.pm'
[MSG] [Mon Feb 5 14:56:40 2007] Extracted 'onto-perl-latest/CCO/Util/'
[MSG] [Mon Feb 5 14:56:40 2007] Extracted 'onto-perl-latest/CCO/Util/DbxrefSet.pm'
[MSG] [Mon Feb 5 14:56:40 2007] Extracted 'onto-perl-latest/CCO/Util/SynonymSet.pm'
[MSG] [Mon Feb 5 14:56:40 2007] Extracted 'onto-perl-latest/CCO/Util/Set.pm'
[MSG] [Mon Feb 5 14:56:40 2007] Extracted 'onto-perl-latest/CCO/Util/GoaAssociationSet.pm'
[MSG] [Mon Feb 5 14:56:40 2007] Extracted 'onto-perl-latest/CCO/Util/TermSet.pm'
[MSG] [Mon Feb 5 14:56:40 2007] Extracted 'onto-perl-latest/doc/'
[MSG] [Mon Feb 5 14:56:40 2007] Extracted 'onto-perl-latest/scripts/'
[MSG] [Mon Feb 5 14:56:40 2007] Extracted 'onto-perl-latest/scripts/go2owl.pl'
[MSG] [Mon Feb 5 14:56:40 2007] Extracted 'onto-perl-latest/scripts/names.xsl'
[MSG] [Mon Feb 5 14:56:40 2007] Extracted 'onto-perl-latest/scripts/obo2xml.pl'
[MSG] [Mon Feb 5 14:56:40 2007] Extracted 'onto-perl-latest/scripts/xml2html.xsl'
[MSG] [Mon Feb 5 14:56:40 2007] Extracted 'onto-perl-latest/scripts/obo2owl.pl'
[MSG] [Mon Feb 5 14:56:40 2007] Extracted 'onto-perl-latest/onto-perl.pod'
[MSG] [Mon Feb 5 14:56:40 2007] Extracted 'onto-perl-latest/MANIFEST'
[MSG] [Mon Feb 5 14:56:40 2007] Extracted 'onto-perl-latest/INSTALL'
[MSG] [Mon Feb 5 14:56:40 2007] Extracted 'onto-perl-latest/Makefile.PL'
[MSG] [Mon Feb 5 14:56:40 2007] Extracted 'onto-perl-latest/Changes'
[MSG] [Mon Feb 5 14:56:40 2007] Extracted 'onto-perl-latest/README'
[MSG] [Mon Feb 5 14:56:40 2007] Extracted 'onto-perl-latest/pm_to_blib'
[MSG] [Mon Feb 5 14:56:40 2007] Extracted 'onto-perl-latest/Makefile'
[MSG] [Mon Feb 5 14:56:40 2007] Extracted 'onto::perl' to '/usr/home/chris/.cpanplus/5.8.7/build/onto-perl-latest'
[MSG] [Mon Feb 5 14:56:43 2007] Writing Makefile for CCO
[MSG] [Mon Feb 5 14:56:43 2007] DEFAULT 'filter_prereqs' HANDLER RETURNING 'sub return value'
[MSG] [Mon Feb 5 14:56:49 2007] cp onto-perl.pod blib/lib/onto-perl.pod
cp CCO/Core/Dbxref.pm blib/lib/CCO/Core/Dbxref.pm
cp CCO/Core/GoaAssociation.pm blib/lib/CCO/Core/GoaAssociation.pm
cp CCO/Util/DbxrefSet.pm blib/lib/CCO/Util/DbxrefSet.pm
cp CCO/Core/Relationship.pm blib/lib/CCO/Core/Relationship.pm
cp CCO/Core/RelationshipType.pm blib/lib/CCO/Core/RelationshipType.pm
cp CCO/Util/TermSet.pm blib/lib/CCO/Util/TermSet.pm
cp CCO/Util/GoaAssociationSet.pm blib/lib/CCO/Util/GoaAssociationSet.pm
cp CCO/Util/SynonymSet.pm blib/lib/CCO/Util/SynonymSet.pm
cp CCO/Parser/GoaParser.pm blib/lib/CCO/Parser/GoaParser.pm
cp CCO/Core/Ontology.pm blib/lib/CCO/Core/Ontology.pm
cp CCO/Core/Synonym.pm blib/lib/CCO/Core/Synonym.pm
cp CCO/Core/Def.pm blib/lib/CCO/Core/Def.pm
cp CCO/Util/Set.pm blib/lib/CCO/Util/Set.pm
cp CCO/Core/Term.pm blib/lib/CCO/Core/Term.pm
cp CCO/Parser/NCBIParser.pm blib/lib/CCO/Parser/NCBIParser.pm
cp CCO/Parser/OBOParser.pm blib/lib/CCO/Parser/OBOParser.pm
Manifying blib/man3/onto-perl.3
Manifying blib/man3/CCO::Core::Dbxref.3
Manifying blib/man3/CCO::Util::DbxrefSet.3
Manifying blib/man3/CCO::Core::GoaAssociation.3
Manifying blib/man3/CCO::Core::Relationship.3
Manifying blib/man3/CCO::Util::TermSet.3
Manifying blib/man3/CCO::Core::RelationshipType.3
Manifying blib/man3/CCO::Util::GoaAssociationSet.3
Manifying blib/man3/CCO::Core::Ontology.3
Manifying blib/man3/CCO::Parser::GoaParser.3
Manifying blib/man3/CCO::Util::SynonymSet.3
Manifying blib/man3/CCO::Core::Def.3
Manifying blib/man3/CCO::Core::Synonym.3
Manifying blib/man3/CCO::Util::Set.3
Manifying blib/man3/CCO::Core::Term.3
Manifying blib/man3/CCO::Parser::NCBIParser.3
Manifying blib/man3/CCO::Parser::OBOParser.3
[ERROR] [Mon Feb 5 14:57:49 2007] MAKE TEST failed: PERL_DL_NONLAZY=1 /usr/local/bin/perl "-MExtUtils::Command::MM" "-e" "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t
t/Dbxref...............ok
t/DbxrefSet............ok
t/Def..................ok
t/GoaAssociation.......ok
t/GoaAssociationSet....ok
t/GoaParser............Can't locate CCO_ID_Term_Map.pm in @INC (@INC contains: /usr/home/chris/.cpanplus/5.8.7/build/onto-perl-latest/blib/lib /usr/home/chris/.cpanplus/5.8.7/build/onto-perl-latest/blib/arch /usr/home/chris/.cpanplus/5.8.7/build/onto-perl-latest/blib /usr/local/lib/perl5/site_perl/5.8.7/mach /usr/local/lib/perl5/site_perl/5.8.7 /usr/local/lib/perl5/site_perl/5.8.7 /usr/local/lib/perl5/site_perl /usr/local/lib/perl5/5.8.7/BSDPAN /usr/local/lib/perl5/5.8.7/mach /usr/local/lib/perl5/5.8.7 . /usr/local/lib/perl5/site_perl/5.8.7/mach /usr/local/lib/perl5/site_perl/5.8.7 /usr/local/lib/perl5/site_perl /usr/local/lib/perl5/5.8.7/BSDPAN /usr/local/lib/perl5/5.8.7/mach /usr/local/lib/perl5/5.8.7 . ../cco/scripts/pipeline) at /usr/home/chris/.cpanplus/5.8.7/build/onto-perl-latest/blib/lib/CCO/Parser/GoaParser.pm line 25.
BEGIN failed--compilation aborted at /usr/home/chris/.cpanplus/5.8.7/build/onto-perl-latest/blib/lib/CCO/Parser/GoaParser.pm line 25.
Compilation failed in require at t/GoaParser.t line 15.
BEGIN failed--compilation aborted at t/GoaParser.t line 15.
dubious
Test returned status 2 (wstat 512, 0x200)
DIED. FAILED tests 1-5
Failed 5/5 tests, 0.00% okay
t/NCBIParser...........Can't locate CCO_ID_Term_Map.pm in @INC (@INC contains: /usr/home/chris/.cpanplus/5.8.7/build/onto-perl-latest/blib/lib /usr/home/chris/.cpanplus/5.8.7/build/onto-perl-latest/blib/arch /usr/home/chris/.cpanplus/5.8.7/build/onto-perl-latest/blib /usr/local/lib/perl5/site_perl/5.8.7/mach /usr/local/lib/perl5/site_perl/5.8.7 /usr/local/lib/perl5/site_perl/5.8.7 /usr/local/lib/perl5/site_perl /usr/local/lib/perl5/5.8.7/BSDPAN /usr/local/lib/perl5/5.8.7/mach /usr/local/lib/perl5/5.8.7 . /usr/local/lib/perl5/site_perl/5.8.7/mach /usr/local/lib/perl5/site_perl/5.8.7 /usr/local/lib/perl5/site_perl /usr/local/lib/perl5/5.8.7/BSDPAN /usr/local/lib/perl5/5.8.7/mach /usr/local/lib/perl5/5.8.7 . ../cco/scripts/pipeline) at /usr/home/chris/.cpanplus/5.8.7/build/onto-perl-latest/blib/lib/CCO/Parser/NCBIParser.pm line 21.
BEGIN failed--compilation aborted at /usr/home/chris/.cpanplus/5.8.7/build/onto-perl-latest/blib/lib/CCO/Parser/NCBIParser.pm line 21.
Compilation failed in require at t/NCBIParser.t line 17.
BEGIN failed--compilation aborted at t/NCBIParser.t line 17.
dubious
Test returned status 2 (wstat 512, 0x200)
DIED. FAILED tests 1-3
Failed 3/3 tests, 0.00% okay
t/OBOParser............ok
t/Ontology.............ok
t/Relationship.........ok
t/RelationshipType.....ok
t/Set..................ok
t/Synonym..............ok
t/SynonymSet...........ok
t/Term.................ok
t/TermSet..............ok
Failed Test Stat Wstat Total Fail List of Failed
-------------------------------------------------------------------------------
t/GoaParser.t 2 512 5 10 1-5
t/NCBIParser.t 2 512 3 6 1-3
Failed 2/16 test scripts. 8/488 subtests failed.
Files=16, Tests=488, 59 wallclock secs (28.00 cusr + 0.89 csys = 28.89 CPU)
Failed 2/16 test programs. 8/488 subtests failed.
*** Error code 35
Stop in /usr/home/chris/.cpanplus/5.8.7/build/onto-perl-latest.
MISSING PREREQUISITES:
It was observed that the test suite seem to fail without these modules:
CCO_ID_Term_Map
As such, adding the prerequisite module(s) to 'PREREQ_PM' in your
Makefile.PL should solve this problem. For example:
WriteMakefile(
AUTHOR => 'EASR (cpanplus-info@lists.sf.net)',
... # other information
PREREQ_PM => {
'CCO_ID_Term_Map' => '0', # or a minimum working version
}
);
If you are interested in making a more flexible Makefile.PL that can
probe for missing dependencies and install them, ExtUtils::AutoInstall
at <http://search.cpan.org/dist/ExtUtils-AutoInstall/> may be
worth a look.
Thanks! :-)
******************************** NOTE ********************************
The comments above are created mechanically, possibly without manual
checking by the sender. As there are many people performing automatic
tests on each upload to CPAN, it is likely that you will receive
identical messages about the same problem.
If you believe that the message is mistaken, please reply to the first
one with correction and/or additional informations, and do not take
it personally. We appreciate your patience. :)
**********************************************************************
Additional comments:
This report was machine-generated by CPAN::YACSmoke 0.0307.
------------------------------
ENVIRONMENT AND OTHER CONTEXT
------------------------------
Environment variables:
AUTOMATED_TESTING = 1
PATH = /sbin:/bin:/usr/sbin:/usr/bin:/usr/games:/usr/local/sbin:/usr/local/bin:/usr/X11R6/bin:/home/chris/bin
PERL5LIB = :/usr/home/chris/.cpanplus/5.8.7/build/onto-perl-latest/blib/lib:/usr/home/chris/.cpanplus/5.8.7/build/onto-perl-latest/blib/arch:/usr/home/chris/.cpanplus/5.8.7/build/onto-perl-latest/blib
PERL5_CPANPLUS_IS_RUNNING = 10841
PERL_MM_USE_DEFAULT = 1
SHELL = /bin/sh
TERM = screen
Perl special variables (and OS-specific diagnostics, for MSWin32):
Perl: $^X = /usr/local/bin/perl
UID: $< = 1001
EUID: $> = 1001
GID: $( = 0 0 0
EGID: $) = 0 0 0
-------------------------------
--
Summary of my perl5 (revision 5 version 8 subversion 7) configuration:
Platform:
osname=freebsd, osvers=6.0-release, archname=alpha-freebsd
uname='freebsd alpha.bingosnet.co.uk 6.0-release freebsd 6.0-release #0: thu nov 3 01:10:43 utc 2005 root@ds10.freebie.xs4all.nl:usrobjusrsrcsysgeneric alpha '
config_args='-sde -Dprefix=/usr/local -Darchlib=/usr/local/lib/perl5/5.8.7/mach -Dprivlib=/usr/local/lib/perl5/5.8.7 -Dman3dir=/usr/local/lib/perl5/5.8.7/perl/man/man3 -Dman1dir=/usr/local/man/man1 -Dsitearch=/usr/local/lib/perl5/site_perl/5.8.7/mach -Dsitelib=/usr/local/lib/perl5/site_perl/5.8.7 -Dscriptdir=/usr/local/bin -Dsiteman3dir=/usr/local/lib/perl5/5.8.7/man/man3 -Dsiteman1dir=/usr/local/man/man1 -Ui_malloc -Ui_iconv -Uinstallusrbinperl -Dcc=cc -Duseshrplib -Dccflags=-DAPPLLIB_EXP="/usr/local/lib/perl5/5.8.7/BSDPAN" -Doptimize=-O2 -fno-strict-aliasing -pipe -mcpu=ev4 -mtune=ev5 -mieee -Ud_dosuid -Ui_gdbm -Dusethreads=n -Dusemymalloc=y -Duse64bitint'
hint=recommended, useposix=true, d_sigaction=define
usethreads=undef use5005threads=undef useithreads=undef usemultiplicity=undef
useperlio=define d_sfio=undef uselargefiles=define usesocks=undef
use64bitint=define use64bitall=define uselongdouble=undef
usemymalloc=y, bincompat5005=undef
Compiler:
cc='cc', ccflags ='-DAPPLLIB_EXP="/usr/local/lib/perl5/5.8.7/BSDPAN" -DHAS_FPSETMASK -DHAS_FLOATINGPOINT_H -fno-strict-aliasing -pipe',
optimize='-O2 -fno-strict-aliasing -pipe -mcpu=ev4 -mtune=ev5 -mieee',
cppflags='-DAPPLLIB_EXP="/usr/local/lib/perl5/5.8.7/BSDPAN" -DHAS_FPSETMASK -DHAS_FLOATINGPOINT_H -fno-strict-aliasing -pipe'
ccversion='', gccversion='3.4.4 [FreeBSD] 20050518', gccosandvers=''
intsize=4, longsize=8, ptrsize=8, doublesize=8, byteorder=12345678
d_longlong=define, longlongsize=8, d_longdbl=define, longdblsize=8
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'
libpth=/usr/lib
libs=-lm -lcrypt -lutil
perllibs=-lm -lcrypt -lutil
libc=, so=so, useshrplib=true, libperl=libperl.so
gnulibc_version=''
Dynamic Linking:
dlsrc=dl_dlopen.xs, dlext=so, d_dlsymun=undef, ccdlflags=' -Wl,-R/usr/local/lib/perl5/5.8.7/mach/CORE'
cccdlflags='-DPIC -fPIC', lddlflags='-shared '
-
FAIL onto-perl-0.26 alpha-freebsd 6.0-release
by chris