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This queue is for tickets about the Bio-LITE-Taxonomy-NCBI CPAN distribution.

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The Basics
Id: 63285
Status: resolved
Priority: 0/
Queue: Bio-LITE-Taxonomy-NCBI
People
Owner: Nobody in particular
Requestors: GAURAV [...] cpan.org
Cc:
AdminCc:
Bug Information
Severity: Normal
Broken in: 0.02
Fixed in: (no value)

History Show all quoted text
  Tue Nov 23 12:18:53 2010 GAURAV [...] cpan.org - Ticket created
Subject: Pod coverage and syntax tests fail on MacOS X 10.6/Perl 5.10.1
Hi there, Thanks so much for this excellent module! I had a bit of trouble installing it, since two of the included tests failed (see attached). It's only Pod coverage failures, so I force-installed the module using 'cpan -f' and it's working great. Just thought I'd let you know about those test failures: it seems like a pretty small fix and, if the source is available on Git somewhere, I don't mind cleaning it up myself. cheers, Gaurav
Subject: CPAN output and Perl version.txt
-- CPAN OUTPUT -- CPAN: Storable loaded ok (v2.20) Going to read '/Users/vaidyagi/Library/Application Support/.cpan/Metadata' Database was generated on Mon, 22 Nov 2010 16:34:47 GMT Running install for module 'Bio::LITE::Taxonomy::NCBI' CPAN: YAML loaded ok (v0.70) Running make for M/MO/MOTIF/Bio-LITE-Taxonomy-NCBI-0.01.tar.gz CPAN: Digest::SHA loaded ok (v5.47) CPAN: Compress::Zlib loaded ok (v2.023) Checksum for /Users/vaidyagi/Library/Application Support/.cpan/sources/authors/id/M/MO/MOTIF/Bio-LITE-Taxonomy-NCBI-0.01.tar.gz ok CPAN: Archive::Tar loaded ok (v1.54) Bio-LITE-Taxonomy-NCBI-0.01/ Bio-LITE-Taxonomy-NCBI-0.01/lib/ Bio-LITE-Taxonomy-NCBI-0.01/lib/Bio/ Bio-LITE-Taxonomy-NCBI-0.01/lib/Bio/LITE/ Bio-LITE-Taxonomy-NCBI-0.01/lib/Bio/LITE/Taxonomy/ Bio-LITE-Taxonomy-NCBI-0.01/lib/Bio/LITE/Taxonomy/NCBI.pm Bio-LITE-Taxonomy-NCBI-0.01/README Bio-LITE-Taxonomy-NCBI-0.01/t/ Bio-LITE-Taxonomy-NCBI-0.01/t/pod-coverage.t Bio-LITE-Taxonomy-NCBI-0.01/t/NCBI.t Bio-LITE-Taxonomy-NCBI-0.01/t/data/ Bio-LITE-Taxonomy-NCBI-0.01/t/data/dict.bin Bio-LITE-Taxonomy-NCBI-0.01/t/data/nodes.dmp Bio-LITE-Taxonomy-NCBI-0.01/t/data/names.dmp Bio-LITE-Taxonomy-NCBI-0.01/t/00-load.t Bio-LITE-Taxonomy-NCBI-0.01/t/pod.t Bio-LITE-Taxonomy-NCBI-0.01/t/manifest.t Bio-LITE-Taxonomy-NCBI-0.01/Changes Bio-LITE-Taxonomy-NCBI-0.01/Makefile.PL Bio-LITE-Taxonomy-NCBI-0.01/META.yml Bio-LITE-Taxonomy-NCBI-0.01/MANIFEST CPAN: File::Temp loaded ok (v0.22) CPAN.pm: Going to build M/MO/MOTIF/Bio-LITE-Taxonomy-NCBI-0.01.tar.gz Argument "6.55_02" isn't numeric in numeric ge (>=) at Makefile.PL line 5. Checking if your kit is complete... Looks good Writing Makefile for Bio::LITE::Taxonomy::NCBI cp lib/Bio/LITE/Taxonomy/NCBI.pm blib/lib/Bio/LITE/Taxonomy/NCBI.pm Manifying blib/man3/Bio::LITE::Taxonomy::NCBI.3 MOTIF/Bio-LITE-Taxonomy-NCBI-0.01.tar.gz /usr/bin/make -- OK Running make test PERL_DL_NONLAZY=1 /opt/perl5/bin/perl "-MExtUtils::Command::MM" "-e" "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t t/00-load.t ....... 1/1 # Testing Bio::LITE::Taxonomy::NCBI 0.01, Perl 5.010001, /opt/perl5/bin/perl t/00-load.t ....... ok t/manifest.t ...... skipped: Author tests not required for installation t/NCBI.t .......... ok t/pod-coverage.t .. 1/1 # Failed test 'Pod coverage on Bio::LITE::Taxonomy::NCBI' # at /opt/perl5/lib/site_perl/5.10.0/Test/Pod/Coverage.pm line 126. # Coverage for Bio::LITE::Taxonomy::NCBI is 50.0%, with 2 naked subroutines: # get_taxonomy_with_levels_from_gi # get_term_at_level_from_gi # Looks like you failed 1 test of 1. t/pod-coverage.t .. Dubious, test returned 1 (wstat 256, 0x100) Failed 1/1 subtests t/pod.t ........... 1/1 # Failed test 'blib/lib/Bio/LITE/Taxonomy/NCBI.pm' # at /opt/perl5/lib/site_perl/5.10.0/Test/Pod.pm line 159. # blib/lib/Bio/LITE/Taxonomy/NCBI.pm (68): You forgot a '=back' before '=head1' # blib/lib/Bio/LITE/Taxonomy/NCBI.pm (85): You forgot a '=back' before '=head1' # Looks like you failed 1 test of 1. t/pod.t ........... Dubious, test returned 1 (wstat 256, 0x100) Failed 1/1 subtests Test Summary Report ------------------- t/pod-coverage.t (Wstat: 256 Tests: 1 Failed: 1) Failed test: 1 Non-zero exit status: 1 t/pod.t (Wstat: 256 Tests: 1 Failed: 1) Failed test: 1 Non-zero exit status: 1 Files=5, Tests=21, 41 wallclock secs ( 0.04 usr 0.02 sys + 34.62 cusr 1.22 csys = 35.90 CPU) Result: FAIL Failed 2/5 test programs. 2/21 subtests failed. make: *** [test_dynamic] Error 1 MOTIF/Bio-LITE-Taxonomy-NCBI-0.01.tar.gz /usr/bin/make test -- NOT OK //hint// to see the cpan-testers results for installing this module, try: reports MOTIF/Bio-LITE-Taxonomy-NCBI-0.01.tar.gz -- PERL VERSION -- Summary of my perl5 (revision 5 version 10 subversion 1) configuration: Platform: osname=darwin, osvers=9.8.0, archname=darwin-2level uname='darwin simhgad 9.8.0 darwin kernel version 9.8.0: wed jul 15 16:55:01 pdt 2009; root:xnu-1228.15.4~1release_i386 i386 ' config_args='-des -Dprefix=/opt/perl5' hint=recommended, useposix=true, d_sigaction=define useithreads=undef, usemultiplicity=undef useperlio=define, d_sfio=undef, uselargefiles=define, usesocks=undef use64bitint=undef, use64bitall=undef, uselongdouble=undef usemymalloc=n, bincompat5005=undef Compiler: cc='cc', ccflags ='-fno-common -DPERL_DARWIN -no-cpp-precomp -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include', optimize='-O3', cppflags='-no-cpp-precomp -fno-common -DPERL_DARWIN -no-cpp-precomp -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include' ccversion='', gccversion='4.0.1 (Apple Inc. build 5465)', gccosandvers='' intsize=4, longsize=4, ptrsize=4, doublesize=8, byteorder=1234 d_longlong=define, longlongsize=8, d_longdbl=define, longdblsize=16 ivtype='long', ivsize=4, 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=/usr/local/lib /usr/lib libs=-ldbm -ldl -lm -lutil -lc perllibs=-ldl -lm -lutil -lc libc=/usr/lib/libc.dylib, 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: PERL_DONT_CREATE_GVSV PERL_MALLOC_WRAP USE_LARGE_FILES USE_PERLIO Built under darwin Compiled at Nov 14 2009 11:47:39 @INC: /opt/perl5/lib/5.10.1/darwin-2level /opt/perl5/lib/5.10.1 /opt/perl5/lib/site_perl/5.10.1/darwin-2level /opt/perl5/lib/site_perl/5.10.1 /opt/perl5/lib/site_perl/5.10.0/darwin-2level /opt/perl5/lib/site_perl/5.10.0 /opt/perl5/lib/site_perl .
  Wed Nov 24 08:44:15 2010 MOTIF [...] cpan.org - Correspondence added
Hi Gaurav, Thanks a lot for your interest in these modules and for taking time for reporting this annoying issue. Though I was aware of it I hadn't much time last week to fix it. Sorry for that. I have uploaded a fixed version that should install smooth now. Any other comment or suggestion regarding these modules is welcome. Also, if you want to collaborate in any of the improvements for these modules that I have in mind you are welcome to contact me again (emepyc@gmail.com) Regards, M; On Tue Nov 23 12:18:53 2010, GAURAV wrote: Show quoted text
> Hi there, > > Thanks so much for this excellent module! I had a bit of trouble > installing it, since two of the included tests failed (see attached). > It's only Pod coverage failures, so I force-installed the module using > 'cpan -f' and it's working great. Just thought I'd let you know about > those test failures: it seems like a pretty small fix and, if the
source Show quoted text
> is available on Git somewhere, I don't mind cleaning it up myself. > > cheers, > Gaurav
  Wed Nov 24 08:44:15 2010 The RT System itself - Status changed from 'new' to 'open'
  Tue Nov 30 11:35:39 2010 MOTIF [...] cpan.org - Correspondence added
POD issues solved
  Tue Nov 30 11:35:40 2010 MOTIF [...] cpan.org - Status changed from 'open' to 'resolved'