Open cjfields opened 8 years ago
cjfields
commented
8 years ago Original Redmine Comment Author Name: Chris Fields Original Date: 2010-04-05T10:14:13Z
Fernan, this doesn’t seem to be very widespread (it’s the first time I’ve heard of it since the 1.6.1 release, and it wasn’t one of the fail reasons on CPAN Testers).
We will need to know the (perl version|CPAN version|OS) to try reproducing this.
cjfields
commented
8 years ago Original Redmine Comment Author Name: Fernan Aguero Original Date: 2010-04-05T10:48:22Z
(In reply to comment #1)
Fernan, this doesn’t seem to be very widespread (it’s the first time I’ve heard of it since the 1.6.1 release, and it wasn’t one of the fail reasons on CPAN Testers).
This is happening since ~ 1.5.x. Though I always thought someone would notice and fix it :)
It doesn’t cause a failure when installing … so I would not expect to be detected by CPAN Testers. It’s a cosmetic issue that only affects listing of updates in the CPAN shell. It doesn’t affect looking for information on a specific module, e.g. the following works fine:
cpan> i /BioPerl/ cpan[3]> i /BioPerl/ Bundle Bundle::BioPerl (CRAFFI/Bundle-BioPerl-2.1.8.tar.gz) Distribution BIRNEY/bioperl-1.2.2.tar.gz Distribution BIRNEY/bioperl-1.2.3.tar.gz Distribution BIRNEY/bioperl-1.2.tar.gz Distribution BIRNEY/bioperl-1.4.tar.gz Distribution BIRNEY/bioperl-db-0.1.tar.gz Distribution BIRNEY/bioperl-ext-1.4.tar.gz Distribution BIRNEY/bioperl-gui-0.7.tar.gz Distribution BIRNEY/bioperl-run-1.4.tar.gz Distribution BOZO/Fry-Lib-BioPerl-0.15.tar.gz Distribution CJFIELDS/BioPerl-1.6.0.tar.gz Distribution CJFIELDS/BioPerl-1.6.1.tar.gz Distribution CJFIELDS/BioPerl-db-1.6.0.tar.gz Distribution CJFIELDS/BioPerl-network-1.6.0.tar.gz Distribution CJFIELDS/BioPerl-run-1.6.1.tar.gz Distribution CRAFFI/Bundle-BioPerl-2.1.8.tar.gz Module < Bio::LiveSeq::IO::BioPerl (CJFIELDS/BioPerl-1.6.1.tar.gz) Module Fry::Lib::BioPerl (BOZO/Fry-Lib-BioPerl-0.15.tar.gz) Author BIOPERLML (“Bioperl-l” bioperl-l@lists.open-bio.org) 19 items found
Seems like CPAN-shell is looking inside modules for version information, maybe comparing what’s installed to what’s available, and failing … apparently this is only done at this stage (looking for out of date modules) so it’s not preventing installation of the Distribution.
We will need to know the (perl version|CPAN version|OS) to try reproducing this.
CPAN 1.9402 (ANDK/CPAN-1.9402.tar.gz) perl 5.10.0 Ubuntu Linux 9.10
cjfields
commented
8 years ago Original Redmine Comment Author Name: Chris Fields Original Date: 2010-04-05T11:20:59Z
(In reply to comment #2)
(In reply to comment #1)
Fernan, this doesn’t seem to be very widespread (it’s the first time I’ve heard of it since the 1.6.1 release, and it wasn’t one of the fail reasons on CPAN Testers).
This is happening since ~ 1.5.x. Though I always thought someone would notice and fix it :)
Nope, never noticed it. It’s the first time I recall it being reported.
Seems like CPAN-shell is looking inside modules for version information, maybe comparing what’s installed to what’s available, and failing … apparently this is only done at this stage (looking for out of date modules) so it’s not preventing installation of the Distribution.
We will need to know the (perl version|CPAN version|OS) to try reproducing this.
CPAN 1.9402 (ANDK/CPAN-1.9402.tar.gz) perl 5.10.0 Ubuntu Linux 9.10
Okay, I’ll check it out. I will be installing a local perl 5.10.1 and perl 5.12 on my Ubuntu box for testing later this week, I can probably try replicating this there.
Author Name: Fernan Aguero (Fernan Aguero) Original Redmine Issue: 3041, https://redmine.open-bio.org/issues/3041 Original Date: 2010-04-05 Original Assignee: Bioperl Guts
When using CPAN to install modules, bioperl breaks the listing of modules that can be updated.
Bio/Ontology/SimpleGOEngine/GraphAdaptor.pm seems to be the culprit.
How to reproduce:
First, make sure BioPerl is installed:
1) open a CPAN shell and install BioPerl cpan> install CJFIELDS/BioPerl-1.6.0.tar.gz
When BioPerl is installed, you can ask CPAN about modules that need updating
2) in your CPAN shell type ‘r’ cpan> r
and notice how BioPerl breaks the listing of modules
Package namespace installed latest in CPAN file Any::Moose 0.11 0.12 SARTAK/Any-Moose-0.12.tar.gz JSON 2.19 2.20 MAKAMAKA/JSON-2.20.tar.gz … Bio::Align::AlignI undef 1.006001 CJFIELDS/BioPerl-1.6.1.tar.gz Could not eval ’ package ExtUtils::MakeMaker::_version; no strict; BEGIN { eval {
Ensure any version() routine which might have leaked
into this package has been deleted. Interferes with
version->import()
undef *version; require version; “version”->import; } }
local $Graph::VERSION; $Graph::VERSION=undef; do { ( defined $Graph::VERSION && $Graph::VERSION >= 0.5 ) ? }; $Graph::VERSION; ‘ in /usr/local/share/perl/5.10.0/Bio/Ontology/SimpleGOEngine/GraphAdaptor.pm: syntax error at (eval 3244) line 17, at EOF Could not eval ’ package ExtUtils::MakeMaker::_version; no strict; BEGIN { eval {
Ensure any version() routine which might have leaked
into this package has been deleted. Interferes with
version->import()
undef *version; require version; “version”->import; } }
local $Graph::VERSION; $Graph::VERSION=undef; do { ( defined $Graph::VERSION && $Graph::VERSION >= 0.5 ) ? }; $Graph::VERSION; ‘ in /usr/local/share/perl/5.10.0/Bio/Ontology/SimpleGOEngine/GraphAdaptor.pm: syntax error at (eval 3244) line 17, at EOF Could not eval ’ package ExtUtils::MakeMaker::_version; no strict; BEGIN { eval {
Ensure any version() routine which might have leaked
into this package has been deleted. Interferes with
version->import()
undef *version; require version; “version”->import; } }
local $Graph::VERSION; $Graph::VERSION=undef; do { ( defined $Graph::VERSION && $Graph::VERSION >= 0.5 ) ? }; $Graph::VERSION; ’ in /usr/local/share/perl/5.10.0/Bio/Ontology/SimpleGOEngine/GraphAdaptor.pm: syntax error at (eval 3245) line 17, at EOF Compress::Zlib 2.020 2.025 PMQS/IO-Compress-2.025.tar.gz Image::Magick 6.5.1 6.005009 JCRISTY/PerlMagick-6.59.tar.gz