{"action":"created","issue":{"url":"https://api.github.com/repos/cjfields/redmine-test/issues/31","labels_url":"https://api.github.com/repos/cjfields/redmine-test/issues/31/labels{/name}","comments_url":"https://api.github.com/repos/cjfields/redmine-test/issues/31/comments","events_url":"https://api.github.com/repos/cjfields/redmine-test/issues/31/events","html_url":"https://github.com/cjfields/redmine-test/issues/31","id":108469045,"number":31,"title":"BioPerl breaks listing of updateable modules in a CPAN shell","user":{"login":"cjfields","id":49265,"avatar_url":"https://avatars.githubusercontent.com/u/49265?v=3","gravatar_id":"","url":"https://api.github.com/users/cjfields","html_url":"https://github.com/cjfields","followers_url":"https://api.github.com/users/cjfields/followers","following_url":"https://api.github.com/users/cjfields/following{/other_user}","gists_url":"https://api.github.com/users/cjfields/gists{/gist_id}","starred_url":"https://api.github.com/users/cjfields/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/cjfields/subscriptions","organizations_url":"https://api.github.com/users/cjfields/orgs","repos_url":"https://api.github.com/users/cjfields/repos","events_url":"https://api.github.com/users/cjfields/events{/privacy}","received_events_url":"https://api.github.com/users/cjfields/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/cjfields/redmine-test/labels/Category:%20Core%20Components","name":"Category: Core Components","color":"006699"},{"url":"https://api.github.com/repos/cjfields/redmine-test/labels/Priority:%20Normal","name":"Priority: Normal","color":"666600"},{"url":"https://api.github.com/repos/cjfields/redmine-test/labels/Status:%20New","name":"Status: New","color":"FF6600"},{"url":"https://api.github.com/repos/cjfields/redmine-test/labels/Tracker:%20Bug","name":"Tracker: Bug","color":"FF0000"}],"state":"open","locked":false,"assignee":null,"milestone":{"url":"https://api.github.com/repos/cjfields/redmine-test/milestones/2","html_url":"https://github.com/cjfields/redmine-test/milestones/1.6%20branch","labels_url":"https://api.github.com/repos/cjfields/redmine-test/milestones/2/labels","id":1324963,"number":2,"title":"1.6 branch","description":null,"creator":{"login":"cjfields","id":49265,"avatar_url":"https://avatars.githubusercontent.com/u/49265?v=3","gravatar_id":"","url":"https://api.github.com/users/cjfields","html_url":"https://github.com/cjfields","followers_url":"https://api.github.com/users/cjfields/followers","following_url":"https://api.github.com/users/cjfields/following{/other_user}","gists_url":"https://api.github.com/users/cjfields/gists{/gist_id}","starred_url":"https://api.github.com/users/cjfields/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/cjfields/subscriptions","organizations_url":"https://api.github.com/users/cjfields/orgs","repos_url":"https://api.github.com/users/cjfields/repos","events_url":"https://api.github.com/users/cjfields/events{/privacy}","received_events_url":"https://api.github.com/users/cjfields/received_events","type":"User","site_admin":false},"open_issues":7,"closed_issues":0,"state":"open","created_at":"2015-09-26T14:12:47Z","updated_at":"2015-09-26T14:20:26Z","due_on":null,"closed_at":null},"comments":3,"created_at":"2015-09-26T14:20:26Z","updated_at":"2015-09-26T14:20:36Z","closed_at":null,"body":"---\n\n\nAuthor Name: **Fernan Aguero** (Fernan Aguero)\nOriginal Redmine Issue: 3041, https://redmine.open-bio.org/issues/3041\nOriginal Date: 2010-04-05\nOriginal Assignee: Bioperl Guts\n\n---\n\nWhen using CPAN to install modules, bioperl breaks the listing of modules that can be updated.\n\nBio/Ontology/SimpleGOEngine/GraphAdaptor.pm seems to be the culprit.\n\nHow to reproduce:\n\nFirst, make sure BioPerl is installed:\n\n1) open a CPAN shell and install BioPerl\ncpan\\> install CJFIELDS/BioPerl-1.6.0.tar.gz\n\n1.  we’re installing an older version on purpose so that later CPAN will show there is an update for this package\n\nWhen BioPerl is installed, you can ask CPAN about modules that need updating\n\n2) in your CPAN shell type ‘r’\ncpan\\> r\n\nand notice how BioPerl breaks the listing of modules\n\nPackage namespace installed latest in CPAN file\nAny::Moose 0.11 0.12 SARTAK/Any-Moose-0.12.tar.gz\nJSON 2.19 2.20 MAKAMAKA/JSON-2.20.tar.gz\n…\nBio::Align::AlignI undef 1.006001 CJFIELDS/BioPerl-1.6.1.tar.gz\nCould not eval ’\n package ExtUtils::MakeMaker::\\_version;\n no strict;\n BEGIN { eval {\n \\# Ensure any version() routine which might have leaked\n \\# into this package has been deleted. Interferes with\n \\# version-\\>import()\n undef \\*version;\n require version;\n “version”-\\>import;\n } }\n\nlocal $Graph::VERSION;\n $Graph::VERSION=undef;\n do {\n ( defined $Graph::VERSION && $Graph::VERSION \\>= 0.5 ) ?\n };\n $Graph::VERSION;\n ‘ in /usr/local/share/perl/5.10.0/Bio/Ontology/SimpleGOEngine/GraphAdaptor.pm: syntax error at (eval 3244) line 17, at EOF\nCould not eval ’\n package ExtUtils::MakeMaker::\\_version;\n no strict;\n BEGIN { eval {\n \\# Ensure any version() routine which might have leaked\n \\# into this package has been deleted. Interferes with\n \\# version-\\>import()\n undef \\*version;\n require version;\n “version”-\\>import;\n } }\n\nlocal $Graph::VERSION;\n $Graph::VERSION=undef;\n do {\n ( defined $Graph::VERSION && $Graph::VERSION \\>= 0.5 ) ?\n };\n $Graph::VERSION;\n ‘ in /usr/local/share/perl/5.10.0/Bio/Ontology/SimpleGOEngine/GraphAdaptor.pm: syntax error at (eval 3244) line 17, at EOF\nCould not eval ’\n package ExtUtils::MakeMaker::\\_version;\n no strict;\n BEGIN { eval {\n \\# Ensure any version() routine which might have leaked\n \\# into this package has been deleted. Interferes with\n \\# version-\\>import()\n undef \\*version;\n require version;\n “version”-\\>import;\n } }\n\nlocal $Graph::VERSION;\n $Graph::VERSION=undef;\n do {\n ( defined $Graph::VERSION && $Graph::VERSION \\>= 0.5 ) ?\n };\n $Graph::VERSION;\n ’ in /usr/local/share/perl/5.10.0/Bio/Ontology/SimpleGOEngine/GraphAdaptor.pm: syntax error at (eval 3245) line 17, at EOF\nCompress::Zlib 2.020 2.025 PMQS/IO-Compress-2.025.tar.gz\nImage::Magick 6.5.1 6.005009 JCRISTY/PerlMagick-6.59.tar.gz\n\n\n\n\n"},"comment":{"url":"https://api.github.com/repos/cjfields/redmine-test/issues/comments/143450805","html_url":"https://github.com/cjfields/redmine-test/issues/31#issuecomment-143450805","issue_url":"https://api.github.com/repos/cjfields/redmine-test/issues/31","id":143450805,"user":{"login":"cjfields","id":49265,"avatar_url":"https://avatars.githubusercontent.com/u/49265?v=3","gravatar_id":"","url":"https://api.github.com/users/cjfields","html_url":"https://github.com/cjfields","followers_url":"https://api.github.com/users/cjfields/followers","following_url":"https://api.github.com/users/cjfields/following{/other_user}","gists_url":"https://api.github.com/users/cjfields/gists{/gist_id}","starred_url":"https://api.github.com/users/cjfields/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/cjfields/subscriptions","organizations_url":"https://api.github.com/users/cjfields/orgs","repos_url":"https://api.github.com/users/cjfields/repos","events_url":"https://api.github.com/users/cjfields/events{/privacy}","received_events_url":"https://api.github.com/users/cjfields/received_events","type":"User","site_admin":false},"created_at":"2015-09-26T14:20:35Z","updated_at":"2015-09-26T14:20:35Z","body":"---\n\nOriginal Redmine Comment\nAuthor Name: **Chris Fields** (Chris Fields)\nOriginal Date: 2010-04-05T11:20:59Z\n\n---\n\n(In reply to comment \\#2)\n\\> (In reply to comment \\#1)\n\\> \\> Fernan, this doesn’t seem to be very widespread (it’s the first time I’ve heard\n\\> \\> of it since the 1.6.1 release, and it wasn’t one of the fail reasons on CPAN\n\\> \\> Testers).\n\\>\n\\> This is happening since ~ 1.5.x. Though I always thought someone would notice\n\\> and fix it :)\n\nNope, never noticed it. It’s the first time I recall it being reported.\n\n\\> Seems like CPAN-shell is looking inside modules for version information, maybe\n\\> comparing what’s installed to what’s available, and failing … apparently this\n\\> is only done at this stage (looking for out of date modules) so it’s not\n\\> preventing installation of the Distribution.\n\\>\n\\>\n\\> \\> We will need to know the (perl version|CPAN version|OS) to try reproducing\n\\> \\> this.\n\\>\n\\> CPAN 1.9402 (ANDK/CPAN-1.9402.tar.gz)\n\\> perl 5.10.0\n\\> Ubuntu Linux 9.10\n\nOkay, 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.\n\n"}}