Perl 6 - the future is here, just unevenly distributed

IRC log for #bioperl, 2014-04-29

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All times shown according to UTC.

Time Nick Message
01:00 mnb_ joined #bioperl
10:55 carandraug joined #bioperl
16:52 cdiesh I am having a problem running jbrowse's perl tests on linux platforms. i am not sure if it is a bioperl issue though.
16:54 cdiesh i am wondering if there was an updated package that caused it
16:56 cdiesh i dunno if anyone is able to help, but here are my test results from jbrowse on ubuntu 14 http://nopaste.info/78c3e79aaf.html
16:56 cdiesh the tests run fine on Mac OSX for me (github tip)
17:11 cdiesh added note: the tests also do not work on older versions of JBrowse either, leading me to believe that something else (like a package update) might have caused the problem
17:20 trs cdiesh: Perl version?
17:22 trs I don't know what the test code is doing, but if it's relying on the order of keys %hash or values %hash somewhere being stable, that'll fail on Perl >= 5.18.0
17:30 cdiesh trs: oo. i think it is perl 5.18 on these ubuntu machines
17:54 trs older versions of Perl's hashing scheme let you slip by in many cases with subtle assumptions about the ordering of keys/values because the order was more stable (though not guaranteed) so it was harder to see the lurking bug.
17:55 trs 5.18 changed the hashing scheme to close a security problem and in doing so made the ordering much more random.
17:55 trs cdiesh: does jbrowse get uploaded to cpan?
18:05 cdiesh some jbrowse perl packages are on cpan
18:05 cdiesh trs: but not everything
18:06 cdiesh but these packages might be sensitive to this change, given the tests failing
18:08 cdiesh one package: http://search.cpan.org/~rbuels/Bio-GFF3-2.0/
18:17 cdiesh i think this package does not fail tests  though.
18:19 trs cdiesh: I was only asking about cpan because if jbrowse was on cpan, it'd get the benefit of cpantesters and you'd be able to see test failure reports and analysis (such as reports that would quickly point to 5.18 being the issue)
18:22 cdiesh trs: ah yes. there are quite a few perl modules that are internal to jbrowse
18:23 cdiesh but no cpan for them
18:33 trs I mostly meant a CPAN distribution for the entire jbrowse dist.
18:33 trs if only to run the tests
18:37 cdiesh i will definitely consider that
18:37 cdiesh I'm waiting on another older version of perl to run the tests on this ubuntu machine. that way i can see if the 5.18 is the problem..
18:37 cdiesh would be easier with cpan testers :)
18:57 cdiesh yep...looks like older version of perl works..
22:02 github [bioperl-live] fjossandon pushed 4 new commits to master: https://github.com/bioperl/bioperl-liv​e/compare/aa377fce499e...b9afc6c7a535
22:02 github bioperl-live/master 53e3c8b Francisco J. Ossandon: Changed argument "requires_modules" to "require_module"...
22:02 github bioperl-live/master 7142389 Francisco J. Ossandon: Added 'Data::Stag' requirement to many tests files...
22:02 github bioperl-live/master 637aab3 Francisco J. Ossandon: BioFetch.t & SwissProt.t: Fixed some number of skipped tests...
22:41 byte48 joined #bioperl

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