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This queue is for tickets about the bioperl CPAN distribution.

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The Basics
Id: 91880
Status: resolved
Priority: 0/
Queue: bioperl
People
Owner: Nobody in particular
Requestors: SREZIC [...] cpan.org
tsibley [...] cpan.org
Cc:
AdminCc:
Bug Information
Severity: (no value)
Broken in: 1.6.923
Fixed in: (no value)

History Show all quoted text
  Sun Jan 05 14:16:51 2014 SREZIC [...] cpan.org - Ticket created
Subject: Some tests fail with "Can't store CODE items" error
The complete error message is: Can't store CODE items at Bio/Root/Root.pm line 223. A sample test report can be seen in http://www.cpantesters.org/cpan/report/88f32df6-6c7c-11e3-bf3e-b51f7bc94557 I assume the error happens if Storable is chosen as serializer. Storable cannot serialize CODE references by default. To do so, one has explicitely set the $Storable::Deparse variable (and a deserializer has to set the $Storable::Eval variable). Regards, Slaven
  Thu Jun 05 14:11:43 2014 tsibley [...] cpan.org - Requestor TSIBLEY added
  Thu Jun 05 18:58:00 2014 tsibley [...] cpan.org - Correspondence added
On Sun Jan 05 11:16:51 2014, SREZIC wrote: Show quoted text
> The complete error message is: > > Can't store CODE items at Bio/Root/Root.pm line 223. > > A sample test report can be seen in > http://www.cpantesters.org/cpan/report/88f32df6-6c7c-11e3-bf3e- > b51f7bc94557 > > I assume the error happens if Storable is chosen as serializer. > Storable cannot serialize CODE references by default. To do so, one > has explicitely set the $Storable::Deparse variable (and a > deserializer has to set the $Storable::Eval variable).
Current BioPerl git branch v1.6.x and master address this by ripping out Storable usage in Bio::Root::Root. I also submitted an alternate solution which keeps Storable and simply uses the appropriate flags. https://github.com/bioperl/bioperl-live/pull/73 A quick fix for anyone finding this ticket is to install Clone from CPAN before attempting to install BioPerl again.
  Sun Jul 10 23:23:15 2016 cjfields [...] uiuc.edu - Correspondence added
Pull request was merged back in 2014 but ticket wasn't closed, now doing so. Thanks! On Thu Jun 05 17:58:00 2014, TSIBLEY wrote: Show quoted text
> On Sun Jan 05 11:16:51 2014, SREZIC wrote:
> > The complete error message is: > > > > Can't store CODE items at Bio/Root/Root.pm line 223. > > > > A sample test report can be seen in > > http://www.cpantesters.org/cpan/report/88f32df6-6c7c-11e3-bf3e- > > b51f7bc94557 > > > > I assume the error happens if Storable is chosen as serializer. > > Storable cannot serialize CODE references by default. To do so, one > > has explicitely set the $Storable::Deparse variable (and a > > deserializer has to set the $Storable::Eval variable).
> > Current BioPerl git branch v1.6.x and master address this by ripping > out Storable usage in Bio::Root::Root. I also submitted an alternate > solution which keeps Storable and simply uses the appropriate flags. > > https://github.com/bioperl/bioperl-live/pull/73 > > A quick fix for anyone finding this ticket is to install Clone from > CPAN before attempting to install BioPerl again.
  Sun Jul 10 23:23:15 2016 The RT System itself - Status changed from 'new' to 'open'
  Sun Jul 10 23:23:16 2016 cjfields [...] uiuc.edu - Status changed from 'open' to 'resolved'