cjfields / bioperl6 Goto Github PK

Tried installing with panda but got a load of error output:

$ panda install bioperl6
==> Fetching bioperl6
==> Building bioperl6
Compiling lib/Configure.pm to pir
Useless declaration of a has-scoped method in mainline
Compiling lib/Bio/Alphabet.pm to pir
Compiling lib/Bio/AnnotationCollectionI.pm to pir
Compiling lib/Bio/AnnotationI.pm to pir
1 #!/usr/bin/env perl6
Compiling lib/Bio/Annotation/Comment.pm to pir
1 >id comment
===SORRY!=== Error while compiling lib/Bio/Annotation/Comment.pm
Attribute $!text not declared in class Bio::Annotation::Comment
at lib/Bio/Annotation/Comment.pm:23
------> return "Comment: "~ $!text⏏;
Passing an object candidate to Mu.bless is deprecated in method new at /Users/mo8122/rakudo/rakudo-star-2013.09/install/lib/parrot/5.5.0/languages/perl6/lib/Panda/Common.pm:55

build stage failed for bioperl6: Failed building lib/Bio/Annotation/Comment.pm

Then I git cloned the whole repo and tried using the SeqIO library locally and just got endless chains of compile time errors in a fair chunk of code that looked a bit shaky.
Line 81 in lib/Bio/Role/Location/Simple.pm failed with "Attribute $!min_ not declared in role Bio::Role::Location::Simple"

The line in question is
$pos_str = '(' ~ %data{"$!min_$pos"} ~ '.' ~ %data{"$!max_$pos"} ~ ')';
I thought this might have been
$pos_str = '(' ~ %data{"{$!min}$pos"} ~ '.' ~ %data{"{$!max}$pos"} ~ ')';
but there weren't any attributes by those names. If I just escape the first $ to $ in the assumption a mapping to some attribute names is being created I just reach the next in what I assume to be a long list of compiler errors.

Has bioperl6 been abandoned? Considering I've never really liked the class layout of bioperl and that it's relatively easy to create parsers in Perl6 I'm tempted to just go it alone. But if someone is willing to help get bioperl6 building again I'm happy to help out too.

Hi i am using MacOS Catalina, i am facing this error. i have tried through conda and CPAN to fix this. i am facing this error from last 2 weeks, Before this module was working . Can you guide me, How i can fix it.

Can't locate Bio/SeqIO.pm in @inc (you may need to install the Bio::SeqIO module) (@inc contains: /Users/padana/opt/anaconda3/lib/site_perl/5.26.2/darwin-thread-multi-2level /Users/padana/opt/anaconda3/lib/site_perl/5.26.2 /Users/padana/opt/anaconda3/lib/5.26.2/darwin-thread-multi-2level /Users/padana/opt/anaconda3/lib/5.26.2 .)

Hi Chris,

there might come a moment in my copious amounts of spare time where I'd like to try out perl6 implementations of phylogenetic trees, nodes and taxa. Might as well do this as part of bioperl6, so if you trust me enough not to make too much of a mess, may I have push access?

Thanks,

Rutger

We can start pushing releases to CPAN, completely missed this:

https://docs.perl6.org/language/modules.html#Upload_your_Module_to_CPAN

With recent repository update, I cannot install with panda

Testing OK, but I get this message before error:

===SORRY!===
Could not find Bio::Role::Annotation in:
/home/toniher/.perl6/2015.12
/home/toniher/.rakudobrew/moar-nom/install/share/perl6/site
/home/toniher/.rakudobrew/moar-nom/install/share/perl6/vendor
/home/toniher/.rakudobrew/moar-nom/install/share/perl6
CompUnit::Repository::AbsolutePath<139824386661280>
CompUnit::Repository::NQP<139824386632352>
CompUnit::Repository::Perl5<139824386602016>
CompUnit::Repository::AbsolutePath<139824386291912>
CompUnit::Repository::NQP<139824386288504>
CompUnit::Repository::Perl5<139824386285344>
Return status 256

Hi,
has there been any discussion on phylogenetic trees and nodes? Any ideas about package names? I'd like to try my hand at that, having built up some experience both with the BioPerl implementation and the Bio::Phylo objects. Would you be interested in pull requests from my side?
Rutger

===> Testing: BioPerl6:ver<0.0.1>
# Failed test 'is-fuzzy'
# at t/Location/Simple.t line 28
# Failed test 'is-fuzzy'
# at t/Location/Simple.t line 36
# Looks like you failed 2 tests of 35

------------- WARNING -------------
MSG: foo
-----------------------------------



------------- WARNING -------------
MSG: foo
-----------------------------------



------------- WARNING -------------
MSG: foo
-----------------------------------


===> Testing [FAIL]: BioPerl6:ver<0.0.1>

perl6 version:

% perl6 -v                                                                                                                 (master|✔)
This is Rakudo version 2017.09-353-g1ea3297b2 built on MoarVM version 2017.09.1-575-gd4e230a6
implementing Perl 6.c.

the last travis run was 11 months ago; we do include this in toaster runs during release preparation, but you can get early warning if something in rakudo changes that makes your module sad :)

master branch does not work with Rakudo master (previously, ng). This is mainly a placeholder until we get back contextuals or PERL6LIB.