Opened 14 years ago

Closed 9 years ago

#26468 closed submission (fixed)

New Port: p5-bioperl

Reported by: tonym@… Owned by: ryandesign (Ryan Carsten Schmidt)
Priority: Normal Milestone:
Component: ports Version:
Keywords: Cc: uzilday@…, andreas.wilm@…, mojca (Mojca Miklavec), jason@…, dbevans (David B. Evans)
Port: p5-bioperl

Description

BioPerl is a collection of Perl Modules for Bioinformatics.

HomePage::

http://www.bioperl.org/wiki/Main_Page

CPAN Page::

http://search.cpan.org/~cjfields/BioPerl-1.6.1/BioPerl.pm

Requested in ticket #24022.

Attachments (4)

Portfile (1.5 KB) - added by tonym@… 14 years ago.
Portfile.2 (1.7 KB) - added by ryandesign (Ryan Carsten Schmidt) 14 years ago.
revised portfile
Portfile.3 (1.7 KB) - added by jason@… 13 years ago.
1.6.9 was released, here is a portfile that includes more dependencies
Portfile.4 (2.8 KB) - added by dbevans (David B. Evans) 9 years ago.
Revised Portfile version 1.6.924

Download all attachments as: .zip

Change History (20)

Changed 14 years ago by tonym@…

Attachment: Portfile added

comment:1 Changed 14 years ago by mf2k (Frank Schima)

Keywords: haspatch removed
Version: 1.9.1

comment:2 Changed 14 years ago by mf2k (Frank Schima)

Cc: uzilday@… added

comment:3 Changed 14 years ago by ryandesign (Ryan Carsten Schmidt)

Owner: changed from macports-tickets@… to ryandesign@…
Status: newassigned

Changed 14 years ago by ryandesign (Ryan Carsten Schmidt)

Attachment: Portfile.2 added

revised portfile

comment:4 Changed 14 years ago by ryandesign (Ryan Carsten Schmidt)

Attached is a revised portfile with these changes:

  • reformatted
  • added "universal_variant no" because dependency p5-libwww-perl does not have a universal variant
  • added dependency on p5-io-string because I noticed it was downloading IO::String
  • added dependency on p5-data-stag because I noticed it was downloading Data::Stag

Unfortunately we have no port p5-data-stag yet so please create and submit a port p5-data-stag. Please add any other required dependencies also.

comment:5 in reply to:  4 ; Changed 14 years ago by tonym@…

Replying to ryandesign@…:

Unfortunately we have no port p5-data-stag yet so please create and submit a port p5-data-stag. Please add any other required dependencies also.

Will do.

comment:6 in reply to:  5 Changed 14 years ago by tonym@…

Replying to ryandesign@…:

Unfortunately we have no port p5-data-stag yet so please create and submit a port p5-data-stag. Please add any other required dependencies also.

p5-data-stag has been submitted in ticket #26529

comment:7 Changed 13 years ago by larry+macports@…

It looks to me like the only showstopper for this issue has been resolved.

comment:8 Changed 13 years ago by andreas.wilm@…

Works fine for me

MacPorts 1.9.2
perl5                          @5.8.9          lang/perl5
expat                          @2.0.1          textproc/expat
p5-data-stag                   @0.11           perl/p5-data-stag
p5-io-string                   @1.08           perl/p5-io-string
p5-module-build                @0.3607         perl/p5-module-build
p5-libwww-perl                 @5.837          perl/p5-libwww-perl
OS X 10.6.6

Andreas

comment:9 Changed 13 years ago by andreas.wilm@…

Cc: andreas.wilm@… added

Cc Me!

comment:10 Changed 13 years ago by ryandesign (Ryan Carsten Schmidt)

Sorry for forgetting about this submission.

I remember now what the next problem was. When installing, it tries to download DB::File. It says "DB_File is absolutely required prior to installation: shall I install it now using a CPAN shell?" We don't have a p5-db-file port yet.

comment:11 in reply to:  10 Changed 13 years ago by ryandesign (Ryan Carsten Schmidt)

Replying to ryandesign@…:

We don't have a p5-db-file port yet.

I filed #28174 for this and will write some notes there about what I know about this.

Changed 13 years ago by jason@…

Attachment: Portfile.3 added

1.6.9 was released, here is a portfile that includes more dependencies

comment:12 Changed 9 years ago by mojca (Mojca Miklavec)

Cc: mojca@… added

Cc Me!

Changed 9 years ago by dbevans (David B. Evans)

Attachment: Portfile.4 added

Revised Portfile version 1.6.924

comment:13 Changed 9 years ago by dbevans (David B. Evans)

Cc: jason@… added

Seeing that this submission has been struck for some time now, I've attached a revised version of the Portfile that works with the current perl5 PortGroup. Version is updated to 1.6.924 and dependencies have been updated as well to match META.json.

This builds and test runs without errors (for me), although a few tests are skipped due to absence of some optional modules.

Any further changes needed?

Last edited 9 years ago by dbevans (David B. Evans) (previous) (diff)

comment:14 Changed 9 years ago by dbevans (David B. Evans)

FYI, related module p5-bio-phylo (recommended by p5-bioperl) has been committed in r135149, r135150 as nomaintainer.
Additionally, module p5-bio-asn1-entrezgene which depends on p5-bioperl has been submitted for review in #47480, also nomaintainer.

Perhaps someone from the bioperl community would like to take up maintainership of one or both of these ports.

comment:15 Changed 9 years ago by dbevans (David B. Evans)

Cc: devans@… added

Cc Me!

comment:16 Changed 9 years ago by dbevans (David B. Evans)

Resolution: fixed
Status: assignedclosed

Hearing no objections, committed in r135244.

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