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Port details
p5-bioperl-devel 1.5.2 biology Deleted on this many watch lists=2 search for ports that depend on this port
Deprecated DEPRECATED: no longer under development
Expired This port expired on: 2009-05-31
A collection of Perl modules for bioinformatics (developer release)
Was Maintained by: mauricio@arareko.net search for ports maintained by this maintainer
Port Added: 14 Aug 2001 06:36:36
Also Listed In: perl5
License: not specified in port


The Bioperl Project is an international association of developers of open
source Perl tools for bioinformatics, genomics and life science research. 

Bioperl is a collection of object-oriented Perl modules created by the
Bioperl Project.  It forms the basis of a large number of bioinformatics and
genomics applications.

(For an interesting aside on "How Perl saved the Human Genome Project", see
http://bioperl.org/GetStarted/tpj_ls_bio.html)

WWW: http://bioperl.org/
SVNWeb : Main Web Site : Distfiles Availability : PortsMon

NOTE: FreshPorts displays only required dependencies information. Optional dependencies are not covered.

Required To Build:
  1. lang/perl5.8
  2. lang/perl5.8
  3. biology/p5-Bio-ASN1-EntrezGene
  4. devel/p5-Class-AutoClass
  5. devel/p5-Data-Stag
  6. devel/p5-Data-Stag
  7. devel/p5-Data-Stag
  8. graphics/p5-GD-SVG
  9. math/p5-Graph
  10. www/p5-libwww
  11. devel/p5-IO-stringy
  12. devel/p5-IO-String
  13. www/p5-libwww
  14. devel/p5-Set-Scalar
  15. net/p5-SOAP-Lite
  16. textproc/p5-Spreadsheet-ParseExcel
  17. textproc/p5-SVG
  18. graphics/p5-SVG-Graph
  19. devel/p5-Test-Harness
  20. textproc/p5-Text-Shellwords
  21. textproc/p5-XML-DOM
  22. textproc/p5-XML-DOM-XPath
  23. textproc/p5-libxml
  24. textproc/p5-XML-SAX
  25. textproc/p5-XML-SAX
  26. textproc/p5-XML-SAX-Writer
  27. textproc/p5-XML-Twig
  28. textproc/p5-XML-Writer
  29. biology/p5-AcePerl
  30. devel/p5-Clone
  31. converters/p5-Convert-Binary-C
  32. databases/p5-DBD-mysql
  33. graphics/p5-GD
  34. www/p5-HTML-Parser
  35. www/p5-HTML-Parser
  36. devel/p5-Storable
  37. textproc/p5-XML-Parser
  38. devel/p5-Module-Build
  39. lang/perl5.8
Required To Run:
  1. lang/perl5.8
  2. lang/perl5.8
  3. biology/p5-Bio-ASN1-EntrezGene
  4. devel/p5-Class-AutoClass
  5. devel/p5-Data-Stag
  6. devel/p5-Data-Stag
  7. devel/p5-Data-Stag
  8. graphics/p5-GD-SVG
  9. math/p5-Graph
  10. www/p5-libwww
  11. devel/p5-IO-stringy
  12. devel/p5-IO-String
  13. www/p5-libwww
  14. devel/p5-Set-Scalar
  15. net/p5-SOAP-Lite
  16. textproc/p5-Spreadsheet-ParseExcel
  17. textproc/p5-SVG
  18. graphics/p5-SVG-Graph
  19. devel/p5-Test-Harness
  20. textproc/p5-Text-Shellwords
  21. textproc/p5-XML-DOM
  22. textproc/p5-XML-DOM-XPath
  23. textproc/p5-libxml
  24. textproc/p5-XML-SAX
  25. textproc/p5-XML-SAX
  26. textproc/p5-XML-SAX-Writer
  27. textproc/p5-XML-Twig
  28. textproc/p5-XML-Writer
  29. biology/p5-AcePerl
  30. devel/p5-Clone
  31. converters/p5-Convert-Binary-C
  32. databases/p5-DBD-mysql
  33. graphics/p5-GD
  34. www/p5-HTML-Parser
  35. www/p5-HTML-Parser
  36. devel/p5-Storable
  37. textproc/p5-XML-Parser
  38. devel/p5-Module-Build
  39. lang/perl5.8
  40. lang/perl5.8
There are no ports dependent upon this port

No installation instructions: this port has been deleted.

The package name of this deleted port was: p5-bioperl-devel


Configuration Options
     No options to configure

Master Sites:
  1. ftp://ftp.FreeBSD.org/pub/FreeBSD/ports/distfiles/
  2. http://bioperl.org/DIST/
Port Moves
  • port deleted on 2009-06-05
    REASON: Has expired: no longer under development

Number of commits found: 18

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
05 Jun 2009 20:38:36
Original commit files touched by this commit  1.5.2
miwi search for other commits by this committer
2009-05-31 biology/p5-bioperl-devel: no longer under development
2009-05-31 biology/p5-bioperl-run-devel: no longer under development
2009-06-01 net-p2p/deluge05: use net-p2p/deluge instead
2009-06-03 textproc/gmat: failed to build for a long time, no maintainer and
apparently no users either
19 Mar 2009 19:29:34
Original commit files touched by this commit  1.5.2
miwi search for other commits by this committer
- Mark DEPRECATED (no longer under development)

PR:             132122
Submitted by:   Mauricio Herrera Cuadra <mauricio@arareko.net> (maintainer)
07 Mar 2009 19:51:02
Original commit files touched by this commit  1.5.2
skv search for other commits by this committer
Rename PERL_VER to PERL_VERSION.

Pointed by:     pav
21 Oct 2008 15:24:46
Original commit files touched by this commit  1.5.2
rafan search for other commits by this committer
- Unbreak

PR:             ports/128193
Submitted by:   Mauricio Herrera Cuadra <mauricio at arareko.net> (maintainer)
07 Jul 2008 22:57:49
Original commit files touched by this commit  1.5.2
pav search for other commits by this committer
- Mark BROKEN: missing cpan dependency (interactive loop)
06 Jul 2008 23:27:12
Original commit files touched by this commit  1.5.2
lippe search for other commits by this committer
- Update to 1.5.2.

PR:             ports/124648
Submitted by:   Mauricio Herrera Cuadra <mauricio@arareko.net> (maintainer)
Reviewed by:    lippe
Approved by:    gabor (mentor, implicit)
08 Sep 2007 00:53:15
Original commit files touched by this commit  1.5.1_1
linimon search for other commits by this committer
Welcome bsd.perl.mk.  Add support for constructs such as USE_PERL5=5.8.0+.
Drop support for antique perl.

Work done by:   gabor
Sponsored by:   Google Summer of Code 2007
Hat:            portmgr
19 May 2007 20:32:57
Original commit files touched by this commit  1.5.1_1
flz search for other commits by this committer
- Welcome X.org 7.2 \o/.
- Set X11BASE to ${LOCALBASE} for recent ${OSVERSION}.
- Bump PORTREVISION for ports intalling files in ${X11BASE}.
22 Jan 2006 01:25:24
Original commit files touched by this commit  1.5.1
edwin search for other commits by this committer
Replace ugly "@unexec rmdir %D... 2>/dev/null || true" with @dirrmtry

Approved by:    krion@
PR:             ports/88711 (related)
04 Dec 2005 22:12:48
Original commit files touched by this commit  1.5.1
edwin search for other commits by this committer
Add conflicts:

    CONFLICTS= p5-bioperl-1.[02468]*

Submitted by:   Fernan Aguero <fernan@iib.unsam.edu.ar>, Mauricio Herrera Cuadra
<arareko@yahoo.com>
04 Dec 2005 06:24:05
Original commit files touched by this commit  1.5.1
edwin search for other commits by this committer
Fix port: biology/p5-bioperl-devel

      This patch adds a LATEST_LINK line in the Makefile to avoid
      duplication with the 'p5-bioperl' port in the packages/Latest
      directory.

PR:             ports/89916
Submitted by:   Mauricio Herrera Cuadra <mauricio@arareko.net>
02 Dec 2005 21:40:12
Original commit files touched by this commit  1.5.1
barner search for other commits by this committer
- Re-add p5-bioperl-devel, development version of biology/p5-bioperl
  (A collection of Perl modules for bioinformatics)

PR:             ports/89497
Submitted by:   Mauricio Herrera Cuadra <arareko@yahoo.com>
08 Aug 2003 03:29:16
Original commit files touched by this commit  0.9.0
kris search for other commits by this committer
As announced on May 6, remove the broken p5-bioperl-devel port.
06 May 2003 23:36:56
Original commit files touched by this commit  0.9.0
kris search for other commits by this committer
BROKEN: Broken pkg-plist
07 Mar 2003 05:56:43
Original commit files touched by this commit  0.9.0
ade search for other commits by this committer
Clear moonlight beckons.
Requiem mors pacem pkg-comment,
And be calm ports tree.

E Nomini Patri, E Fili, E Spiritu Sancti.
20 Sep 2001 16:11:14
files touched by this commit
wjv search for other commits by this committer
- Add NO_LATEST_LINK, which should've been there in the first place.  :-(    
20 Aug 2001 13:41:11
files touched by this commit
wjv search for other commits by this committer
- Move the (very) long list of manpages from the port Makefile to a separate    
file.    
14 Aug 2001 10:36:36
files touched by this commit
wjv search for other commits by this committer
Add p5-bioperl-devel 0.9.0,   a collection of Perl modules for   bioinformatics
(developer's release).    

Number of commits found: 18

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