Number of commits found XX: 46

- Remove unnecessary USES=shebangfix
- Convert to new options target helper

Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c.

With hat:	portmgr
Sponsored by:	Absolight

- Fix shebangs
- Add NO_ARCH
- Add missing EXAMPLES option

Approved by:	portmgr blanket
MFH:		2015Q2

Reassign biology/ perl modules to perl@.

While here:

Regenerate p5-AcePerl's patches using makepatch.
Make p5-Bio-ASN1-EntrezGene depend on p5-bioperl, instead of the
other way around. Bump PORTREVISION on those two ports.

Some OCD cleanups on some of the perl@ ports.

- Remove dependencies in core
- Put testing depends in TEST_DEPENDS
- Remove unnecessary bsd.port.options.mk inclusions
- Remove checks for Perl versions that no longer exist in the ports tree
- Sort plists, some of which were so jumbled that I have to assume
  the plist was randomized before committing

A lot of the plist changes in this commit are moving PERL5_MAN3 after
SITE_PERL. It's repo churn now, but it makes updating the ports later
far easier.

Change the way Perl modules are installed, update the default Perl to 5.18.

Before, we had:

  site_perl :           lib/perl5/site_perl/5.18
  site_perl/perl_arch : lib/perl5/site_perl/5.18/mach
  perl_man3 :           lib/perl5/5.18/man/man3

Now we have:

  site_perl : lib/perl5/site_perl
  site_arch : lib/perl5/site_perl/mach/5.18
  perl_man3 : lib/perl5/site_perl/man/man3

Modules without any .so will be installed at the same place regardless of the

(Only the first 15 lines of the commit message are shown above )

- Update to 1.6.924 [1]
- Reset maintainer to perl@

PR:		192088 [1]
Submitted by:	Kurt Jaeger<pi@FreeBSD.org> [1]

- Update to 1.6.923
- Add STAGE support

PR:		190342
Submitted by:	Muhammad Moinur Rahman <5u623l20@gmail.com>

Mark as broken unstaged perl ports

With hat:	portmgr

Remove trailing whitespaces from category biology

According to the Porter's Handbook (5.12.2.3.) default options must be added to
OPTIONS_DEFINE. This policy has been implemented only recently that's why we
have many ports violating this policy.

This patch adds the default options specified in the Porter's Handbook to
OPTIONS_DEFINE where they are being used. Ports maintained by
gnome@FreeBSD.org, kde@FreeBSD.org and x11@FreeBSD.org have been excluded.

Approved by:    portmgr (bapt)

Convert biology to MDOCS and MEXAMPLES

Add NO_STAGE all over the place in preparation for the staging support (cat:
biology)

- Convert to new perl framework
- Trim Makefile header

Approved by:	wen@ (maintainer)

- Avoid of using SITE_PERL
- Remove depend on DB_File.pm since it part of perl distribution

PR:		ports/178877
Submitted by:	az
Approved by:	matainer (timeout)

- Take maintainership

- Reassign to the heap at maintainer's request

- Remove SITE_PERL from *_DEPENDS

Approved by: portmgr@ (bapt@)

- update png to 1.5.10

At the moment 1385 ports use BUILD_DEPENDS= ${RUN_DEPENDS} and 450
ports use BUILD_DEPENDS:= ${RUN_DEPENDS}. This patch fixes ports that are
currently broken. This is a temporary measure until we organically stop using
:= or someone(s) spend a lot of time changing all the ports over.

Explicit duplication > := > = and this just moves ports one step to the left

Approved by:    portmgr

- update to 1.4.1
Reviewed by:    exp8 run on pointyhat
Supported by:   miwi

- update to jpeg-8

- Remove unneeded dependencies which is in perl-5.8.9 dist
  (part 19; last!).

Approved by:    portmgr (itetcu)

- Update to 1.6.1

Approved by:    maintainer (via Email)

- bump all port that indirectly depends on libjpeg and have not yet been bumped
or updated
Requested by:   edwin

- lang/perl5.6 is dead, remove PERL_LEVEL/PERL_VERSION < 500801 checks

PR:             ports/135398
Tested by:      2 -exp runs by pav
Approved by:    portmgr (pav)

Remove variable PERL_VER from the ports tree at all - because
it is obsolete since Perl 5.6.0.

- Update to 1.6.0

PR:             ports/131989
Submitted by:   maintainer

Fix plist with perl 5.8.9.

Approved by:    portmgr (pav, implicit)

- Take advantage of CPAN macro from bsd.sites.mk, change
${MASTER_SITE_PERL_CPAN} to CPAN.

PR:             ports/122674
Submitted by:   Philip M. Gollucci <pgollucci@p6m7g8.com>
Reworked by:    araujo (myself)
Approved by:    portmgr (pav)

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

- Welcome X.org 7.2 \o/.
- Set X11BASE to ${LOCALBASE} for recent ${OSVERSION}.
- Bump PORTREVISION for ports intalling files in ${X11BASE}.

Add conflicst:
CONFLICTS=     p5-bioperl-1.[13579]*

Submitted by:   Mauricio Herrera Cuadra <arareko@yahoo.com>,Fernan Aguero
<fernan@iib.unsam.edu.ar>

- add missing MAN1 and MAN3
- apply DATADIR, EXAMPLESDIR, and DOCSDIR in PLIST
- update the usage of NOPORTDOCS

PR:             71322
Submitted by:   leeym
Approved by:    Fernan Aguero <fernan@iib.unsam.edu.ar>

After devel/p5-File-Temp has gained an IGNORE for PERL_LEVEL > 500800, all
these ports were broken because they always depended on it. I've rearranged all
the dependencies to fit the new scheme.

Unmark as broken for 4.x; instead, mark as ignore for perl < 5.6.

BROKEN on 4.x: Configure fails

Major update from 0.7.2 to 1.4 by new maintainer.  This is almost a complete
rework of the port.

See the page http://news.open-bio.org/archives/cat_bioperl.html for the
changes between 1.2 and 1.4.  The older changes are in the CVS tree.

From the new maintainer:

        Note that this new port just handles the installation of bioperl and
        not of additional extra stuff (bioperl-gui, bioperl-corba-server,
        bioperl-corba-client). This is unlike the behaviour of the current
        port.

        The extra stuff, though still functional, had very little adoption
        among users, and does not appear to be currently supported/maintained.

PR:             ports/47303 (and subsequent)
Submitted by:   Fernan Aguero <fernan@iib.unsam.edu.ar> (new maintainer)

utilize SITE_PERL

PR:             58166
Submitted by:   Cheng-Lung Sung <clsung@dragon2.net>

Clear moonlight beckons.
Requiem mors pacem pkg-comment,
And be calm ports tree.

E Nomini Patri, E Fili, E Spiritu Sancti.

- Update to version 0.7.2, somewhat overdue.  :-)    

- Properly list run-time dependencies in RUN_DEPENDS in Makefile.   - Deploy
%%PERL_VER%% and %%PERL_ARCH%% pragmas consistently throughout     pkg-plist. 
(Ouch, that was embarrassing.)   - Bump PORTREVISION due to the above.   -
Update my email address and the project's URL in pkg-descr.    

- Update to version 0.7.1   - Add a build-time message to inform the user of
available options.    

Embarrassingly long overdue update to 0.7.0, including optional support for  
GUI (Tk) and CORBA extensions.    

Update to version 0.6.2    

Add BioPerl, a collection of Perl5 mods for bioinformatics/genomics    

Number of commits found XX: 46

9 vulnerabilities affecting 70 ports have been reported in the past 14 days

^* - modified, not new

All vulnerabilities

Last updated:
2021-01-26 20:33:26