Number of commits found XX: 16

- Convert to option helper install target (add OPTIONS_DEFINE=DOCS
  when it was missing)
- Invoke INSTALL_DATA where appropriate instead of INSTALL_MAN
- Fix some whitespace and formatting bugs along the way

Designatate 4 ports as unsafe for parallel building

All had similar errors that it couldn't find something during the build,
yet built on a subsequent pass with no adjustments.  Most I've seen before
on previous bulk runs.

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 )

- Convert ports from benchmarks/ and biology/ to new USES=python

Approved by:	portmgr (implicit)

Convert a bunch of EXTRACT_SUFX=... into USES=tar:...

Approved by:	portmgr (not really, but touches unstaged ports)

Fix shebang line in Perl and Python scripts.

PR:		191146
Submitted by:	mzaki@m.u-tokyo.ac.jp (maintainer)

Update to 1.2.10.

PR:		191129
Submitted by:	mzaki@m.u-tokyo.ac.jp (maintainer)

- add stage support

- Convert USE_GMAKE to USES

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 the new perl5 framework

Approved by:	portmgr (bapt@, blanket)

Update to 1.1.04

PR:             ports/157527
Submitted by:   Motomichi Matsuzaki <mzaki@m.u-tokyo.ac.jp>
Approved by:    bapt (mentor)

Velvet is a de novo genomic assembler specially designed for short read
sequencing technologies, such as Solexa or 454, developed by Daniel Zerbino
and Ewan Birney at the European Bioinformatics Institute (EMBL-EBI).

Citation:

Velvet: algorithms for de novo short read assembly using de Bruijn graphs.
D.R. Zerbino and E. Birney. Genome Research 18: 821-829 (2008)

WWW: http://www.ebi.ac.uk/~zerbino/velvet/

PR:             140147
Submitted by:   Motomichi Matsuzaki <mzaki@m.u-tokyo.ac.jp>

Number of commits found XX: 16

12 vulnerabilities affecting 113 ports have been reported in the past 14 days

^* - modified, not new

All vulnerabilities

Last updated:
2021-01-14 20:39:03