Commit Graph

25 Commits

Author SHA1 Message Date
Piotr Kubaj 4c1ed61171 biology/mummer: fix build on powerpc64 elfv2 and powerpc64le
Error:
src/tigr/postnuc.cc:174:37: error: non-constant-expression cannot be narrowed from type 'signed char' to 'char' in initializer list [-Wc++11-narrowing]
        Alignments.push_back({ *Mp, CurrCp->dirB } );

Since it may also fix runtime issues on powerpc64 elfv1, bump PORTREVISION.
2020-10-25 23:03:14 +00:00
Gerald Pfeifer ea8c8ec7da Bump PORTREVISION for ports depending on the canonical version of GCC
as defined in Mk/bsd.default-versions.mk which has moved from GCC 8.3
to GCC 9.1 under most circumstances now after revision 507371.

This includes ports
 - with USE_GCC=yes or USE_GCC=any,
 - with USES=fortran,
 - using Mk/bsd.octave.mk which in turn features USES=fortran, and
 - with USES=compiler specifying openmp, nestedfct, c11, c++0x, c++11-lang,
   c++11-lib, c++14-lang, c++17-lang, or gcc-c++11-lib
plus, everything INDEX-11 shows with a dependency on lang/gcc9 now.

PR:		238330
2019-07-26 20:46:53 +00:00
Gerald Pfeifer a9f015d155 Bump PORTREVISION for ports depending on the canonical version of GCC
defined via Mk/bsd.default-versions.mk which has moved from GCC 7.4 t
GCC 8.2 under most circumstances.

This includes ports
 - with USE_GCC=yes or USE_GCC=any,
 - with USES=fortran,
 - using Mk/bsd.octave.mk which in turn features USES=fortran, and
 - with USES=compiler specifying openmp, nestedfct, c11, c++0x, c++11-lang,
   c++11-lib, c++14-lang, c++17-lang, or gcc-c++11-lib
plus, as a double check, everything INDEX-11 showed depending on lang/gcc7.

PR:		231590
2018-12-12 01:35:33 +00:00
Yuri Victorovich df1cfe66a6 biology/mummer: Add USES=compiler:c++11-lang 2018-12-11 07:48:12 +00:00
Yuri Victorovich da87b8a1d5 biology/mummer: Update 3.23 -> 4.0.0beta2-2
Port changes:
* Moved to github
* It now installs itself
* It uses yaggo during build
2018-12-11 07:43:45 +00:00
Yuri Victorovich 5054438501 biology/mummer: Take maintainership 2018-12-11 07:23:54 +00:00
Wen Heping eaf75bad8d - Fix installing scripts and support binaries
- Add LICENSE

PR:		223098
Submitted by:	mzaki@niid.go.jp
2017-10-30 02:27:23 +00:00
Dmitry Marakasov a70208be74 Fix build on mips by properly respecting compiler and flags 2015-08-05 12:18:41 +00:00
Baptiste Daroussin 99a3e8559c Cleanup plist 2014-10-20 07:10:48 +00:00
John Marino 4fa4056388 biology/mummer: Use OPSYS with OSVERSION
I don't think selecting clang as a function of OSVERSION is generally
desired, but if it's going to happen, make sure FreeBSD-specific
conditions are limited to FreeBSD by comparing OPSYS first.
2014-07-19 22:00:16 +00:00
Martin Wilke 2a912e1c5e Fix compilation on 10+ (clang)
Fix format of WWW entry in pkg-descr

PR:		190798
2014-06-27 14:14:01 +00:00
John Marino d0bb05930a Reset the 99 ports still listed under sylvio@
Sylvio's last commit was 17 months ago, a full 5 months after all of his
ports could have been reset per policy.  Given the push to complete
staging (48 ports are still unstaged, something like 70+ have already
been staged by other committers) and given that PRs are automatically
assigned but never addressed, it's better just to reset all the ports and
PRs so that it's clear to others that these ports are free to maintain.

Approved by:	portmgr (implicit)
2014-06-11 18:55:29 +00:00
Jimmy Olgeni 37e782dfbc Remove indefinite articles and trailing periods from COMMENT, plus
minor COMMENT typos and surrounding whitespace fixes. Categories A-C.

CR:		D196
Approved by:	portmgr (bapt)
2014-06-09 11:21:52 +00:00
Olli Hauer c3fa596129 - add stage support 2014-06-01 10:54:33 +00:00
Martin Wilke 059bf913b9 - Convert USE_GMAKE to USES 2014-03-13 07:41:34 +00:00
Emanuel Haupt 094043c26a Remove trailing whitespaces from category biology 2014-02-21 13:35:26 +00:00
Emanuel Haupt 5005b67362 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)
2014-02-10 13:54:26 +00:00
Adam Weinberger 955d37365b Convert biology to MDOCS and MEXAMPLES 2014-01-03 15:46:52 +00:00
Baptiste Daroussin 7055ff02f1 Add NO_STAGE all over the place in preparation for the staging support (cat: biology) 2013-09-20 15:55:44 +00:00
Sylvio Cesar Teixeira aad73e57ae - Update to 3.23 2012-01-17 00:51:39 +00:00
Martin Wilke a9481afc8a - Get Rid MD5 support 2011-03-19 12:38:54 +00:00
Sylvio Cesar Teixeira f1cd5913ef - Update to 3.22
Approved by: 	itetcu (mentor)
2010-03-21 17:18:20 +00:00
Sylvio Cesar Teixeira ba072d1713 - Update my mail address to FreeBSD
Approved by:	miwi (mentor)
2009-11-27 22:52:30 +00:00
Marcelo Araujo 7c7ff787ef - Update to 3.21.
- Reset maintainer to submitter.

PR:		ports/138192
Submitted by:	Sylvio Cesar <scjamorim@bsd.com.br>
2009-08-28 14:52:05 +00:00
Martin Wilke 9326ebd9c8 MUMmer is a modular system for the rapid whole genome alignment of finished
or draft sequence. This package provides an efficient suffix tree library,
seed-and-extend alignment, SNP detection, repeat detection, and
visualization tools.

WWW:	http://mummer.sourceforge.net/

PR:		ports/118142
Submitted by:	Tony Maher
2007-12-14 20:54:47 +00:00