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Commit Graph

1868 Commits

Author SHA1 Message Date
Danilo Egea Gondolfo
09e9fc3c2f - Update to 1.14.2 2015-09-17 12:54:47 +00:00
Baptiste Daroussin
e0de738591 Remove ansi version fo wxGTK 2.8 and only keep the unicode version
All applications in the ports tree works correctly with unicode version of wxGTK

Newer version of wxGTK are unicode only (3.0+)

Note that now WX_UNICODE macro is noop
2015-09-16 19:51:26 +00:00
Muhammad Moinur Rahman
9787ec44da biology/seaview: Update version 4.5.4.4=>4.5.4.6 2015-09-15 14:44:47 +00:00
Mathieu Arnold
afae652a2a Make it so that the default Perl is always called perl5.
- Move Perl's man1 files along with its man3 files.
- Move where Perl installs its modules man1 pages.
- Convert the ports installing man1 pages.
- Make different Perl versions installable at the same time.
  Though you should note that only the default version can be used to
  install Perl modules, and the non default Perl versions cannot use the
  modules installed via ports if they contain .so as they are installed
  in a version specific directory.

Reviewed by:	bapt (the Mk bits)
Exp-run by:	antoine
Sponsored by:	Absolight
Differential Revision:	https://reviews.freebsd.org/D3542
2015-09-14 12:19:48 +00:00
Baptiste Daroussin
d59c43836a Enfoce unicode version of wxGTK 2015-09-13 18:45:47 +00:00
Danilo Egea Gondolfo
ac8989c768 - Update to 1.14.1 2015-09-13 18:05:54 +00:00
Sunpoet Po-Chuan Hsieh
c9368d48f9 - Add LICENSE
- Add NO_ARCH
- Use BROKEN_RUBY22
- While I'm here, use single space after WWW:

Approved by:	portmgr (blanket)
With hat:	ruby
2015-09-03 16:23:37 +00:00
Alexey Dokuchaev
4abd2afa2c - Unbreak on PowerPC by using atomicops implementation for Linux and GCC
__sync_* functions family
- Remove BROKEN_ia64: it never had been first-class architecture, killed
  officially in -CURRENT for a while now
- Sanitize installation commands and sort the knobs while I am here
2015-09-02 12:29:09 +00:00
Alexey Dokuchaev
052e315217 - Do not falsely advertise that PowerPC build runs out of space and fails
- Remove redundant PKGMESSAGE assignment and sanitize symlinks while here
2015-09-02 10:35:25 +00:00
Alexey Dokuchaev
670f0e0e42 Unbreak the build on PowerPC (at least) by always using va_copy() macro for
copying variable argument lists, not just on AMD64.
2015-09-02 10:10:06 +00:00
Alexey Dokuchaev
a56efba135 Unbreak the build on PowerPC, it had nothing to do with "error in pthreads":
configure script was passing `-faltivec' to the compiler, while this flag is
non-standard and only supported on Mac OS X/Darwin systems.

Also replace Apple-specific Altivec detection with querying the "hw.altivec"
sysctl instead.
2015-09-02 09:23:05 +00:00
Dmitry Marakasov
83235e7fc9 - Switch to options helpers 2015-09-02 03:04:09 +00:00
Raphael Kubo da Costa
3705667db1 Switch to USES=iconv:build.
The port does not use iconv on its own, the only dependency comes via
libxml2, which has one header that includes iconv.h.
2015-08-25 13:15:17 +00:00
Mathieu Arnold
bc0d524329 Fix previous commit.
Pointy hat to:	mat
Sponsored by:	Absolight
2015-08-19 13:41:51 +00:00
Mathieu Arnold
bb271f0bf7 Convert ports to use the options helpers in categories [abc]*, and minor fixes.
Sponsored by:	Absolight
Differential Revision:	https://reviews.freebsd.org/D3412?
2015-08-19 13:29:59 +00:00
Philip M. Gollucci
71f877793d biology/ugene: qt4-linguist -> qt4-linguisttools
- add USES=desktop-file-utils

PR:                  202138
Submitted by:        s3erios@gmail.com
Approved by:         h2+fbsdports@fsfe.org
2015-08-18 20:02:45 +00:00
Mathieu Arnold
21a283f3be Remove UNIQUENAME and LATEST_LINK.
UNIQUENAME was never unique, it was only used by USE_LDCONFIG and now,
we won't have conflicts there.

Use PKGBASE instead of LATEST_LINK in PKGLATESTFILE, the *only* consumer
is pkg-devel, and it works just fine without LATEST_LINK as pkg-devel
has the correct PKGNAME anyway.

Now that UNIQUENAME is gone, OPTIONSFILE is too. (it's been called
OPTIONS_FILE now.)

Reviewed by:	antoine, bapt
Exp-run by:	antoine
Sponsored by:	Absolight
Differential Revision:	https://reviews.freebsd.org/D3336
2015-08-17 14:20:40 +00:00
Kurt Jaeger
0269d640fc biology/seqtools: 4.35 -> 4.36
Minor under-the-hood changes
2015-08-08 11:22:24 +00:00
Dmitry Marakasov
a70208be74 Fix build on mips by properly respecting compiler and flags 2015-08-05 12:18:41 +00:00
Mathieu Arnold
53cb289f4a Update to 1.65.
PR:		201888
Submitted by:	brueffer
Approved by:	maintainer
Sponsored by:	Absolight
2015-08-05 10:32:31 +00:00
Antoine Brodin
afe5727737 Unbreak
Reported by:	pkg-fallout
2015-07-28 17:52:11 +00:00
Alexey Dokuchaev
856105bda2 - Fix four cases of an obvious typo: LICENSE_FILES -> LICENSE_FILE
- While here: move knobs to their expected location, remove useless check
  for ${PORT_OPTIONS:MDOCS} when installing documentation, standardize
  Makefile headers
2015-07-25 15:06:48 +00:00
Alexey Dokuchaev
0a216b375c - Update Unipro UGENE to version 1.17.0 (documentation was also rerolled)
- Remove no longer required local source code tweaks (picked up upstream)
2015-07-15 07:18:08 +00:00
Danilo Egea Gondolfo
88e7c8d386 - Update to 1.14.0
- Use install-strip
2015-07-12 18:25:07 +00:00
Kurt Jaeger
97a21e2f53 biology/seqtools: 4.34.1 -> 4.35
- Blixem bug fix in sorting features, RT 473624
- Compilation of the seqtools in parallel, RT 467905
- Fix bug with sorting by similarity/identity to first sequence (RT:473624)
- Fix an error compiling with multiple threads (RT:467905)
2015-07-07 14:17:51 +00:00
Adam Weinberger
26f58ed1c0 After r390893, chmod u+w/u-w for stripping perl XS modules is unnecessary,
and in fact now leads to incorrect permissions.

Remove all instances of it from perl@ ports.
2015-06-29 15:47:44 +00:00
Wen Heping
0c0c24c6a2 - Update options 2015-06-28 15:30:41 +00:00
Wen Heping
65167a114c - Update to 3.6.11
- Convert to optionsNG
2015-06-28 13:31:38 +00:00
Baptiste Daroussin
16cbf75f61 Use BROKEN helpers 2015-06-27 14:30:19 +00:00
Baptiste Daroussin
58dc978e42 Use BROKEN helpers 2015-06-27 14:29:25 +00:00
Dmitry Marakasov
043cdf9d8f - Add LICENSE
- Fix shebangs

Approved by:	porgmgr (bapt)
2015-06-25 09:32:18 +00:00
Adam Weinberger
34ed372f38 Start removing MASTER_SITE_SUBDIR=CPAN:username where possible. The
downside to having this set is that portscout cannot find new releases
when the username changes (which happens often in large projects with
multiple maintainers).
2015-06-24 15:16:23 +00:00
Baptiste Daroussin
2e55acc16d Convert to COPYTREE_SHARE
Use options helpers
2015-06-23 06:58:19 +00:00
Antoine Brodin
6e5719ca80 Convert to USES=jpeg 2015-06-22 18:33:20 +00:00
Dmitry Marakasov
ca76221d98 - Fix shebangs
MFH:		2015Q2
2015-06-11 10:17:24 +00:00
Kurt Jaeger
def75b1a0f New port: biology/bcftools
BCFtools is a set of utilities that manipulate variant calls in the
Variant Call Format (VCF) and its binary counterpart BCF. All
commands work transparently with both VCFs and BCFs, both
uncompressed and BGZF-compressed.

WWW: http://www.htslib.org/

PR:		199747
Submitted by:	cartwright@asu.edu
2015-06-05 21:01:13 +00:00
Dmitry Marakasov
fa5163da2f - Strip binaries 2015-06-03 17:27:08 +00:00
Bartek Rutkowski
b23eb33111 biology/mafft: update 7.149 -> 7.221
PR:		200603
Submitted by:	Reed A. Cartwright <cartwright@asu.edu> (maintainer)
2015-06-03 17:04:19 +00:00
Dmitry Marakasov
4d4b259bcd - Add NO_ARCH
Approved by:	portmgr blanket
2015-05-31 13:37:20 +00:00
Dmitry Marakasov
9464d224ca - Fix shebangs
- Add NO_ARCH
- Add missing EXAMPLES option

Approved by:	portmgr blanket
MFH:		2015Q2
2015-05-30 12:31:59 +00:00
Alexey Dokuchaev
14e4d92279 Update Unipro UGENE to version 1.16.2. 2015-05-28 08:11:59 +00:00
Mathieu Arnold
8dab11a002 Remove $FreeBSD$ from patches files in categories a-j.
With hat:	portmgr
Sponsored by:	Absolight
2015-05-22 13:34:20 +00:00
Muhammad Moinur Rahman
9885162820 biology/seaview: Update version 4.5.4=>4.5.4.4 2015-05-22 11:09:23 +00:00
Wen Heping
f028652e52 - Update to 7.1.3 2015-05-18 01:27:46 +00:00
Wen Heping
e05d953fd2 - Update to 3.6.9 and unbreak 2015-05-18 00:24:33 +00:00
Mathieu Arnold
60d1a83c2a MASTER_SITES cleanup.
- Replace ${MASTER_SITE_FOO} with FOO.
- Merge MASTER_SITE_SUBDIR into MASTER_SITES when possible. (This means 99.9%
  of the time.)
- Remove occurrences of MASTER_SITE_LOCAL when no subdirectory was present and
  no hint of what it should be was present.
- Fix some logic.
- And generally, make things more simple and easy to understand.

While there, add magic values to the FESTIVAL, GENTOO, GIMP, GNUPG, QT and
SAMBA macros.

Also, replace some EXTRACT_SUFX occurences with USES=tar:*.

Checked by:	make fetch-urlall-list
With hat:	portmgr
Sponsored by:	Absolight
2015-05-14 10:15:04 +00:00
Wen Heping
e277ea8c7b - Update to 5.11.4 2015-05-12 08:58:14 +00:00
Mathieu Arnold
88bfe4bd43 Cleanup DIST* variables.
When appropriate:
- Try to use DISTVERSION{SUF,PRE}FIX
- Replace PORTNAME-PORTVERSION by DISTNAME
- Convert MASTER_SITES to use macros
- Other light cleanup

With hat:	portmgr
Sponsored by:	Absolight
2015-05-11 18:34:57 +00:00
Adam Weinberger
03f1abf704 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.
2015-05-08 18:12:36 +00:00
Wen Heping
fac1a2b00f - Update to 36.3.7a 2015-05-07 02:33:57 +00:00