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Commit Graph

1827 Commits

Author SHA1 Message Date
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
Kurt Jaeger
681df24d3b biology/seqtools: 4.33 -> 4.34.1
Blixem
- Added functionality to shift-select a range of coordinates,
  and copy the reference/match sequence for that range.
- DNA search now highlights the resultant range of coordinates.
- Added a splitter bar to allow the variations track to be resized.
- Dotter
  Fix a crash pressing Esc on an undocked alignment or greyramp tool.
- All
  Code reorganisation: the codebase is now in C++ rather than C,
  and a new module 'gbtools' has been created for generic
  utility functions.
2015-05-06 20:30:53 +00:00
Mathieu Arnold
c6457ffef4 Update ports in the [bcd]* categories to not use GH_COMMIT.
With minor cleanups to make things simpler.

With hat:	portmgr
Sponsored by:	Absolight
2015-05-06 15:16:53 +00:00
Wen Heping
7fc484154b - Unbreak
PR:		199734
Submitted by:	jwbacon@tds.net(maintainer)
2015-05-04 06:08:59 +00:00
Antoine Brodin
9a9b4fb54c Mark BROKEN: fails to configure
===>  Configuring for ncbi-blast+-2.2.30_2
configure: error: --localstatedir=/var:  unknown option;  use --help to show usage

Reported by:	pkg-fallout
2015-04-28 12:29:12 +00:00
John Marino
c66b4d5283 biology/ncbi-blast+: Add additionl MASTER_SITE to unbreak fetch
The distfile was rerolled but nobody knows why (not a good sign).  The
maintainer has added a new MASTER_SITE with the original distfile in
order to unbreak fetch.

PR:		199474
Submitted by:	maintainer (Jason Bacon)
2015-04-25 14:21:58 +00:00
Mathieu Arnold
18d6818fe4 ${ENV} does not exist, it is called ${SETENV}. 2015-04-13 14:49:37 +00:00
John Marino
0d28709839 biology/seaview: Unbreak -- it fetches fine
The second MASTER_SITES entry worked fine, so this must have been a
transient fetch problem.  I removed the first entry which is still
failing though.

Approved by:	blanket
2015-04-11 15:49:57 +00:00
John Marino
24651f6747 biology/platon: Upgrade from 05 MAR 2015 => 30 MAR 2015 to unbreak
As noted by previous commit, upstream rerolls the same distfile
frequently.  When FreeBSD cache was removed, the port broke.  I'm fixing
it again with a new digest, but I'm also defining DIST_SUBDIR, which is
the correct thing to do with rerolls-by-policy.

Also I removed the bad backup MASTER_SITES and tested in poudriere.
2015-04-11 15:41:22 +00:00
John Marino
1402a5b211 biology/p5-Bio-ASN1-EntrezGene: bump PORTEPOCH
Apparently in some world I don't live in 1.091 > 1.70
pkg needs this port's epoch to be bumped

reported by: 	wen
2015-04-11 15:19:03 +00:00
John Marino
ddfbdcb255 biology/p5-Bio-ASN1-EntrezGene: Upgrade 1.09 => 1.70 to unbreak
While here, reset the port.  The last time the maintainer was seen was
in 2005, when the port was created.  Also, rewrap the package description
such that it keeps within 75 characters; also move the url so it won't
wrap across lines.
2015-04-11 15:00:12 +00:00
Brad Davis
4417c1e084 Update biology/paml to 4.8a and unbreak.
PR:		199264
Submitted by:	Joseph Mingrone <jrm@ftfl.ca>
Approved by:	bdrewery (mentor)
2015-04-10 15:39:01 +00:00
Baptiste Daroussin
06f79b66f2 Convert bsd.gnustep.mk to USES=gnustep
Simplify gnustep ports
Hook into the regular ports framework:
- LIB_DEPENDS for library dependencies
- Use regular USE_LDCONFIG

Reuse USES=objc (automatic)
USE_GNUSTEP is now a macro to set the dependencies and build feature needed.
Accepted arguments: back base build gui

Merge deskutils/preferencepanes into deskutils/systempreferences
2015-04-09 07:44:41 +00:00
Baptiste Daroussin
f4e1a5b6b2 Mark as broken unfetchable ports 2015-04-05 17:55:35 +00:00
Steve Wills
3e74a84730 biology/ruby-bio: mark broken with ruby 2.2 2015-04-03 13:50:38 +00:00
Dmitry Marakasov
5ae457bc49 - Remove deprecated option
- Tweak compiler flags
- Add LICENSE
- Pass maintainership to submitter

PR:		199066
Submitted by:	jwbacon@tds.net
2015-04-02 15:41:31 +00:00
Kurt Jaeger
fd18692b42 biology/seqtools: 4.32 -> 4.33
- Blixem/Dotter
  Multi-dotter support; may now start multiple dotters from blixem
2015-03-31 18:04:25 +00:00
Sunpoet Po-Chuan Hsieh
3f7a3c8d4a - Add LICENSE
- Space/Tab fix
2015-03-28 17:20:45 +00:00
Mikhail Teterin
8c46a40c1a Upgrade from 3.6.6 to 3.6.7. Be sure to not extract the zlib
subdirectory.
2015-03-24 16:56:27 +00:00
John Marino
64ee7e63bf 6 ports categories: Remove $PTHREAD_LIBS
Categories: cad, devel, java, x11-fm, biology, deskutils

approved by:	PTHREAD blanket
2015-03-24 16:01:21 +00:00
Muhammad Moinur Rahman
219a0f8115 biology/seaview: Update version 4.5.3.4=>4.5.4
- Remove dependency for libpdf as removed by upstream
2015-03-24 10:15:30 +00:00
Alexey Dokuchaev
70f863c983 - Update to version 1.16.1
- Explicitly list all required Qt components in USE_QT4 instead of relying
  on them being silently picked up through `www/webkit-qt4' dependency
- Group *_build components together while here
- Remove one REINPLACE_CMD call that is no longer needed
2015-03-23 01:44:43 +00:00
John Marino
ed9f597563 biology/segan: Limit GCC to 4.8 while waiting for update
Due to questionable c++, GCC 4.9 and newer cannot build seqan.  An update
has been in the works that will enable clang compilers and all versions
of GCC to build seqan, but it is not quite ready yet.  While waiting for
it, limit the version of GCC used to 4.8.

PR:	196851
2015-03-21 11:53:27 +00:00
Bryan Drewery
37a1520519 For the new USE_GITHUB with only GH_TAGNAME set default DISTNAME to
include GH_PROJECT/GH_ACCOUNT/GH_TAGNAME. This prevents the distfile
having the same name despite changing one of these values and causing
a bad checksum.

Differential Revision:	https://reviews.freebsd.org/D2103
Reviewed by:	mat
With hat:	bdrewery
2015-03-20 20:07:50 +00:00
Mathieu Arnold
45ca777110 Convert to new USE_GITHUB.
While there, cleanup.

Sponsored by:	Absolight
2015-03-20 09:43:20 +00:00
Baptiste Daroussin
873adcf645 Fix packaging as a user (pkg already takes care of credentials)
Strip binaries
2015-03-18 21:52:19 +00:00
Dmitry Marakasov
409a9aff40 - Simplify MASTER_SITES
- Strip libraries
2015-03-17 03:09:25 +00:00
Muhammad Moinur Rahman
da8394e59b biology/seaview: UNBREAK
- Update version 4.5.2=>4.5.3.4
- Add LICENSE (GPLv3)
- Remove PDFLIBS as OPTIONS as it is no loner an optional requirement

PR:		198602
Submitted by:	pi
Approved by:	bapt marino (implicit)
2015-03-16 12:07:49 +00:00
Adam Weinberger
9e00ce3f62 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.
2015-03-12 23:00:02 +00:00
Dmitry Marakasov
a28b904955 - Add empty directory to plist 2015-03-11 14:41:53 +00:00
Mikhail Teterin
44305716cb Update from 7.1.1 to 7.1.2. 2015-03-11 13:44:21 +00:00
Mikhail Teterin
05b84dd275 Unbreak by upgrading to March 5, 2015 "release" from upstream.
Reduce restrictions from RESTRICTED to NO_CDROM -- the licensing
allows use by academic community as long as it is not redistributed.

Upstream still do not version their "releases", so next time they
reroll the tarball, the download will start breaking again. But
this time, it will be possible to fetch it from FreeBSD mirrors.

Hide most of the optional data files under the DOCS-option and
streamline various build-related scriptlets.
2015-03-08 23:13:21 +00:00
Mikhail Teterin
95461ffde0 Unbreak by updating from 7.0.1 to 7.1.1. Hopefully, the authors will
stop rerolling releases (and breaking downstream checksums) now.

While here, allow parallel builds (seems to work again now) and stop
extraction of unused subdirectories.
2015-03-08 18:34:42 +00:00
Bartek Rutkowski
9b9d6e55f6 biology/samtools: update 1.1 -> 1.2
PR:		198292
Submitted by:	Reed Cartwright <cartwright@asu.edu>
2015-03-06 12:53:58 +00:00
Bartek Rutkowski
e478a19bbf biology/htslib: update 1.1 -> 1.2.1
PR:		198291
Submitted by:	Reed Cartwright <cartwright@asu.edu>
2015-03-06 12:45:22 +00:00
Tilman Keskinoz
8281385109 Add a run dependency used by update_blastdb.pl
PR:		198331
Submitted by:	maintainer
2015-03-06 10:39:31 +00:00
Danilo Egea Gondolfo
de357d9a0c - Update to 1.13.10 2015-03-04 13:17:46 +00:00
Baptiste Daroussin
35c339abf0 Remove Authors from pkg-descr 2015-03-02 23:09:43 +00:00
Adam Weinberger
e2098037aa Remove TEST dependency on p5-Test-Simple when the version in core is
sufficient.

Thanks to az for showing me the light here.
2015-02-26 16:54:41 +00:00
Alexey Dokuchaev
4be0124f6e Update Unipro UGENE to version 1.16.0 (documentation was also rerolled). 2015-02-24 11:42:53 +00:00
Antoine Brodin
9939b90892 Mark BROKEN: Fails to link, tries to use internal fltk symbols
c++ -o seaview   seaview.o custom.o use_mase_files.o regions.o load_seq.o align.o xfmatpt.o comlines.o resource.o nexus.o viewasprots.o racnuc_fetch.o concatenate.o statistics.o trees.o treedraw.o addbootstrap.o least_squares_brl.o pseudoterminal.o unrooted.o pdf_or_ps.o svg.o threads.o Fl_Native_File_Chooser_FLTK.o raa_acnuc.o parser.o md5.o zsockr.o misc_acnuc.o dnapars.o protpars.o seq.o phylip.o lwl.o bionj.o phyml_util.o  \
      -L/usr/local/lib -lfltk_images -lfltk  \
     -lXft -lXext -lfontconfig -ljpeg -lpng -lXinerama -L/usr/local/lib -lpdf \
         -lX11 -lm -lz -pthread
seaview.o: In function `clipboard_contains_alignment(char const*)':
seaview.cxx:(.text+0x1c14): undefined reference to `fl_selection_buffer'

Reported by:	pkg-fallout
2015-02-21 07:35:32 +00:00
Kurt Jaeger
507078b95f biology/seqtools: 4.31 -> 4.32
- Blixem
  o Previously-unsupported GFF feature types can now be displayed
    as a new 'basic feature' type.
  o Styles are now applied to the detail view as well as the big
    picture, so feature display is more consistent across the two
    views.
  o Fix a bug where styles were not being applied to
    dynamically-loaded features.
- Dotter
  o Added a 'maximise' button for the greyramp tool.
  o Small fixes to inconsistencies in context-sensitive menus and
    keyboard shortcuts.
2015-02-12 12:04:09 +00:00