20:51 antoine 

Deprecate ports broken for more than 6 months

 

12:48 antoine 

Mark a few ports BROKEN, unfetchable

 

21:08 zeising 

Add USES=xorg USES=gl, ports categories b

Add USES=xorg, USES=gl and in a few cases USES=gnome to ports in categories
starting with 'b'.

 

20:46 gerald 

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

 

19:54 pi 

biology/seqtools: fix build on current, if lld is lld7

- fixed by LLD_UNSAFE=yes

PR:		230609
Submitted by:	jbeich

 

01:35 gerald 

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

 

03:38 jbeich 

biology/seqtools: re-try on powerpc* after r449590

 

10:48 mat 

Remove USES=execinfo.

PR:		220271
Submitted by:	mat (review), Yasuhiro KIMURA (PR)
Sponsored by:	Absolight
Differential Revision:	https://reviews.freebsd.org/D11488

 

20:55 gerald 

Bump PORTREVISION for ports depending on the canonical version of GCC
(via Mk/bsd.default-versions.mk and lang/gcc) which has moved from
GCC 5.4 to GCC 6.4 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, c++11-lib, c++11-lang,
   c++14-lang, c++0x, c11, or gcc-c++11-lib.

PR:		219275

 

21:55 linimon 

Mark some ports failing on power64.  In cases where the error message
was a stub, provide a real one.

While here, pet portlint.

Approved by:	portmgr (tier-2 blanket)
Reported by:	swills

 

15:23 gerald 

Bump PORTREVISIONs for ports depending on the canonical version of GCC and
lang/gcc which have moved from GCC 4.9.4 to GCC 5.4 (at least under some
circumstances such as versions of FreeBSD or platforms).

This includes ports
 - with USE_GCC=yes or USE_GCC=any,
 - with USES=fortran,
 - using using Mk/bsd.octave.mk which in turn has USES=fortran, and
 - with USES=compiler specifying openmp, nestedfct, c++11-lib, c++14-lang,
   c++11-lang, c++0x, c11, or gcc-c++11-lib.

PR:		216707

 

03:45 sunpoet 

Remove BROKEN_FreeBSD_9

Approved by:	portmgr (blanket)

 

06:19 pi 

biology/seqtools: update 4.43.0 -> 4.44.1

- Blixem: Features can now be added to multiple different groups/filters.
- Belvu: Fix a problem where column highlighting can get out of sync
  with the text.

 

14:19 pi 

biology/seqtools: 4.42.1 -> 4.43.0

 
ftp://ftp.sanger.ac.uk/pub4/resources/software/seqtools/PRODUCTION/release_notes.html

- Mark broken on 9.x: Fails to build due to C++ std issues

 

16:27 pi 

biology/seqtools: 4.41.1 -> 4.42.1

- fixes build on 9.x
- Added a feedback box to show the read depth at the selected coord.
  Hover over this box to see the specific base support (i.e. the
  number of A/C/G/Ts).

 

13:29 mat 

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

With hat:	portmgr
Sponsored by:	Absolight

 

19:40 pi 

biology/seqtools: 4.40.0 -> 4.41.1

- mostly internal changes, some build fixes

 

10:17 pi 

biology/seqtools: 4.39.3 -> 4.40.0

- Blixem can now accept a 'command' tag in a gff line for a region
  feature. The given command should return gff and will be run by
  blixem on the given region.
- Blixem now supports fetching sequence data over https.

 

13:20 pi 

biology/seqtools: 4.39.2 -> 4.39.3

- Blixem
  Further improve the display of features in the detail view
  when they have transparent fill, making sure that they have a
  visible border.

 

20:50 pi 

biology/seqtools: 4.39.1 -> 4.39.2

- Blixem:
  Improve the display of features in the detail view when they
  have transparent fill.

 

18:46 pi 

biology/seqtools: 4.39.0 -> 4.39.1

- Fix a bug in Belvu where the display was being initialised in
  command-line-only modes.

 

16:39 pi 

biology/seqtools: 4.36 -> 4.39.0

- Blixem
  o There is now an optional setting to highlight "maybe-canonical"
    splice sites in Blixem. This can be used to help identify
    problems where the strand is incorrect in the input data - it
    highlights splice sites in a different colour if they would be
    canonical were they on the other strand.
  o Fixed a bug with colinearity lines when an alignment's cigar
    string contains introns.
  o There are now separate feedback boxes for the selected sequence
    name coordinates. Hover over each box to see a tooltip describing
    its contents.

 

11:22 pi 

biology/seqtools: 4.35 -> 4.36

Minor under-the-hood changes

 

14:17 pi 

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)

 

20:30 pi 

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.

 

18:04 pi 

biology/seqtools: 4.32 -> 4.33

- Blixem/Dotter
  Multi-dotter support; may now start multiple dotters from blixem

 

12:04 pi 

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.

 

18:10 pi 

biology/seqtools: 4.30 -> 4.31

Some changes to sqlite dependencies

 

13:19 pi 

biology/seqtools: 4.29 -> 4.30

- Blixem
  o Fix potential crash with internal processing
  o Fix two bugs in data input

 

18:46 pi 

biology/seqtools: 4.28 -> 4.29

- Blixem
  o Added the facility to run Dotter on an ad-hoc sequence (RT:408836).
  o Added the facility to run Dotter against a transcript.
- Dotter
  Minimise the greyramp tool to a simple contrast slider. Use
  Ctrl-G to toggle between this and the full greyramp tool.
- Belvu
  Fix a bug with tree bootstrapping in Belvu.

 

23:06 bapt 

USES=execinfo

 

03:17 pi 

biology/seqtools: 4.27 -> 4.28

 

23:11 adamw 

Add OPTIONS_DEFINE=DOCS for ports with %%PORTDOCS%% in the plist.

Where possible, correct a few instances where PORTDOCS was being used
to flag stuff in EXAMPLESDIR. For some ports, mostly those owned by
ruby@, PORTDOCS is applied to pretty much everything whether it's
documentation or example.

 

18:56 pi 

biology/seqtools: 4.26 -> 4.27

 

17:21 miwi 

- Chase database/sqlite3 slib bump

Approved by:	portmgr (myself)

 

19:51 olgeni 

Remove all space characters from Makefile assignments.

No functional changes included.

CR:		D193 (except math/sedumi)
Approved by:	portmgr (bapt)

 

19:00 pi 

biology/seqtools: 4.25 -> 4.26, fix broken distinfo by upgrading

Submitted by:   pi (myself)
Approved by:    jadawin (mentor)

 

16:50 pi 

biology/seqtools: 4.24 -> 4.25

PR:             ports/186299
Submitted by:   pi (myself)
Approved by:    jadawin (mentor)

 

14:03 mat 

Fix old makeplist bug.

Pointy hat to:	people who blindly use makeplist
Sponsored by:	Absolight

 

17:23 wg 

biology/seqtools: update to 4.24

PR:		ports/185162
Submitted by:	maintainer

 

20:09 wg 

biology/seqtools: update to 4.23

PR:		ports/183960
Submitted by:	maintainer

 

11:01 wg 

biology/seqtools: Tools for visualising sequence alignments

Blixem is an interactive browser of pairwise alignments that have
been stacked up in a "master-slave" multiple alignment; it is not
a 'true' multiple alignment but a 'one-to-many' alignment.

Belvu is a multiple sequence alignment viewer and phylogenetic tool.

Dotter is a graphical dot-matrix program for detailed comparison
of two sequences.

WWW: http://www.sanger.ac.uk/resources/software/seqtools/

PR:		ports/183801
Submitted by:	Kurt Jaeger <fbsd-ports opsec.eu>