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* Remove expired ports:Rene Ladan2020-05-051-34/+0
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more than 6 months 2020-05-05 www/p5-WWW-Google-Video: Broken for more than 6 months 2020-05-05 www/p5-WWW-Shorten-KUSO: Broken for more than 6 months 2020-05-05 www/p5-WWW-Shorten-isgd: Broken for more than 6 months 2020-05-05 www/photo_gallery: Broken for more than 6 months 2020-05-05 www/pwebstats: Broken for more than 6 months 2020-05-05 www/py-django-profiles: Broken for more than 6 months 2020-05-05 www/red5: Broken for more than 6 months 2020-05-05 www/redmine-sidebar_hide: Broken for more than 6 months 2020-05-05 www/rssowl: Broken for more than 6 months 2020-05-05 www/skytemplate: Broken for more than 6 months 2020-05-05 www/surfraw: Broken for more than 6 months 2020-05-05 www/sws: Broken for more than 6 months 2020-05-05 www/tickr: Broken for more than 6 months 2020-05-05 www/tinytinyhttpd: Broken for more than 6 months 2020-05-05 www/udmsearch: Broken for more than 6 months 2020-05-05 www/vee: Broken for more than 6 months 2020-05-05 www/webreport: Broken for more than 6 months 2020-05-05 www/webstats: Broken for more than 6 months 2020-05-05 www/www6to4: Broken for more than 6 months 2020-05-05 x11/deskpaint: Broken for more than 6 months 2020-05-05 x11/dmenu2: Broken for more than 6 months 2020-05-05 x11/gcb: Broken for more than 6 months 2020-05-05 x11/gpctool: Broken for more than 6 months 2020-05-05 x11/ipager: Broken for more than 6 months 2020-05-05 x11/keylaunch: Broken for more than 6 months 2020-05-05 x11/props: 64-bit unsupported 2020-05-05 x11/roxbg: Broken for more than 6 months 2020-05-05 x11/sisctrl: Broken for more than 6 months 2020-05-05 x11/wdm: Broken for more than 6 months 2020-05-05 x11/xaniroc: Broken for more than 6 months 2020-05-05 x11/xmove: Broken for more than 6 months 2020-05-05 x11/xnodecor: Broken for more than 6 months 2020-05-05 x11/xvattr: Broken for more than 6 months 2020-05-05 x11-clocks/tktz: Broken for more than 6 months 2020-05-05 x11-clocks/xtimer: Broken for more than 6 months 2020-05-05 x11-themes/gnome-icons-dropline-neu: Broken for more than 6 months 2020-05-05 x11-themes/gnome-icons-dropline-nou: Broken for more than 6 months 2020-05-05 x11-themes/gnome-icons-gion: Broken for more than 6 months 2020-05-05 x11-themes/gnome-icons-jini: Broken for more than 6 months 2020-05-05 x11-themes/gtk-aurora-engine: Broken for more than 6 months 2020-05-05 x11-themes/gtk-blueprint-engine: Broken for more than 6 months 2020-05-05 x11-themes/gtk-murrina-fancy-clearlooks: Broken for more than 6 months 2020-05-05 x11-themes/gtk-murrina-lightblue: Broken for more than 6 months 2020-05-05 x11-themes/gtk-murrine-themes: Broken for more than 6 months 2020-05-05 x11-themes/murrine-configurator: Broken for more than 6 months 2020-05-05 x11-themes/nimbus: Broken for more than 6 months 2020-05-05 x11-themes/openbox-themes: Broken for more than 6 months 2020-05-05 x11-themes/rezlooks: Broken for more than 6 months 2020-05-05 x11-themes/ubuntulooks: Broken for more than 6 months 2020-05-05 x11-toolkits/slingshot: 64-bit unsupported 2020-05-05 x11-toolkits/xview-clients: 64-bit unsupported 2020-05-05 x11-wm/fluxconf: Broken for more than 6 months 2020-05-05 x11-wm/ion: Broken for more than 6 months 2020-05-05 x11-wm/matwm2: Broken for more than 6 months 2020-05-05 x11-wm/nickleby: Broken for more than 6 months 2020-05-05 x11-wm/olvwm: 64-bit unsupported 2020-05-05 x11-wm/ratmenu: Broken for more than 6 months Notes: svn path=/head/; revision=534093
* Deprecate ports broken for more than 6 monthsAntoine Brodin2020-04-041-0/+2
| | | | Notes: svn path=/head/; revision=530719
* Mark a few ports BROKEN, unfetchableAntoine Brodin2019-11-061-0/+2
| | | | Notes: svn path=/head/; revision=516880
* Add USES=xorg USES=gl, ports categories bNiclas Zeising2019-11-041-1/+1
| | | | | | | | Add USES=xorg, USES=gl and in a few cases USES=gnome to ports in categories starting with 'b'. Notes: svn path=/head/; revision=516742
* Bump PORTREVISION for ports depending on the canonical version of GCCGerald Pfeifer2019-07-261-1/+1
| | | | | | | | | | | | | | | | | | 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 Notes: svn path=/head/; revision=507372
* biology/seqtools: fix build on current, if lld is lld7Kurt Jaeger2019-01-071-0/+1
| | | | | | | | | | - fixed by LLD_UNSAFE=yes PR: 230609 Submitted by: jbeich Notes: svn path=/head/; revision=489613
* Bump PORTREVISION for ports depending on the canonical version of GCCGerald Pfeifer2018-12-121-1/+1
| | | | | | | | | | | | | | | | | | 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 Notes: svn path=/head/; revision=487272
* biology/seqtools: re-try on powerpc* after r449590Jan Beich2017-12-121-2/+0
| | | | Notes: svn path=/head/; revision=456096
* Remove USES=execinfo.Mathieu Arnold2017-09-221-1/+1
| | | | | | | | | | PR: 220271 Submitted by: mat (review), Yasuhiro KIMURA (PR) Sponsored by: Absolight Differential Revision: https://reviews.freebsd.org/D11488 Notes: svn path=/head/; revision=450351
* Bump PORTREVISION for ports depending on the canonical version of GCCGerald Pfeifer2017-09-101-1/+1
| | | | | | | | | | | | | | | | | (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 Notes: svn path=/head/; revision=449591
* Mark some ports failing on power64. In cases where the error messageMark Linimon2017-05-211-0/+2
| | | | | | | | | | | | was a stub, provide a real one. While here, pet portlint. Approved by: portmgr (tier-2 blanket) Reported by: swills Notes: svn path=/head/; revision=441429
* Bump PORTREVISIONs for ports depending on the canonical version of GCC andGerald Pfeifer2017-04-011-0/+1
| | | | | | | | | | | | | | | | | 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 Notes: svn path=/head/; revision=437439
* Remove BROKEN_FreeBSD_9Sunpoet Po-Chuan Hsieh2017-01-011-2/+0
| | | | | | | Approved by: portmgr (blanket) Notes: svn path=/head/; revision=430235
* biology/seqtools: update 4.43.0 -> 4.44.1Kurt Jaeger2016-11-111-1/+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. Notes: svn path=/head/; revision=425863
* biology/seqtools: 4.42.1 -> 4.43.0Kurt Jaeger2016-07-311-5/+9
| | | | | | | | | 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 Notes: svn path=/head/; revision=419380
* biology/seqtools: 4.41.1 -> 4.42.1Kurt Jaeger2016-04-221-3/+3
| | | | | | | | | | - 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). Notes: svn path=/head/; revision=413787
* Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c.Mathieu Arnold2016-04-011-2/+2
| | | | | | | | With hat: portmgr Sponsored by: Absolight Notes: svn path=/head/; revision=412344
* biology/seqtools: 4.40.0 -> 4.41.1Kurt Jaeger2016-03-141-2/+2
| | | | | | | - mostly internal changes, some build fixes Notes: svn path=/head/; revision=411109
* biology/seqtools: 4.39.3 -> 4.40.0Kurt Jaeger2016-02-061-1/+1
| | | | | | | | | | - 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. Notes: svn path=/head/; revision=408287
* biology/seqtools: 4.39.2 -> 4.39.3Kurt Jaeger2015-12-051-1/+1
| | | | | | | | | | - Blixem Further improve the display of features in the detail view when they have transparent fill, making sure that they have a visible border. Notes: svn path=/head/; revision=403064
* biology/seqtools: 4.39.1 -> 4.39.2Kurt Jaeger2015-12-011-1/+1
| | | | | | | | | - Blixem: Improve the display of features in the detail view when they have transparent fill. Notes: svn path=/head/; revision=402787
* biology/seqtools: 4.39.0 -> 4.39.1Kurt Jaeger2015-11-131-1/+1
| | | | | | | | - Fix a bug in Belvu where the display was being initialised in command-line-only modes. Notes: svn path=/head/; revision=401527
* biology/seqtools: 4.36 -> 4.39.0Kurt Jaeger2015-11-081-1/+1
| | | | | | | | | | | | | | | | | - 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. Notes: svn path=/head/; revision=401065
* biology/seqtools: 4.35 -> 4.36Kurt Jaeger2015-08-081-1/+1
| | | | | | | Minor under-the-hood changes Notes: svn path=/head/; revision=393723
* biology/seqtools: 4.34.1 -> 4.35Kurt Jaeger2015-07-071-3/+3
| | | | | | | | | | - 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) Notes: svn path=/head/; revision=391503
* biology/seqtools: 4.33 -> 4.34.1Kurt Jaeger2015-05-061-1/+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. Notes: svn path=/head/; revision=385561
* biology/seqtools: 4.32 -> 4.33Kurt Jaeger2015-03-311-1/+1
| | | | | | | | - Blixem/Dotter Multi-dotter support; may now start multiple dotters from blixem Notes: svn path=/head/; revision=382855
* biology/seqtools: 4.31 -> 4.32Kurt Jaeger2015-02-121-1/+1
| | | | | | | | | | | | | | | | | | - 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. Notes: svn path=/head/; revision=378870
* biology/seqtools: 4.30 -> 4.31Kurt Jaeger2014-12-131-1/+1
| | | | | | | Some changes to sqlite dependencies Notes: svn path=/head/; revision=374668
* biology/seqtools: 4.29 -> 4.30Kurt Jaeger2014-11-041-2/+1
| | | | | | | | | - Blixem o Fix potential crash with internal processing o Fix two bugs in data input Notes: svn path=/head/; revision=372142
* biology/seqtools: 4.28 -> 4.29Kurt Jaeger2014-10-151-1/+1
| | | | | | | | | | | | | | - 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. Notes: svn path=/head/; revision=370943
* USES=execinfoBaptiste Daroussin2014-08-041-2/+1
| | | | Notes: svn path=/head/; revision=364067
* biology/seqtools: 4.27 -> 4.28Kurt Jaeger2014-07-311-1/+1
| | | | Notes: svn path=/head/; revision=363530
* Add OPTIONS_DEFINE=DOCS for ports with %%PORTDOCS%% in the plist.Adam Weinberger2014-07-151-0/+2
| | | | | | | | | | 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. Notes: svn path=/head/; revision=362014
* biology/seqtools: 4.26 -> 4.27Kurt Jaeger2014-07-121-2/+1
| | | | Notes: svn path=/head/; revision=361635
* - Chase database/sqlite3 slib bumpMartin Wilke2014-06-271-0/+1
| | | | | | | Approved by: portmgr (myself) Notes: svn path=/head/; revision=359586
* Remove all space characters from Makefile assignments.Jimmy Olgeni2014-06-081-1/+1
| | | | | | | | | | No functional changes included. CR: D193 (except math/sedumi) Approved by: portmgr (bapt) Notes: svn path=/head/; revision=357070
* biology/seqtools: 4.25 -> 4.26, fix broken distinfo by upgradingKurt Jaeger2014-05-021-2/+3
| | | | | | | | Submitted by: pi (myself) Approved by: jadawin (mentor) Notes: svn path=/head/; revision=352838
* biology/seqtools: 4.24 -> 4.25Kurt Jaeger2014-05-011-3/+2
| | | | | | | | | PR: ports/186299 Submitted by: pi (myself) Approved by: jadawin (mentor) Notes: svn path=/head/; revision=352761
* Fix old makeplist bug.Mathieu Arnold2014-02-121-0/+1
| | | | | | | | Pointy hat to: people who blindly use makeplist Sponsored by: Absolight Notes: svn path=/head/; revision=343923
* biology/seqtools: update to 4.24William Grzybowski2013-12-241-1/+1
| | | | | | | | PR: ports/185162 Submitted by: maintainer Notes: svn path=/head/; revision=337375
* biology/seqtools: update to 4.23William Grzybowski2013-11-141-2/+2
| | | | | | | | PR: ports/183960 Submitted by: maintainer Notes: svn path=/head/; revision=333786
* biology/seqtools: Tools for visualising sequence alignmentsWilliam Grzybowski2013-11-101-0/+25
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> Notes: svn path=/head/; revision=333374
generated by cgit v1.2.3 (git 2.25.1) at 2024-11-20 15:11:52 +0000