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non port: biology/ugene/Makefile
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Number of commits found: 33

Wed, 16 Jan 2019
[ 11:13 tijl ] Original commit   Revision:490472
490472 accessibility/kdeaccessibility/Makefile
490472 accessibility/kmag/Makefile
490472 accessibility/kmousetool/Makefile
490472 accessibility/kmouth/Makefile
490472 accessibility/qt5-speech/Makefile
490472 archivers/ark/Makefile
490472 archivers/kf5-karchive/Makefile
490472 archivers/peazip/Makefile
490472 archivers/quazip/Makefile
490472 astro/gpsbabel/Makefile

(Only the first 10 of 1089 ports in this commit are shown above. View all ports for this commit)
Fix Qt5 symbol version scripts to put the catch-all clause first.  When
a symbol matches multiple clauses the last one takes precedence.  If the
catch-all is last it captures everything.  In the case of Qt5 libraries
this caused all symbols to have a Qt_5 label while some should have
Qt_5_PRIVATE_API.  This only affects lld because GNU ld always gives the
catch-all lowest priority.

Older versions of Qt5Webengine exported some memory allocation symbols from
the bundled Chromium.  Version 5.9 stopped exporting these [1] but the
symbols were kept as weak wrappers for the standard allocation functions to
maintain binary compatibility. [2][3]  The problem is that the call to the
standard function in these weak wrappers is only resolved to the standard
function if there's a call to this standard function in other parts of
Qt5Webengine, because only then is there a non-weak symbol that takes
precedence over the weak one.  If there's no such non-weak symbol the call
(Only the first 15 lines of the commit message are shown above View all of this commit message)
Sun, 2 Sep 2018
[ 20:47 jhale ] Original commit   Revision:478818
478818 biology/ugene/Makefile
478818 biology/ugene/distinfo
478818 biology/ugene/files/patch-git_279756e4
478818 biology/ugene/files/patch-git_578c949
478818 biology/ugene/files/patch-src_corelibs_U2Private_U2Private.pro
478818 biology/ugene/files/patch-src_libs__3rdparty_QSpec_src_drivers_GTKeyboardDriverLinux.cpp
478818 biology/ugene/files/patch-src_libs__3rdparty_QSpec_src_drivers_GTMouseDriverLinux.cpp
478818 biology/ugene/files/patch-src_libs__3rdparty_samtools_samtools.pri
478818 biology/ugene/files/patch-src_plugins__3rdparty_phylip_src_phylip.h
478818 biology/ugene/files/patch-src_plugins__3rdparty_umuscle_src_MuscleWorkPool.cpp

(Only the first 10 of 17 ports in this commit are shown above. View all ports for this commit)
Update to 1.31.0

PR:		229463
Approved by:	Hannes Hauswedell <h2+fbsdports@fsfe.org> (maintainer)
Thu, 28 Jun 2018
[ 17:39 tcberner ] Original commit   Revision:473503
473503 CHANGES
473503 Mk/Scripts/qa.sh
473503 Mk/Uses/qmake.mk
473503 Mk/Uses/qt-dist.mk
473503 Mk/Uses/qt.mk
473503 Mk/bsd.port.mk
473503 Mk/bsd.qt.mk
473503 Mk/bsd.sanity.mk
473503 accessibility/jovie-kde4/Makefile
473503 accessibility/kaccessible-kde4/Makefile

(Only the first 10 of 1416 ports in this commit are shown above. View all ports for this commit)
Replace bsd.qt.mk by Uses/qt.mk and Uses/qt-dist.mk

From now on, ports that depend on Qt4 will have to set
	USES=		qt:4
	USE_QT=		foo bar
ports depending on Qt5 will use
	USES=		qt:5
	USE_QT=		foo bar

PR:		229225
Exp-run by:	antoine
Reviewed by:	mat
Approved by:	portmgr (antoine)
Differential Revision:	-https://reviews.freebsd.org/D15540
Tue, 15 May 2018
[ 18:51 rakuco ] Original commit   Revision:470045
470045 biology/ugene/Makefile
470045 biology/ugene/files/patch-git_279756e4
Add upstream patch to fix the build with Qt 5.10.

    _tmp/ui/ui_Bowtie2Settings.h:189:35: error: no viable conversion from
'QLatin1String' to 'const QKeySequence'
            gbarCheckBox->setShortcut(QLatin1String(""));
                                      ^~~~~~~~~~~~~~~~~

PR:		228213
Fri, 22 Sep 2017
[ 10:48 mat ] Original commit   Revision:450351
450351 Mk/Scripts/qa.sh
450351 Mk/Uses/execinfo.mk
450351 astro/opencpn/Makefile
450351 audio/clementine-player/Makefile
450351 audio/deadbeef/Makefile
450351 audio/pulseaudio/Makefile
450351 audio/sayonara/Makefile
450351 biology/seqtools/Makefile
450351 biology/ugene/Makefile
450351 cad/klayout/Makefile

(Only the first 10 of 175 ports in this commit are shown above. View all ports for this commit)
Remove USES=execinfo.

PR:		220271
Submitted by:	mat (review), Yasuhiro KIMURA (PR)
Sponsored by:	Absolight
Differential Revision:	https://reviews.freebsd.org/D11488
Tue, 23 May 2017
[ 05:03 rezny ] Original commit   Revision:441503
441503 accessibility/redshift/Makefile
441503 astro/boinc-astropulse/Makefile
441503 astro/boinc-setiathome-v7/Makefile
441503 astro/celestia/Makefile
441503 astro/nightfall/Makefile
441503 astro/opencpn/Makefile
441503 astro/openuniverse/Makefile
441503 astro/qlandkartegt/Makefile
441503 audio/amarok-kde4/Makefile
441503 audio/aylet/Makefile

(Only the first 10 of 711 ports in this commit are shown above. View all ports for this commit)
Revision bump of all ports with USE_GL after consolidation of mesa-libs

Approved by:	swills (mentor)
Differential Revision:	https://reviews.freebsd.org/D10845
Mon, 9 Jan 2017
[ 13:16 amdmi3 ] Original commit   Revision:430947
430947 archivers/unarchiver/Makefile
430947 audio/csound/Makefile
430947 audio/csound6/Makefile
430947 audio/optimfrog/Makefile
430947 audio/praat/Makefile
430947 audio/shoutcast/Makefile
430947 audio/sndio/Makefile
430947 benchmarks/fio/Makefile
430947 biology/seqan-apps/Makefile
430947 biology/ugene/Makefile

(Only the first 10 of 104 ports in this commit are shown above. View all ports for this commit)
- Remove always-true/false conditions after FreeBSD 9, 10.1, 10.2 EOL

Approved by:	portmgr blanket
Tue, 8 Nov 2016
[ 19:29 linimon ] Original commit   Revision:425758
425758 audio/bristol/Makefile
425758 biology/avida/Makefile
425758 biology/gmap/Makefile
425758 biology/ugene/Makefile
425758 databases/p5-Tie-LevelDB/Makefile
425758 devel/avro-c/Makefile
425758 devel/gecode/Makefile
425758 devel/libdouble-conversion/Makefile
425758 devel/libhoard/Makefile
425758 devel/php-uprofiler/Makefile

(Only the first 10 of 45 ports in this commit are shown above. View all ports for this commit)
The 64-bit arm arch is actually spelled 'aarch64', not 'arm64'.
[ 07:20 linimon ] Original commit   Revision:425689
425689 biology/ugene/Makefile
Mark as broken on arm64.

Approved by:	portmgr (tier-2 blanket)
Sat, 7 May 2016
[ 19:38 dim ] Original commit   Revision:414784
414784 biology/ugene/Makefile
414784 biology/ugene/files/patch-src_libs__3rdparty_samtools_samtools.pri
414784 biology/ugene/files/patch-src_plugins__3rdparty_variants_variants.pri
414784 biology/ugene/files/patch-src_ugene__globals.pri
During the exp-run in bug 208158, it was found that biology/ugene gives
errors with libc++ 3.8.0:

In file included from src/QScoreAdapter.cpp:1:
In file included from src/QScoreAdapter.h:4:
In file included from ../../include/U2Core/MAlignment.h:1:
In file included from
../../include/U2Core/../../corelibs/U2Core/src/datatype/MAlignment.h:25:
In file included from
../../include/U2Core/../../corelibs/U2Core/src/datatype/MAlignmentInfo.h:25:
In file included from /usr/local/include/qt5/QtCore/QString:1:
In file included from /usr/local/include/qt5/QtCore/qstring.h:41:
In file included from /usr/local/include/qt5/QtCore/qchar.h:37:
In file included from /usr/local/include/qt5/QtCore/qglobal.h:39:
/usr/include/c++/v1/cstddef:43:15: fatal error: 'stddef.h' file not found
#include_next <stddef.h>
              ^

This is because the port tries to add /usr/include as a system include
directory, using -isystem, and this screws up the order of include
directories.  Fix it by patching up a number of .pri files to avoid
using the -isystem flag.

Approved by:	h2+fbsdports@fsfe.org (maintainer)
PR:		209366
MFH:		2016Q2
Thu, 14 Apr 2016
[ 04:07 danfe ] Original commit   Revision:413242
413242 biology/ugene/Makefile
413242 biology/ugene/distinfo
413242 biology/ugene/files
413242 biology/ugene/files/patch-src_corelibs_U2Private_U2Private.pro
413242 biology/ugene/files/patch-src_plugins__3rdparty_umuscle_src_MuscleWorkPool.cpp
413242 biology/ugene/files/patch-src_plugins__checker_src_Main.cpp
413242 biology/ugene/files/patch-src_ugenecl_src_Main.cpp
413242 biology/ugene/files/patch-src_ugeneui_src_Main.cpp
413242 biology/ugene/files/patch-ugene.pro
413242 biology/ugene/pkg-plist
Update to version 1.22.0, which now unfortunately requires Qt 5.x.  Also
since around v1.18.0, UGENE is using Google's Breakpad library for crash
reporting, which is very system-specific and does not support FreeBSD at
the moment.  Due to lack of resources and interest in porting it, simply
disable crash reporting code for the time being.
Fri, 1 Apr 2016
[ 13:29 mat ] Original commit   Revision:412344
412344 Mk/Uses/gecko.mk
412344 Mk/bsd.fpc.mk
412344 Mk/bsd.gecko.mk
412344 Mk/bsd.port.mk
412344 accessibility/accerciser/Makefile
412344 accessibility/at-spi/Makefile
412344 accessibility/at-spi2-atk/Makefile
412344 accessibility/at-spi2-core/Makefile
412344 accessibility/caribou/Makefile
412344 accessibility/dasher/Makefile

(Only the first 10 of 1009 ports in this commit are shown above. View all ports for this commit)
Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c.

With hat:	portmgr
Sponsored by:	Absolight
Tue, 18 Aug 2015
[ 20:02 pgollucci ] Original commit   Revision:394652
394652 biology/ugene/Makefile
biology/ugene: qt4-linguist -> qt4-linguisttools

- add USES=desktop-file-utils

PR:                  202138
Submitted by:        s3erios@gmail.com
Approved by:         h2+fbsdports@fsfe.org
Wed, 15 Jul 2015
[ 07:18 danfe ] Original commit   Revision:392119
392119 biology/ugene/Makefile
392119 biology/ugene/distinfo
- Update Unipro UGENE to version 1.17.0 (documentation was also rerolled)
- Remove no longer required local source code tweaks (picked up upstream)
Thu, 28 May 2015
[ 08:12 danfe ] Original commit   Revision:387709
387709 biology/ugene/Makefile
387709 biology/ugene/distinfo
387709 biology/ugene/pkg-plist
Update Unipro UGENE to version 1.16.2.
Mon, 23 Mar 2015
[ 01:44 danfe ] Original commit   Revision:381974
381974 biology/ugene/Makefile
381974 biology/ugene/distinfo
381974 biology/ugene/pkg-plist
- 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
Tue, 24 Feb 2015
[ 11:42 danfe ] Original commit   Revision:379787
379787 biology/ugene/Makefile
379787 biology/ugene/distinfo
379787 biology/ugene/pkg-plist
Update Unipro UGENE to version 1.16.0 (documentation was also rerolled).
Tue, 6 Jan 2015
[ 05:28 danfe ] Original commit   Revision:376383
376383 biology/ugene/Makefile
376383 biology/ugene/distinfo
376383 biology/ugene/pkg-plist
Update to version 1.15.1.
Wed, 3 Dec 2014
[ 01:40 danfe ] Original commit   Revision:373799
373799 biology/ugene/Makefile
373799 biology/ugene/distinfo
373799 biology/ugene/pkg-plist
Update to version 1.15.0.
Mon, 13 Oct 2014
[ 11:01 danfe ] Original commit   Revision:370764
370764 biology/ugene/Makefile
370764 biology/ugene/distinfo
370764 biology/ugene/pkg-plist
Update to version 1.14.2.
Wed, 10 Sep 2014
[ 20:50 gerald ] Original commit   Revision:367888
367888 accessibility/accerciser/Makefile
367888 accessibility/jovie/Makefile
367888 accessibility/kaccessible/Makefile
367888 accessibility/kdeaccessibility4/Makefile
367888 accessibility/kmag/Makefile
367888 accessibility/kmousetool/Makefile
367888 accessibility/kmouth/Makefile
367888 accessibility/orca/Makefile
367888 arabic/kde4-l10n/Makefile
367888 arabic/libreoffice/Makefile

(Only the first 10 of 3171 ports in this commit are shown above. View all ports for this commit)
Update the default version of GCC in the Ports Collection from GCC 4.7.4
to GCC 4.8.3.

Part II, Bump PORTREVISIONs.

PR:		192025
Tested by:	antoine (-exp runs)
Approved by:	portmgr (implicit)
Mon, 1 Sep 2014
[ 07:39 danfe ] Original commit   Revision:366842
366842 biology/ugene/Makefile
366842 biology/ugene/distinfo
366842 biology/ugene/files
366842 biology/ugene/pkg-plist
- Update Unipro UGENE and documentation to version 1.14.0
- Remove patches integrated upstream (it's nice to have direct contact)
- Sort USES and pkg-plist, cleanup Makefile a bit while here

Approved by:	maintainer (implicit)
Mon, 4 Aug 2014
[ 23:06 bapt ] Original commit   Revision:364067
364067 biology/seqtools/Makefile
364067 biology/ugene/Makefile
USES=execinfo
Fri, 7 Mar 2014
[ 07:39 danfe ] Original commit   Revision:347340
347340 biology/ugene/Makefile
347340 biology/ugene/distinfo
347340 biology/ugene/files/patch-src-corelibs-U2Core-src-globals-AppResources.cpp
Update to version 1.13.1.
Thu, 30 Jan 2014
[ 13:38 danfe ] Original commit   Revision:341837
341837 biology/ugene/Makefile
341837 biology/ugene/distinfo
Unbreak the fetch: one of the documentation PDF files was rerolled.
[ 13:11 decke ] Original commit   Revision:341835
341835 biology/ugene/Makefile
- Mark BROKEN because it does not fetch
Thu, 16 Jan 2014
[ 17:17 danfe ] Original commit   Revision:339938
339938 biology/ugene/Makefile
339938 biology/ugene/distinfo
339938 biology/ugene/files/patch-clang-fixes
339938 biology/ugene/files/patch-gtest-std::tr1::tuple-fix
339938 biology/ugene/files/patch-src-corelibs-U2Core-src-globals-AppResources.cpp
339938 biology/ugene/files/patch-src-shtirlitz-Shtirlitz.cpp
339938 biology/ugene/files/patch-src-ugenem-src-SendReportDialog.cpp
339938 biology/ugene/files/patch-src-ugeneui-src-Main.cpp
339938 biology/ugene/pkg-plist
- Update to version 1.13.0 and improve FreeBSD support; it also builds
  pretty cleanly with GCC v4.2, v4.6, and Clang (modulo a few warnings)
- Sadly, do not use PORTDOCS: since DOCSDIR is set to be inside DATADIR,
  and will get appended to PLIST after @dirrm %%DATADIR%%, which upsets
  sanity checking tools; instead, list the docs explicitly in DISTFILES
  and add them to pkg-plist (guarded by %%PORTDOCS%%)

Tested on:	i386 (only)
Fri, 1 Nov 2013
[ 15:20 danfe ] Original commit   Revision:332391
332391 biology/ugene/Makefile
332391 biology/ugene/distinfo
332391 biology/ugene/pkg-plist
- Install official UGENE documentation (PDF)
- Utilize DIST_SUBDIR as now it's more than one distfile
Thu, 31 Oct 2013
[ 15:30 danfe ] Original commit   Revision:332256
332256 biology/ugene/Makefile
332256 biology/ugene/distinfo
332256 biology/ugene/files/patch-clang-fixes
332256 biology/ugene/files/patch-gtest-std::tr1::tuple-fix
332256 biology/ugene/files/patch-src-corelibs-U2Private-src-CrashHandler.cpp
332256 biology/ugene/files/patch-src-plugins_3rdparty-umuscle-src-muscle-intmath.cpp
332256 biology/ugene/pkg-descr
332256 biology/ugene/pkg-plist
- Update to version 1.12.3
- Conditionalize dependency on `devel/libexecinfo'
- Try to detect SSE2 support
- Convert to USES=qmake and stafigy
- Improve grammar in port description while here

Approved by:	maintainer (implicit)
Fri, 20 Sep 2013
[ 15:55 bapt ] Original commit   Revision:327709
327709 biology/ariadne/Makefile
327709 biology/artemis/Makefile
327709 biology/avida/Makefile
327709 biology/babel/Makefile
327709 biology/biococoa/Makefile
327709 biology/biojava/Makefile
327709 biology/blast/Makefile
327709 biology/blat/Makefile
327709 biology/boinc-simap/Makefile
327709 biology/chemeq/Makefile

(Only the first 10 of 94 ports in this commit are shown above. View all ports for this commit)
Add NO_STAGE all over the place in preparation for the staging support (cat:
biology)
Wed, 14 Aug 2013
[ 22:35 ak ] Original commit   Revision:324744
324744 accessibility/atkmm/Makefile
324744 accessibility/jovie/Makefile
324744 accessibility/kaccessible/Makefile
324744 accessibility/kmag/Makefile
324744 accessibility/kmousetool/Makefile
324744 accessibility/kmouth/Makefile
324744 accessibility/qt4-accessible/Makefile
324744 accessibility/speech-dispatcher/Makefile
324744 archivers/ark/Makefile
324744 archivers/bicom/Makefile

(Only the first 10 of 1725 ports in this commit are shown above. View all ports for this commit)
- Remove MAKE_JOBS_SAFE variable

Approved by:	portmgr (bdrewery)
Mon, 25 Feb 2013
[ 13:00 danfe ] Original commit   Revision:312918
312918 biology/ugene/Makefile
312918 biology/ugene/files/patch-src-corelibs-U2Private-src-CrashHandler.cpp
312918 biology/ugene/files/patch-src-plugins_3rdparty-umuscle-src-muscle-intmath.cpp
312918 biology/ugene/pkg-plist
Unbreak on 7.X and i386 systems.

Reported by:	QAT
Sat, 23 Feb 2013
[ 04:50 danfe ] Original commit   Revision:312798
312798 biology/Makefile
312798 biology/ugene
312798 biology/ugene/Makefile
312798 biology/ugene/distinfo
312798 biology/ugene/files
312798 biology/ugene/files/patch-src-corelibs-U2Private-src-CrashHandler.cpp
312798 biology/ugene/pkg-descr
312798 biology/ugene/pkg-plist
Add Unipro UGENE, a free open-source crowss-platform bioinformatics software.

PR:		ports/173387
Submitted by:	Hannes Hauswedell

Number of commits found: 33

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