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non port: biology/ugene/Makefile
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Number of commits found: 46

Thu, 16 Sep 2021
[ 09:48 danfe (Alexey Dokuchaev) ]    commit hash:299862ff2afc17f5a415843ba9fc87ee6074fa87  299862f 
biology/ugene: update Unipro UGENE to version 40.0.
Fri, 25 Jun 2021
[ 17:56 danfe (Alexey Dokuchaev) ]    commit hash:05f96c80f8f5cde88a25a3f71a1b6248dd84827a  05f96c8 
biology/ugene: update Unipro UGENE to version 39.0.
Tue, 22 Jun 2021
[ 18:53 kbowling (Kevin Bowling) ]    commit hash:da3162c7c9f01912ba1940e188b253f2b5c7ba77  da3162c  (Only the first 10 of 914 ports in this commit are shown above. View all ports for this commit)
graphics/mesa-libs: Bump reverse deps for libglvnd

Per discussion with bapt on helping pkg handle the changing of these
deps and avoiding impossible upgrade senarios.

PR:		246767
Reviewed by:	manu, bapt
Approved by:	x11
Differential Revision:	https://reviews.freebsd.org/D30824
Tue, 18 May 2021
[ 15:24 danfe (Alexey Dokuchaev) ]    commit hash:6464fe05fe9d896e130503dfc4533d946d787e0f  6464fe0 
- Update Unipro UGENE to version 38.1 and thus unbreak
- CONFIG defaults to 64-bit mode now, adjust the check
Wed, 12 May 2021
[ 11:55 amdmi3 (Dmitry Marakasov) ]    commit hash:4b5a5c6d9c8767e327824d8d20c8d4bf86534904  4b5a5c6 
biology/ugene: mark BROKEN (does not fetch)

Approved by:	portmgr blanket
Tue, 6 Apr 2021
[ 14:31 mat (Mathieu Arnold) ]    commit hash:305f148f482daf30dcf728039d03d019f88344eb  305f148  (Only the first 10 of 29333 ports in this commit are shown above. View all ports for this commit)
Remove # $FreeBSD$ from Makefiles.
Tue, 23 Mar 2021
[ 14:20 danfe ] Original commit   Revision:569026
- Update Unipro UGENE to version 38.0
- Garbage-collect no longer needed patches
- Make COMMENT shorter and closer to upstream
- Stop building bundled SQLite, use ours!
Tue, 19 Jan 2021
[ 02:29 linimon ] Original commit   Revision:562006
Mark BROKEN on riscv64 the same as on aarch64.

While here, pet portlint (Makevar order).

Approved by:	portmgr (tier-2 blanket)
Obtained from:	lonesome.com build testing
Thu, 31 Dec 2020
[ 13:43 danfe ] Original commit   Revision:559737 (Only the first 10 of 13 ports in this commit are shown above. View all ports for this commit)
- Update Unipro UGENE port to version 37.0
- Drop no longer used WebEngine dependencies
- Force SSE2 on i386 (required for the build)
- Chase HTTP 301 redirection in the WWW line
Sun, 10 May 2020
[ 15:42 danfe ] Original commit   Revision:534852
- Resurrect and unbreak by updating to version 34.0
- Stop providing outdated offline PDF documentation,
  users are advised to use the online files instead
Sat, 4 Apr 2020
[ 20:51 antoine ] Original commit   Revision:530719 (Only the first 10 of 520 ports in this commit are shown above. View all ports for this commit)
Deprecate ports broken for more than 6 months
Wed, 6 Nov 2019
[ 12:48 antoine ] Original commit   Revision:516880 (Only the first 10 of 268 ports in this commit are shown above. View all ports for this commit)
Mark a few ports BROKEN, unfetchable
Mon, 4 Nov 2019
[ 21:08 zeising ] Original commit   Revision:516742 (Only the first 10 of 11 ports in this commit are shown above. View all ports for this commit)
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'.
Wed, 16 Jan 2019
[ 11:13 tijl ] Original commit   Revision:490472 (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 (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 (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
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 (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 (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 (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 (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
Mark as broken on arm64.

Approved by:	portmgr (tier-2 blanket)
Sat, 7 May 2016
[ 19:38 dim ] Original commit   Revision:414784
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
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 (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
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
- 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
Update Unipro UGENE to version 1.16.2.
Mon, 23 Mar 2015
[ 01:44 danfe ] Original commit   Revision:381974
- 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
Update Unipro UGENE to version 1.16.0 (documentation was also rerolled).
Tue, 6 Jan 2015
[ 05:28 danfe ] Original commit   Revision:376383
Update to version 1.15.1.
Wed, 3 Dec 2014
[ 01:40 danfe ] Original commit   Revision:373799
Update to version 1.15.0.
Mon, 13 Oct 2014
[ 11:01 danfe ] Original commit   Revision:370764
Update to version 1.14.2.
Wed, 10 Sep 2014
[ 20:50 gerald ] Original commit   Revision:367888 (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
- 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
USES=execinfo
Fri, 7 Mar 2014
[ 07:39 danfe ] Original commit   Revision:347340
Update to version 1.13.1.
Thu, 30 Jan 2014
[ 13:38 danfe ] Original commit   Revision:341837
Unbreak the fetch: one of the documentation PDF files was rerolled.
[ 13:11 decke ] Original commit   Revision:341835
- Mark BROKEN because it does not fetch
Thu, 16 Jan 2014
[ 17:17 danfe ] Original commit   Revision:339938
- 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
- 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
- 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 (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 (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
Unbreak on 7.X and i386 systems.

Reported by:	QAT
Sat, 23 Feb 2013
[ 04:50 danfe ] Original commit   Revision:312798
Add Unipro UGENE, a free open-source crowss-platform bioinformatics software.

PR:		ports/173387
Submitted by:	Hannes Hauswedell

Number of commits found: 46