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non port: biology/ugene/Makefile

Number of commits found: 53

Wednesday, 10 Jan 2024
08:16 Baptiste Daroussin (bapt) search for other commits by this committer
MAN?PREFIX: eleminate its usage  and move man to share/man
commit hash: 1b819e486953bae191a4b8f0da175b55cb6c3070 commit hash: 1b819e486953bae191a4b8f0da175b55cb6c3070 commit hash: 1b819e486953bae191a4b8f0da175b55cb6c3070 commit hash: 1b819e486953bae191a4b8f0da175b55cb6c3070 1b819e4
Sunday, 11 Sep 2022
10:20 Felix Palmen (zirias) search for other commits by this committer
Mk/Uses: always use colon for build/run suffix

Most USES use a colon for build/run(/test) suffixes. Change kde.mk,
qt.mk and pyqt.mk to do the same, and update all ports using that.

Document in CHANGES.

PR:			266034
Exp-run by:		antoine
Approved by:		tcberner (mentor)
Differential Revision:	https://reviews.freebsd.org/D36349
commit hash: ddae4e92d8313a1461145e3b4f0232fe463feaee commit hash: ddae4e92d8313a1461145e3b4f0232fe463feaee commit hash: ddae4e92d8313a1461145e3b4f0232fe463feaee commit hash: ddae4e92d8313a1461145e3b4f0232fe463feaee ddae4e9
Wednesday, 7 Sep 2022
21:10 Stefan E├čer (se) search for other commits by this committer
Add WWW entries to port Makefiles

It has been common practice to have one or more URLs at the end of the
ports' pkg-descr files, one per line and prefixed with "WWW:". These
URLs should point at a project website or other relevant resources.

Access to these URLs required processing of the pkg-descr files, and
they have often become stale over time. If more than one such URL was
present in a pkg-descr file, only the first one was tarnsfered into
the port INDEX, but for many ports only the last line did contain the
port specific URL to further information.

There have been several proposals to make a project URL available as
a macro in the ports' Makefiles, over time.

This commit implements such a proposal and moves one of the WWW: entries
of each pkg-descr file into the respective port's Makefile. A heuristic
attempts to identify the most relevant URL in case there is more than
one WWW: entry in some pkg-descr file. URLs that are not moved into the
Makefile are prefixed with "See also:" instead of "WWW:" in the pkg-descr
files in order to preserve them.

There are 1256 ports that had no WWW: entries in pkg-descr files. These
ports will not be touched in this commit.

The portlint port has been adjusted to expect a WWW entry in each port
Makefile, and to flag any remaining "WWW:" lines in pkg-descr files as
deprecated.

Approved by:		portmgr (tcberner)
commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52 commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52 commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52 commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52 b7f0544
Thursday, 4 Aug 2022
16:35 Yuri Victorovich (yuri) search for other commits by this committer
biology/ugene: Correct BROKEN message

Approved by:	portmgr (blanket)
commit hash: 5d1325cd1bad647d66d9cffb7dc0e5ee57e122e5 commit hash: 5d1325cd1bad647d66d9cffb7dc0e5ee57e122e5 commit hash: 5d1325cd1bad647d66d9cffb7dc0e5ee57e122e5 commit hash: 5d1325cd1bad647d66d9cffb7dc0e5ee57e122e5 5d1325c
07:41 Yuri Victorovich (yuri) search for other commits by this committer
biology/ugene: Broken on systems where OpenMP isn't enabled

Reported by:	fallout
Approved by:	portmgr (blanket)
commit hash: 34c51b63d7ff1399ba51c26cd4ab08ef73d5d335 commit hash: 34c51b63d7ff1399ba51c26cd4ab08ef73d5d335 commit hash: 34c51b63d7ff1399ba51c26cd4ab08ef73d5d335 commit hash: 34c51b63d7ff1399ba51c26cd4ab08ef73d5d335 34c51b6
Wednesday, 20 Jul 2022
14:20 Tobias C. Berner (tcberner) search for other commits by this committer
biology: remove 'Created by' lines

A big Thank You to the original contributors of these ports:

  *  Aaron Dalton <aaron@FreeBSD.org>
  *  Akinori MUSHA aka knu <knu@idaemons.org>
  *  Andrey Zakhvatov
  *  Bob Zimmermann <rpz@cse.wustl.edu>
  *  Camson Huynh <chuynh@biolateral.com.au>
  *  Dan Siercks <dsiercks@uwm.edu>
  *  Fernan Aguero <fernan@iib.unsam.edu.ar>
  *  Hannes Hauswedell <h2+fbsdports@fsfe.org>
  *  J. Bacon <jwb@FreeBSD.org>
  *  Jason Bacon <jwb@FreeBSD.org>
  *  Jeremy <karlj000@unbc.ca>
  *  Johann Visagie <johann@egenetics.com>
  *  Johann Visagie <wjv@FreeBSD.org>
  *  Mauricio Herrera Cuadra <mauricio@arareko.net>
  *  Motomichi Matsuzaki <mzaki@biol.s.u-tokyo.ac.jp>
  *  Motomichi Matsuzaki <mzaki@e-mail.ne.jp>
  *  Motomichi Matsuzaki <mzaki@m.u-tokyo.ac.jp>
  *  Motomichi Matsuzaki <mzaki@niid.go.jp>
  *  Po-Chuan Hsieh <sunpoet@FreeBSD.org>
  *  Razi Khaja <razi@genet.sickkids.on.ca>
  *  Reed A. Cartwright <cartwright@asu.edu>
  *  Ryo MIYAMOTO
  *  Ryo MIYAMOTO <rmiya@cc.hirosaki-u.ac.jp>
  *  Sangwoo Shim <sangwoos@gmail.com>
  *  Sunpoet Po-Chuan Hsieh <sunpoet@FreeBSD.org>
  *  Tassilo Philipp <tphilipp@potion-studios.com>
  *  Tony Maher
  *  Tony Maher <tonym@biolateral.com.au>
  *  Wen Heping <wen@FreeBSD.org>
  *  Wen Heping <wenheping@gmail.com>
  *  Yonatan <onatan@gmail.com>
  *  Yuri Victorovich <yuri@rawbw.com>
  *  ballen
  *  barnhart@genetics.wustl.edu
  *  camson@bilateral.com.au
  *  chuynh@biolateral.com.au
  *  dbader@eece.unm.edu
  *  frankch@waru.life.nthu.edu.tw
  *  h2
  *  lentferj
  *  maho@FreeBSD.org
  *  mzaki@biol.s.u-tokyo.ac.jp
  *  tonym
  *  wen@FreeBSD.org

With hat:	portmgr
commit hash: 37526bbd4e50616d87f70e1c788ae4895d88d671 commit hash: 37526bbd4e50616d87f70e1c788ae4895d88d671 commit hash: 37526bbd4e50616d87f70e1c788ae4895d88d671 commit hash: 37526bbd4e50616d87f70e1c788ae4895d88d671 37526bb
Thursday, 14 Oct 2021
11:23 Alexey Dokuchaev (danfe) search for other commits by this committer
biology/ugene: update UniPro UGENE to version 40.1 (bugfix release).
commit hash: e409be37a880805890a6a3ba0be4aed22042f25b commit hash: e409be37a880805890a6a3ba0be4aed22042f25b commit hash: e409be37a880805890a6a3ba0be4aed22042f25b commit hash: e409be37a880805890a6a3ba0be4aed22042f25b e409be3
Thursday, 16 Sep 2021
09:48 Alexey Dokuchaev (danfe) search for other commits by this committer
biology/ugene: update Unipro UGENE to version 40.0.
commit hash: 299862ff2afc17f5a415843ba9fc87ee6074fa87 commit hash: 299862ff2afc17f5a415843ba9fc87ee6074fa87 commit hash: 299862ff2afc17f5a415843ba9fc87ee6074fa87 commit hash: 299862ff2afc17f5a415843ba9fc87ee6074fa87 299862f
Friday, 25 Jun 2021
17:56 Alexey Dokuchaev (danfe) search for other commits by this committer
biology/ugene: update Unipro UGENE to version 39.0.
commit hash: 05f96c80f8f5cde88a25a3f71a1b6248dd84827a commit hash: 05f96c80f8f5cde88a25a3f71a1b6248dd84827a commit hash: 05f96c80f8f5cde88a25a3f71a1b6248dd84827a commit hash: 05f96c80f8f5cde88a25a3f71a1b6248dd84827a 05f96c8
Tuesday, 22 Jun 2021
18:53 Kevin Bowling (kbowling) search for other commits by this committer
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
commit hash: da3162c7c9f01912ba1940e188b253f2b5c7ba77 commit hash: da3162c7c9f01912ba1940e188b253f2b5c7ba77 commit hash: da3162c7c9f01912ba1940e188b253f2b5c7ba77 commit hash: da3162c7c9f01912ba1940e188b253f2b5c7ba77 da3162c
Tuesday, 18 May 2021
15:24 Alexey Dokuchaev (danfe) search for other commits by this committer
- Update Unipro UGENE to version 38.1 and thus unbreak
- CONFIG defaults to 64-bit mode now, adjust the check
commit hash: 6464fe05fe9d896e130503dfc4533d946d787e0f commit hash: 6464fe05fe9d896e130503dfc4533d946d787e0f commit hash: 6464fe05fe9d896e130503dfc4533d946d787e0f commit hash: 6464fe05fe9d896e130503dfc4533d946d787e0f 6464fe0
Wednesday, 12 May 2021
11:55 Dmitry Marakasov (amdmi3) search for other commits by this committer
biology/ugene: mark BROKEN (does not fetch)

Approved by:	portmgr blanket
commit hash: 4b5a5c6d9c8767e327824d8d20c8d4bf86534904 commit hash: 4b5a5c6d9c8767e327824d8d20c8d4bf86534904 commit hash: 4b5a5c6d9c8767e327824d8d20c8d4bf86534904 commit hash: 4b5a5c6d9c8767e327824d8d20c8d4bf86534904 4b5a5c6
Tuesday, 6 Apr 2021
14:31 Mathieu Arnold (mat) search for other commits by this committer
Remove # $FreeBSD$ from Makefiles.
commit hash: 305f148f482daf30dcf728039d03d019f88344eb commit hash: 305f148f482daf30dcf728039d03d019f88344eb commit hash: 305f148f482daf30dcf728039d03d019f88344eb commit hash: 305f148f482daf30dcf728039d03d019f88344eb 305f148
Tuesday, 23 Mar 2021
14:20 danfe search for other commits by this committer
- 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!
Original commitRevision:569026 
Tuesday, 19 Jan 2021
02:29 linimon search for other commits by this committer
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
Original commitRevision:562006 
Thursday, 31 Dec 2020
13:43 danfe search for other commits by this committer
- 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
Original commitRevision:559737 
Sunday, 10 May 2020
15:42 danfe search for other commits by this committer
- Resurrect and unbreak by updating to version 34.0
- Stop providing outdated offline PDF documentation,
  users are advised to use the online files instead
Original commitRevision:534852 
Saturday, 4 Apr 2020
20:51 antoine search for other commits by this committer
Deprecate ports broken for more than 6 months
Original commitRevision:530719 
Wednesday, 6 Nov 2019
12:48 antoine search for other commits by this committer
Mark a few ports BROKEN, unfetchable
Original commitRevision:516880 
Monday, 4 Nov 2019
21:08 zeising search for other commits by this committer
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'.
Original commitRevision:516742 
Wednesday, 16 Jan 2019
11:13 tijl search for other commits by this committer
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
in the weak wrapper resolves to the weak wrapper itself creating an infinite
call loop that overflows the stack and causes a crash.  Some of the
allocation functions are variants of C++ new and delete and it probably
depends on the compiler whether these variants are used in other parts of
Qt5Webengine.

Remove the weak wrappers (make them Linux specific).  This isn't binary
compatible but we are already breaking that with the changes to the symbol
versions.

[1]
https://github.com/qt/qtwebengine/commit/5c2cbfccf9aafb547b0b30914c4056abd25942a4
[2]
https://github.com/qt/qtwebengine/commit/2ed5054e3a800fa97c2c9e920ba1e6ea4b6ef2a5
[3]
https://github.com/qt/qtwebengine/commit/009f5ebb4bd6e50188671e0815a5dae6afe39db5

Bump all ports that depend on Qt5.

PR:		234070
Exp-run by:	antoine
Approved by:	kde (adridg)
Original commitRevision:490472 
Sunday, 2 Sep 2018
20:47 jhale search for other commits by this committer
Update to 1.31.0

PR:		229463
Approved by:	Hannes Hauswedell <h2+fbsdports@fsfe.org> (maintainer)
Original commitRevision:478818 
Thursday, 28 Jun 2018
17:39 tcberner search for other commits by this committer
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
Original commitRevision:473503 
Tuesday, 15 May 2018
18:51 rakuco search for other commits by this committer
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
Original commitRevision:470045 
Friday, 22 Sep 2017
10:48 mat search for other commits by this committer
Remove USES=execinfo.

PR:		220271
Submitted by:	mat (review), Yasuhiro KIMURA (PR)
Sponsored by:	Absolight
Differential Revision:	https://reviews.freebsd.org/D11488
Original commitRevision:450351 
Tuesday, 23 May 2017
05:03 rezny search for other commits by this committer
Revision bump of all ports with USE_GL after consolidation of mesa-libs

Approved by:	swills (mentor)
Differential Revision:	https://reviews.freebsd.org/D10845
Original commitRevision:441503 
Monday, 9 Jan 2017
13:16 amdmi3 search for other commits by this committer
- Remove always-true/false conditions after FreeBSD 9, 10.1, 10.2 EOL

Approved by:	portmgr blanket
Original commitRevision:430947 
Tuesday, 8 Nov 2016
19:29 linimon search for other commits by this committer
The 64-bit arm arch is actually spelled 'aarch64', not 'arm64'.
Original commitRevision:425758 
07:20 linimon search for other commits by this committer
Mark as broken on arm64.

Approved by:	portmgr (tier-2 blanket)
Original commitRevision:425689 
Saturday, 7 May 2016
19:38 dim search for other commits by this committer
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
Original commitRevision:414784 
Thursday, 14 Apr 2016
04:07 danfe search for other commits by this committer
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.
Original commitRevision:413242 
Friday, 1 Apr 2016
13:29 mat search for other commits by this committer
Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c.

With hat:	portmgr
Sponsored by:	Absolight
Original commitRevision:412344 
Tuesday, 18 Aug 2015
20:02 pgollucci search for other commits by this committer
biology/ugene: qt4-linguist -> qt4-linguisttools

- add USES=desktop-file-utils

PR:                  202138
Submitted by:        s3erios@gmail.com
Approved by:         h2+fbsdports@fsfe.org
Original commitRevision:394652 
Wednesday, 15 Jul 2015
07:18 danfe search for other commits by this committer
- Update Unipro UGENE to version 1.17.0 (documentation was also rerolled)
- Remove no longer required local source code tweaks (picked up upstream)
Original commitRevision:392119 
Thursday, 28 May 2015
08:12 danfe search for other commits by this committer
Update Unipro UGENE to version 1.16.2.
Original commitRevision:387709 
Monday, 23 Mar 2015
01:44 danfe search for other commits by this committer
- 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
Original commitRevision:381974 
Tuesday, 24 Feb 2015
11:42 danfe search for other commits by this committer
Update Unipro UGENE to version 1.16.0 (documentation was also rerolled).
Original commitRevision:379787 
Tuesday, 6 Jan 2015
05:28 danfe search for other commits by this committer
Update to version 1.15.1.
Original commitRevision:376383 
Wednesday, 3 Dec 2014
01:40 danfe search for other commits by this committer
Update to version 1.15.0.
Original commitRevision:373799 
Monday, 13 Oct 2014
11:01 danfe search for other commits by this committer
Update to version 1.14.2.
Original commitRevision:370764 
Wednesday, 10 Sep 2014
20:50 gerald search for other commits by this committer
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)
Original commitRevision:367888 
Monday, 1 Sep 2014
07:39 danfe search for other commits by this committer
- 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)
Original commitRevision:366842 
Monday, 4 Aug 2014
23:06 bapt search for other commits by this committer
USES=execinfo
Original commitRevision:364067 
Friday, 7 Mar 2014
07:39 danfe search for other commits by this committer
Update to version 1.13.1.
Original commitRevision:347340 
Thursday, 30 Jan 2014
13:38 danfe search for other commits by this committer
Unbreak the fetch: one of the documentation PDF files was rerolled.
Original commitRevision:341837 
13:11 decke search for other commits by this committer
- Mark BROKEN because it does not fetch
Original commitRevision:341835 
Thursday, 16 Jan 2014
17:17 danfe search for other commits by this committer
- 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)
Original commitRevision:339938 
Friday, 1 Nov 2013
15:20 danfe search for other commits by this committer
- Install official UGENE documentation (PDF)
- Utilize DIST_SUBDIR as now it's more than one distfile
Original commitRevision:332391 
Thursday, 31 Oct 2013
15:30 danfe search for other commits by this committer
- 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)
Original commitRevision:332256 
Friday, 20 Sep 2013
15:55 bapt search for other commits by this committer
Add NO_STAGE all over the place in preparation for the staging support (cat:
biology)
Original commitRevision:327709 
Wednesday, 14 Aug 2013
22:35 ak search for other commits by this committer
- Remove MAKE_JOBS_SAFE variable

Approved by:	portmgr (bdrewery)
Original commitRevision:324744 
Monday, 25 Feb 2013
13:00 danfe search for other commits by this committer
Unbreak on 7.X and i386 systems.

Reported by:	QAT
Original commitRevision:312918 
Saturday, 23 Feb 2013
04:50 danfe search for other commits by this committer
Add Unipro UGENE, a free open-source crowss-platform bioinformatics software.

PR:		ports/173387
Submitted by:	Hannes Hauswedell
Original commitRevision:312798 

Number of commits found: 53