Unipro UGENE is multiplatform, open-source software with the main goal of
assisting molecular biologists without much expertise in bioinformatics to
manage, analyze, and visualize their data. UGENE integrates widely used
bioinformatics tools within one common user interface.
UGENE toolkit supports multiple biological data formats and allows the
retrieval of data from remote data sources. It provides visualization
modules for biological objects such as annotated genome sequences, Next
Generation Sequencing (NGS) assembly data, multiple sequence alignments,
phylogenetic trees, and 3D structures.
biology/ugene: fix build on aarch64
The bundled copy of htslib is missing required assembly source files,
causing build failure due to undefined symbols an aarch64.
Unbundle htslib and use our working port biology/htslib instead.
Approved by: makc (maintainer)
MFH: 2026Q2
PR: 293379
biology/ugene: Update to 53.1
Release Notes: https://ugene.net/changelist.html
Port changes:
- Fix build on non-x86, mark IGNORE for aarch64.
- Switch to cmake, qmake is not supported anymore.
- Drop unused sqlite, renew Qt components.
- Convert to PORTDATA, use shebangfix.
Special thanks to fuz@ for testing and fixing non-x86 build!
PR: 293379
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
Remove WWW entries moved into port Makefiles
Commit b7f05445c00f has added WWW entries to port Makefiles based on
WWW: lines in pkg-descr files.
This commit removes the WWW: lines of moved-over URLs from these
pkg-descr files.
Approved by: portmgr (tcberner)
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.
(Only the first 15 lines of the commit message are shown above )
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>
(Only the first 15 lines of the commit message are shown above )
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
- 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!
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
- 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
- Resurrect and unbreak by updating to version 34.0
- Stop providing outdated offline PDF documentation,
users are advised to use the online files instead
Remove expired ports:
Adjusted for ports rescued since r534032
2020-05-05 audio/festvox-czech: Broken for more than 6 months
2020-05-05 audio/gkrellmvolume2: Broken for more than 6 months
2020-05-05 audio/mixmos: Broken for more than 6 months
2020-05-05 audio/mma: Broken for more than 6 months
2020-05-05 audio/pd-cyclone: Broken for more than 6 months
2020-05-05 audio/shorten: Broken for more than 6 months
2020-05-05 audio/taglib-sharp: Broken for more than 6 months
2020-05-05 audio/xhippo: Broken for more than 6 months
2020-05-05 biology/consed: Broken for more than 6 months
2020-05-05 biology/plinkseq: Broken for more than 6 months
2020-05-05 biology/seqtools: Broken for more than 6 months
(Only the first 15 lines of the commit message are shown above )
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 )
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
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
Update Qt5 ports to 5.9.3.
This took quite a lot of time because Qt's own build system underwent
several changes in 5.8.0 that took a while to adapt to.
And, of course, qt5-webengine is a behemoth that we need to patch like crazy
due to its bundling of Chromium. In fact, most of the Chromium patches in
qt5-webengine have been imported with no changes from www/chromium@433510
("www/chromium: update to 56.0.2924.87").
New port: accessibility/qt5-speech
Bigger changes to Qt5 ports we had to make:
- Qt now allows using a configure.json file to define configuration options
and specify configuration checks that can be done when qmake is invoked.
(Only the first 15 lines of the commit message are shown above )
Revision bump of all ports with USE_GL after consolidation of mesa-libs
Approved by: swills (mentor)
Differential Revision: https://reviews.freebsd.org/D10845
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
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.
- 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
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)
- 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)
- 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)
- 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)
