The massXpert project aims at providing (bio)chemists with a software
package allowing the following:
* User-specific atom definitions and polymer chemistry definitions;
* Powerful sequence editing with user-defined glyphs for each monomer
and monomer chemical modification. Multi-region selections;
* Polymer sequence chemical/enzymatic cleavage;
* Intramolecular cross-linking, like disulfide bonds with total resolution
of the peptides generated upon enzymatic cleavage;
* Gas-phase fragmentation of oligomers;
* Mass-to-charge ratio calculations with inline change of ionization agent;
* Calculation of net electrical charge and of isoelectric point (even by
taking into account monomer modifications if polymer is a protein);
* Simulation of isotopic patterns for any chemical formula and z charge;
* A number of plugins allow 1) translation of the sequence from one format
to another (using a dictionary, like between the 1-letter code and the 3-letter
code of proteins) 2) conversion of number format according to any localized
number format 3) sort mass lists.
*/*: Drop maintainership for some of my ports
Drop maintainership for ports for which I do not have much interest any
more or for which I do not have as much time as they require, so that I
can focus more on the ports I maintain and other projects both inside
and outside FreeBSD and so that they can be adopted by other
contributors.
bsd.sites.mk: Update all ports using USE_GITLAB
Replace GL_COMMIT by GL_TAGNAME in all ports. The new GL_TAGNAME is
backwards-compatible (accepting any commit hash as before), but also
understands an actual tag name. Moving to tag names where appropriate is
left to individual ports' maintainers.
Approved by: portmgr (tcberner, mentor)
Differential Revision: https://reviews.freebsd.org/D37077
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 )
Regenerate all distfiles using gitlab as source.
This regeneration is required as the new gitlab version changed
the address and the directory the source files can be downloaded.
This commit also applies some small fixes to make sure all ports using
gitlab are buildable.
Reviewed by: mat
Approved by: portmgr
Differential Revision: https://reviews.freebsd.org/D29628
Add USES=xorg USES=gl, ports categories s
Add USES=xorg and USES=gl to ports in categories starting with 's'
While here, try to sprinkle other USES (mostly gnome and sdl) as needed.
Bump PORTREVISION for ports depending on the canonical version of GCC
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
science/massxpert: fix build with GCC-based architectures
Replace USE_GCC=any with USE_GCC=yes to fix build on GCC architectures.
Build failure log:
CMake Error in lib/CMakeLists.txt:
The compiler feature "cxx_decltype" is not known to CXX compiler
"GNU"
version 4.2.1.
Approved by: tcberner (mentor)
Differential Revision: https://reviews.freebsd.org/D20067
science/massxpert: Update 3.4.0 -> 3.6.1
This software seems to be abandoned by its upstream, and rescued by the Debian
team.
I've set its source to Debian's GitLab server, where they source it from now.
Port changes:
* 3.6.1 is Qt5-based: remove the DEPRECATED lines
* USE_GCC seems to be needed due to clang error messages
* MAKE_JOBS_UNSAFE isn't needed
Bump PORTREVISION for ports depending on the canonical version of GCC
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
Mark QT4 ports/functionality for removal on 2019-03-15
While here, chase some KDE4 ports and functionality, these are scheduled for
removal on 2018-12-31. Change the default option/flavor to QT5 where applicable
or use alternative toolkits like GTK.
Submitted by: tcberner
Reviewed by: adridg, jhale, rene, tcberner
Approved by: portmgr (implicit, flavor hook)
Differential Revision: https://reviews.freebsd.org/D17741
Bump PORTREVISION for ports depending on the canonical version of GCC
in the ports tree (via Mk/bsd.default-versions.mk and lang/gcc) which
has now moved from GCC 6 to GCC 7 by default.
This includes ports
- featuring USE_GCC=yes or USE_GCC=any,
- featuring USES=fortran,
- using Mk/bsd.octave.mk which in turn features USES=fortran, and those
- with USES=compiler specifying one of openmp, nestedfct, c11, c++0x,
c++11-lib, c++11-lang, c++14-lang, c++17-lang, or gcc-c++11-lib.
PR: 222542
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
Bump PORTREVISION for ports depending on the canonical version of GCC
(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
Revert r447879.
Apparently the build is indeed broken with parallel jobs, even though I wasn't
able to reproduce it in my tests. Checking what's broken would take time and
anyone interested in that should rather try updating the port to 3.6.0.
PR: 219293
Reported by: John Marino <freebsdml@marino.st>
Add patch to drop a wrong ';' in an if check.
In addition to fixing an actual bug, this also fixes the build with GCC 6:
/wrkdirs/usr/ports/science/massxpert/work/massxpert-3.4.0/lib/propListHolder.cpp:
In member function 'bool massXpert::PropListHolder::removeProp(const QString&)':
/wrkdirs/usr/ports/science/massxpert/work/massxpert-3.4.0/lib/propListHolder.cpp:216:2:
error: this 'if' clause does not guard... [-Werror=misleading-indentation]
if(m_propList.at(iter)->name() == name);
^~
/wrkdirs/usr/ports/science/massxpert/work/massxpert-3.4.0/lib/propListHolder.cpp:217:2:
note: ...this statement, but the latter is misleadingly indented as if it is
guarded by the 'if'
{
PR: 219293
Approved by: maintainer timeout (vg, 18 days)
MFH: 2017Q3
Bump PORTREVISIONs for ports depending on the canonical version of GCC and
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
- Update devel/libpthread-stubs to 0.4
- Chase libpthread-stubs update, and also switch to BUILD_DEPENDS
from LIB_DEPENDS, as port is now only .pc file
PR: 218015
Submitted by: rezny
Bump PORTREVISIONS for ports depending on the canonical version of GCC and
lang/gcc which have moved from GCC 4.8.5 to GCC 4.9.4 (at least under some
circumstances such as versions of FreeBSD or platforms).
In particular that is ports with USE_GCC=yes, USE_GCC=any, or one of
gcc-c++11-lib, openmp, nestedfct, c++11-lib as well as c++14-lang,
c++11-lang, c++0x, c11 requested via USES=compiler.
Drop USES=iconv.
The port's source does not use iconv anywhere, so remove the unnecessary
dependency from the Makefile.
PR: 202717
Approved by: maintainer timeout (vg, 14 days)
science/massxpert: Fix two logical errors (found by gcc5)
There were two boolean logic issues found by gcc5 when compiling
massxpert. One was comparing boolean output to a negative integer
(is always false) and the other applied the "not" operator in the wrong
place. Fix provided per request by maintainer.
PR: 197823
The FreeBSD x11@ and graphics team proudly presents
a zeising, kwm production, with help from dumbbell, bdrewery:
NEW XORG ON FREEBSD 9-STABLE AND 10-STABLE
This update switches over to use the new xorg stack by default on FreeBSD 9
and 10 stable, on osversions where vt(9) is available.
It is still possible to use the old stack by specifying WITHOUT_NEW_XORG in
/etc/make.conf .
FreeBSD 8-STABLE and released versions of FreeBSD still use
the old version.
A package repository with binary packages for new xorg will
be available soon.
This patch also contains updates of libxcb and related ports, pixman, as well
(Only the first 15 lines of the commit message are shown above )
The FreeBSD x11 team proudly presents
an zeising, kwm, miwi, bapt, eadler production:
Xorg 7.7
Starring:
xserver 1.12.4 (new xorg only)
Mesa 8.0.4, including libGL, libGLU and dri (new xorg only)
libX11 1.5.0
libxcb 1.9
libdrm 2.4.42 (new xorg only)
freeglut 2.8.1
Also starring:
Updates to drivers and other libraries and utilities
(Only the first 15 lines of the commit message are shown above )
- Update to version 3.3.0 [1]
- Add missing deps
- Mark MAKE_JOBS_UNSAFE
- tab -> space in WWW: line
PR: ports/174397 [1]
Submitted by: Veniamin Gvozdikov <g.veniamin@googlemail.com> (maintainer)
Remove CMAKE_USE_PTHREAD from the ports using it.
This setting has not had any effect since r1.13 to bsd.cmake.mk, as it
was only useful when we supported FreeBSD < 7.
Approved by: avilla (mentor), portmgr (miwi)
Feature safe: yes
The massXpert project aims at providing (bio)chemists with a software
package allowing the following:
* User-specific atom definitions and polymer chemistry definitions;
* Powerful sequence editing with user-defined glyphs for each monomer
and monomer chemical modification. Multi-region selections;
* Polymer sequence chemical/enzymatic cleavage;
* Intramolecular cross-linking, like disulfide bonds with total resolution
of the peptides generated upon enzymatic cleavage;
* Gas-phase fragmentation of oligomers;
* Mass-to-charge ratio calculations with inline change of ionization agent;
* Calculation of net electrical charge and of isoelectric point (even by
taking into account monomer modifications if polymer is a protein);
* Simulation of isotopic patterns for any chemical formula and z charge;
* A number of plugins allow 1) translation of the sequence from one format
to another (using a dictionary, like between the 1-letter code and the 3-letter
code of proteins) 2) conversion of number format according to any localized
number format 3) sort mass lists.
PR: ports/146564
Submitted by: Gvozdikov Veniamin <g.veniamin@googlemail.com>
