Open Babel is a project designed to pick up where Babel left off, as a
cross-platform program and library designed to interconvert between many
file formats used in molecular modeling and computational chemistry.
Features currently include:
* A huge variety of common chemical file formats
* Recognition of file type based on filename extension
* SMARTS matcher
* Flexible atom typer
* Gasteiger partial charge calculation
* Hydrogen addition and deletion
* Automatic feature perception (rings, hybridization, aromaticity)
* Multiple conformer storage within molecules
* Command line interface development class
* Bitvector class
* Open-source/Free Software under the GNU General Public License
* Cross platform (Windows, Linux, Mac OS X, SGI, Solaris, Dreamcast...)
===> The following configuration options are available for openbabel-3.2.1_1:
CAIRO=on: PNG support via cairo library
GUI=on: GUI (Graphical User Interface) support
===> Use 'make config' to modify these settings
science/openbabel: Fix build with llvm16
This was a bit ambiguous as it uses USE_CXXSTD for GCC while gnu++98 for
clang. However this patch was tested on 12.4-RELEASE i386/amd64,
13.1-RELEASE amd64 and MAIN amd64.
Approved by: portmgr (blanket)
Sponsored by: The FreeBSD Foundation
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 )
science: remove 'Created by' lines
A big Thank You to the original contributors of these ports:
* Andreas Fehlner <fehlner@gmx.de>
* Brad Huntting <huntting@glarp.com>
* Chao Shin <quakelee@cn.FreeBSD.org>
* Cheng-Lung Sung <clsung@FreeBSD.org>
* Chia-Hsing Yu <me@davidyu.org>
* Chris Rees <utisoft@gmail.com>
* David Naylor <dbn@FreeBSD.org>
* Dmitry Sivachenko <demon@FreeBSD.org>
* Ed Schouten <ed@FreeBSD.org>
* Eric Freeman <freebsdports@chillibear.com>
* Erik B Knudsen
(Only the first 15 lines of the commit message are shown above )
textproc/libxml2: bump all LIB_DEPENDS consumers
This is a separate commit to facilitate easier cherry-picking for
quarterly.
PR: 262853, 262940, 262877, 263126
Approved by: fluffy (mentor)
textproc/libxml2: bump all dependencies
This should make sure that all dependent ports will pick
up the new version commited with a13ec21cd733f67a9fc0dc00ab45268bdc236246
*/*: Remove redundant '-*' from CONFLICTS definitions
The conflict checks compare the patterns first against the package
names without version (as reported by "pkg query "%n"), then - if
there was no match - agsinst the full package names including the
version (as reported by "pkg query "%n-%v").
Approved by: portmgr (blanket)
- Upgrade math/eigen3 to 3.3.8;
- Add some dependencies which might be detected by Find_Package but not
registered;
- Bump PORTREVISION of consumers.
PR: 250833
Submitted by: /me
Approved by: tcberner@ (KDE / maintainer) + exp-run
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
Prepare for powerpc-on-clang by deleting hard-coded tests for libstdc++.so
as a stand-in for "are we running on gcc".
For people already testing powerpc on clang, it is possible that they
already have both compilers in base. Thus, the assumption that "gcc is
in base" (e.g. libstdc++.so exists) always means "force use of GCC" is
already broken. It will be for everyone on -CURRENT once the switch is
made.
While here, standardize on compiler:c++11-lang instead of -lib (they are
equivalent these days), pet portlint, and do some other cleanup.
Approved by: portmgr (tier-2 blanket)
Change cmake default behaviour to outsource.
Ports that build out of source now simply can use "USES=cmake"
instead of "USES=cmake:outsource". Ports that fail to build
out of source now need to specify "USES=cmake:insource".
I tried to only set insource where explictely needed.
PR: 232038
Exp-run by: antoine
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
science/openbabel: Take maintainership; Add the GUI option using wxWidgets-3.0
GUI is "on" by default because that's what CMakeLists.txt suggests as default.
Also improve helpers use.
New USES=eigen
Usage:
USES=eigen:<version>[,<type>]
version: 2 or 3 (required)
type: build (default), run
For example:
USES=eigen:2,build,run
will add a BUILD- and RUN_DEPENDS on math/eigen2, and
USES=eigen:3
will add a BUILD_DEPENDS on math/eigen3.
* Convert the existing ports to use it
- biology/iqtree: remove run time dependency (seemed not to be needed)
- graphics/movit: remove run time dependency (seemed not to be needed)
- science/avogadro: add run time dependeny (installed cmake file requires it
to be present)
Reviewed by: rakuco, mat
Differential Revision: https://reviews.freebsd.org/D13702
science/openbabel: unbreak with GCC >= 6
GCC defaults to C++14 since 6.0 which no longer converts istream to
bool by default. Instead of fixing just downgrade to C++98.
PR: 216036
Reassign makc's ports back to the pool.
See "Maintainer Reset" in
https://www.freebsd.org/portmgr/policies_contributors.html. makc's last commit
was in March 31st (r412218), and his ports have been timing out since at least
July (r418155).
I also emailed him 2 weeks ago and have received no response so far.
science/openbabel: Support gcc5 (taken from upstream)
This was really painful. I consolidated numerous shared_ptr (TR1)
patches to a single big patch (including moving part of an existing
patch to it because the target needed yet another change).
Tested on FreeBSD 8/i386 and FreeBSD 10/amd64. This was previously
built on DragonFly with gcc 4.7, but libstdc++ incompatibilities caused
avogadro to break which eventually broken kde4 metapackage.
Those openbabel guys are long overdue for a new release, this was a bit
absurd although maybe some clever sed'ding could have reduced the patch
count.
Approved by: blanket (gcc5 & DF breakage)
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 )
Add upstream patch to fix the build with libc++.
The original commit has been slightly tuned so that it builds with the code
in the latest stable release.
Approved by: makc (maintainer)
science/openbabel:
- Update openbabel to 2.3.2
- Switch to CMake build system
- Add PYTHON and CAIRO options
- Don't rename babel binary, mark conflict with ancient biology/babel
science/py-openbabel:
- Merge py-openbabel to openbabel
other:
- chase openbabel update
Remove USE_GNOME=gnometarget from ports. It has been a empty keyword since
mid 2008.
PR: ports/159624
Submitted by: Ruslan Mahmatkhanov <cvs-src@yandex.ru>
-Repocopy devel/libtool15 -> libtool22 and libltdl15 -> libltdl22.
-Update libtool and libltdl to 2.2.6a.
-Remove devel/libtool15 and devel/libltdl15.
-Fix ports build with libtool22/libltdl22.
-Bump ports that depend on libltdl22 due to shared library version change.
-Explain what to do update in the UPDATING.
It has been tested with GNOME2, XFCE4, KDE3, KDE4 and other many wm/desktop
and applications in the runtime.
With help: marcus and kwm
Pointyhat-exp: a few times by pav
Tested by: pgollucci, "Romain Tartière" <romain@blogreen.org>, and
a few MarcusCom CVS users. Also, I might have missed a few.
Repocopy by: marcus
Approved by: portmgr
- Update boost to 1.39
- Split boost port to separate components, with boost-all metaport
PR: ports/137054
Submitted by: Alexander Churanov <churanov.port.maintainer@gmail.com>
(maintainer)
- Set --mandir and --infodir in CONFIGURE_ARGS if the configure script
supports them. This is determined by running ``configure --help'' in
do-configure target and set the shell variable _LATE_CONFIGURE_ARGS
which is then passed to CONFIGURE_ARGS.
- Remove --mandir and --infodir in ports' Makefile where applicable
Few ports use REINPLACE_CMD to achieve the same effect, remove them too.
- Correct some manual pages location from PREFIX/man to MANPREFIX/man
- Define INFO_PATH where necessary
- Document that .info files are installed in a subdirectory relative to
PREFIX/INFO_PATH and slightly change add-plist-info to use INFO_PATH and
subdirectory detection.
PR: ports/111470
Approved by: portmgr
Discussed with: stas (Mk/*), gerald (info related stuffs)
Tested by: pointyhat exp run
Mass-conversion to the USE_AUTOTOOLS New World Order. The code present
in bsd.autotools.mk essentially makes this a no-op given that all the
old variables set a USE_AUTOTOOLS_COMPAT variable, which is parsed in
exactly the same way as USE_AUTOTOOLS itself.
Moreover, USE_AUTOTOOLS has already been extensively tested by the GNOME
team -- all GNOME 2.12.x ports use it.
Preliminary documentation can be found at:
http://people.FreeBSD.org/~ade/autotools.txt
which is in the process of being SGMLized before introduction into the
Porters Handbook.
Light blue touch-paper. Run.
* Update to 1.100.1
* Remove patches in favor of --program-prefix=open
* Install the .pc file in the correct location
PR: 53845
Submitted by: Pav Lucistnik <pav@oook.cz>
science/openbabel and biology/babel binary names conflict
renamed the binaries and manpages of science/openbabel to
openbabel instead of babel.
PR: ports/47109
Submitted by: Glenn Johnson <gjohnson@srrc.ars.usda.gov>
