pyaixi is a pure Python implementation of the Monte Carlo-AIXI-Context Tree
Weighting (MC-AIXI-CTW) artificial intelligence algorithm.
This is an approximation of the AIXI universal artificial intelligence
algorithm, which describes a model-based, reinforcement-learning agent capable
of general learning.
WWW: https://github.com/gkassel/pyaixi
PR: ports/184572
Submitted by: Johannes Jost Meixner <xmj chaot.net>
wrkdirs/usr/ports/science/minc2/work/minc-2.2.00/libsrc/hdf_convenience.c: In function 'hdf_put_dimorder':
/wrkdirs/usr/ports/science/minc2/work/minc-2.2.00/libsrc/hdf_convenience.c:621: error: too many arguments to function 'H5Acreate'
/wrkdirs/usr/ports/science/minc2/work/minc-2.2.00/libsrc/hdf_convenience.c: In function 'hdf_set_length':
/wrkdirs/usr/ports/science/minc2/work/minc-2.2.00/libsrc/hdf_convenience.c:928: error: too many arguments to function 'H5Acreate'
/wrkdirs/usr/ports/science/minc2/work/minc-2.2.00/libsrc/hdf_convenience.c: In function 'hdf_attput':
/wrkdirs/usr/ports/science/minc2/work/minc-2.2.00/libsrc/hdf_convenience.c:1110: warning: cast to pointer from integer of different size
/wrkdirs/usr/ports/science/minc2/work/minc-2.2.00/libsrc/hdf_convenience.c:1189: error: too many arguments to function 'H5Acreate'
/wrkdirs/usr/ports/science/minc2/work/minc-2.2.00/libsrc/hdf_convenience.c: In function 'hdf_copy_attr':
/wrkdirs/usr/ports/science/minc2/work/minc-2.2.00/libsrc/hdf_convenience.c:2054: warning: cast from pointer to integer of different size
/wrkdirs/usr/ports/science/minc2/work/minc-2.2.00/libsrc/hdf_convenience.c:2071: error: too many arguments to function 'H5Acreate'
Since this patch converts all affected ports, bsd.cran.mk no longer supports
NO_STAGE and errors out if NO_STAGE is set.
Exp-run: ports/184216
Reviewed by: bdrewery
Approved by: portsmgr, wen
one of two ports that makes us keep lang/gcc34 (which does not even
support FreeBSD 10 and later) and general infrastructure and it does
not even build on FreeBSD 9 nor amd64.
Approved by: portmgr (itetcu, 2013-03-31)
one of two ports that makes us keep lang/gcc34 (which does not even
support FreeBSD 10 and later) and general infrastructure.
Approved by: portmgr (itetcu, 2013-03-31)
(*) Actually it seems to depend on textproc/libxml2, but then it was
still broken because of Tcl errors.
PR: ports/183680
Submitted by: myself
Approved by: maintainer timeout (bkoenig@alpha-tierchen.de , 14 days)
- Remove leading article, revise capitalization in COMMENT
- Convert to new options framework
- Support staging
- Add launch script and desktop entry file
PR: ports/182482 [1]
Submitted by: Max Sterling <maxclsb@gmail.com> [1]
- Update to 2.0.1
- Change master sites to SAVANNAH
- Change maintainer email to @FreeBSD.org
- Remove conflict with non existent Port
- USES pathfix pkgconfig
- Add executable
- Add DOCS Option
- Support STAGEDIR and add OPTIONS_SUB
- Use pathfix instead of simple patches
- Adjust patches
- Change WWW
graphics/OpenEXR
- Update to 2.0.1
- Change master sites to SAVANNAH
- Change maintainer email to @FreeBSD.org
- Use the new format for LIB_DEPENDS
- USES gmake pathfix pkgconfig
- Add DOCS and EXAMPLES Options
- Support STAGEDIR and add OPTIONS_SUB
- Change REINPLACE_CMD
- Add extra patch for EXAMPLES
- Remove obsolete patches
- Bump dependent ports' revisions
Approved by: pawel / wg (mentors)
- Remove leading article from COMMENT
- Use default dependency for science/hdf5-18
- Add patch
PR: ports/181483
Submitted by: Johannes Meixner <xmj@chaot.net>
Approved by: wg (mentor)
- Convert to new LIB_DEPENDS format
- Use options helpers and plist substitution
- Add support for STAGEDIR
- Reformat pkg-descr
PR: ports/182802
Submitted by: KATO Tsuguru <tkato432@yahoo.com>
Pydap is an implementation of the Opendap/DODS protocol, written from scratch.
You can use Pydap to access scientific data on the internet without having to
download it; instead, you work with special array and iterable objects that
download data on-the-fly as necessary, saving bandwidth and time. The module
also comes with a robust-but-lightweight Opendap server, implemented as a WSGI
application.
WWW: https://pypi.python.org/pypi/Pydap
PR: ports/181687
Submitted by: Johannes Meixner <xmj chaot.net>
- Switched to automake 1.11.6, see CVE-2012-3386.
- #14669: Fixed extraction of CC from gmp.h.
- Fixed case of intermediate zero real or imaginary part in mpc_fma,
found by hydra with GMP_CHECK_RANDOMIZE=1346362345.
This is on top of the following changes from version 1.0
- Licence change towards LGPLv3+ for the code and GFDLv1.3+ (with no
invariant sections) for the documentation.
- 100% of all lines are covered by tests
- Renamed functions
. mpc_mul_2exp to mpc_mul_2ui
. mpc_div_2exp to mpc_div_2ui
- 0^0, which returned (NaN,NaN) previously, now returns (1,+0).
- Removed compatibility with K&R compilers, which was untestable due
to lack of such compilers.
- New functions
. mpc_log10
. mpc_mul_2si, mpc_div_2si
- Speed-ups
. mpc_fma
- Bug fixes
. mpc_div and mpc_norm now return a value indicating the effective
rounding direction, as the other functions.
. mpc_mul, mpc_sqr and mpc_norm now return correct results even if
there are over- or underflows during the computation.
. mpc_asin, mpc_proj, mpc_sqr: Wrong result when input variable has
infinite part and equals output variable is corrected.
. mpc_fr_sub: Wrong return value for imaginary part is corrected.
Convert to the new LIB_DEPENDS standard and remove hard-coded
.so versions from a couple of dependent ports.
Bump PORTREVISIONS of all dependent ports.
PR: 183141
Approved by: portmgr (bdrewery)
The following ports will not build with a binutils 2.22+ linker built
with standard options. This has been obvious with DPorts, but difficult
to see on FreeBSD. However, setting the ports compiler as a recent gcc
(e.g lang/gcc48) is an excellent way to detect the unspecified but needed
libraries as these recent GCC compilers use the latest binutils linkers.
These patches were tested on FreeBSD 8.4 and DragonFly 3.5
The non-header fix addresses the error, "calls to overloaded operations cannot
appear in a constant-expression". The fix was suggested on various bug
trackers.
Approved by: portmgr (bapt, implicit)
Also, this port unfortunately sets -Werror, and the use of long-long
with c++98 triggers a warning, so also turn off that check.
Approved by: portmgr (bapt, implicit)
All versions of FreeBSD we support are shipped with at least GCC 4.2.1
or Clang. The code seems to build fine with Clang. In fact, on platforms
where we no longer ship libstdc++, this port seems to only build using
Clang.
Pupynere is a Python module for reading and writing NetCDF files, using the same
API as Scientific.IO.NetCDF and pynetcdf. It depends only on Numpy, so you don't
need to have the NetCDF library installed.
WWW: https://pypi.python.org/pypi/pupynere/
PR: ports/179744
Submitted by: Johannes Jost Meixner <xmj@chaot.net>
be IGNOREd regardless of PACKAGE_BUILDING. Soem have no MASTER_SITES
and require manual fetching, others are already marked RESTRICTED.
- Trim headers
- Convert some pre-fetch errors into IGNORE
- Remove needless quoting in java/jdk7-doc IGNORE
With hat: portmgr
The license was defined as "AS-IS" but this license has no definition in
bsd.license*.mk. As a result, this port would not build in bulk because
there was no implied acceptance of the "AS-IS" license. Upon
re-examination, the maintainer believes it is close enough in spirit to
BSD license to be classified as BSD.
Copyright 1993-2000 Peter Neelin and David MacDonald, McConnell Brain
Imaging Centre, Montreal Neurological Institute, McGill University.
Permission to use, copy, modify, and distribute this software and its
documentation for any purpose and without fee is hereby granted,
provided that the above copyright notice appear in all copies. The
author and McGill University make no representations about the
suitability of this software for any purpose. It is provided "as is"
without express or implied warranty.
The PORTREVISION was bumped because when a license is specified, it
modifies the pkg-plist.
PR: 181350
Approved by: bapt/culot (mentors, implicit), jwbacon (maintainer)
Right now this is a noop in the former case and a noop in the latter
case unless lang/gcc44 has been installed explicitly.
This puts a bit more emphasis on standardizing on a canonical version
"current" GCC and makes it easier to update that canonical version
by changing the default in Mk/bsd.gcc.mk and updating the lang/gcc port.
That is, USE_GCC=yes means "use a decent/modern version of GCC" without
having to worry about details.
Approved by: portmgr (bdrewery)
Unfortunately, this also affects some ports using QT3 as a GUI toolkit.
Changes to infrastructure files:
- bsd.kde.mk : obsolete, remove
- bsd.qt.mk : note that a CONFLICTS_BUILD line can probably go after a while
- CHANGES : document the removals from bsd.port.mk
- KNOBS : remove KDE and QT (KDE4 and QT4 should be used instead)
- MOVED : add the removed ports
PR: ports/180745
Submitted by: rene
Approved by: portmgr (bapt)
Exp-run by: bapt
The h5perf program will not run because it is linked to libh5test.so.0
which is not installed. Rather than install this shared library, a patch
was added to prohibit h5perf from installing.
PR: ports/179951
Approved by: bapt (mentor), maintainer timeout (~4 weeks)
Proudly brought to you by the KDE on FreeBSD team. We're sorry to ship two
KDE updates in just a few days, but the work on 4.10.5 was very light
compared to 4.10.4 so it was ready much faster.
The release announcement can be found in [1].
[1] http://www.kde.org/announcements/announce-4.10.5.php
The biggest news for us on FreeBSD is that the Ruby bindings should work
with Ruby 1.9 now.
I will probably add a note to UPDATING later about this, but as avilla@
pointed out, the clang support we mentioned that was improved in 4.10.4
requires a rebuild of the ports that depend on kdelibs4. Most of them are
covered by this update, but those which are not part of the Software
Compilation need to be rebuilt manually to make sure the previous issues
(proper symbol visibility being the most annoying of them) are solved.
With commits from avilla@, makc@, rakuco@ and Schaich Alonso.
The upstream announcement can be found in [1].
[1] http://www.kde.org/announcements/announce-4.10.4.php
clang support should be more stable now, with clang being recognized by
kdelibs4 and being passed the correct flags to build other ports.
Additionally, all ports being committed have been verified to build with
-CURRENT's clang 3.3 on an amd64 tinderbox (special thanks go to swills@ for
providing it).
Work on the newly-released 4.10.5 will begin shortly.
. create EXAMPLES option;
. bump PORTREVISION (EXAMPLES are on by default now);
. use PLIST_FILES, PORTDOCS and PORTEXAMPLES at Makefile;
. remove pkg-plist;
. unmute install and cp commands;
. trim Makefile headers.
Coards is a parser for time values represented using the COADS convention.
WWW: https://pypi.python.org/pypi/coards
PR: ports/179576
Submitted by: Johannes Meixner <xmj@chaot.net>
quite some time.
- Switch all remaining consumers to depend on www/libxul
- Mark ports that don't work with the new libxul BROKEN
- Mark some old ports DEPRECATED with a reasonable timeout
Approved by: portmgr (miwi)
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
Additional notes:
Change pkgconf to be a build dependency.
Add a new USE_XORG, xcb, to depend on libxcb and update all ports to use
this.
Trim makefile headers.
Take maintanership of x11/xcb-proto, ok'd by ashish.
If you are running WITH_NEW_XORG=, you need to rebuild all installed
drivers, see UPDATING for more information.
Various fixes to make ports compile.
PR: ports/177942
Exp-run by: miwi
Approved by: portmgr (miwi)
Thanks to all who helped testing!
TEX_DEFAULT:
A knob to choose teTeX or TeXLive. One can specify in /etc/make.conf.
USE_TEX:
A knob for port developers. Valid keywords are listed in
bsd.tex.mk.
Voro++ is a software library for carrying out three-dimensional computations
of the Voronoi tessellation. A distinguishing feature of the Voro++ library
is that it carries out cell-based calculations, computing the Voronoi cell
for each particle individually. It is particularly well-suited for
applications that rely on cell-based statistics, where features of Voronoi
cells (eg. volume, centroid, number of faces) can be used to analyze a
system of particles.
WWW: http://math.lbl.gov/voro++/
PR: 177678
Submitted by: jwbacon@tds.net
Feature safe: yes
ports/155546 may fix this. The issue is that the libtool linking stage
is not respecting the CC=gcc46 environment that is used to compile
the rest of the port first. This causes the linking to use 'cc' instead.
.libs/ctl.o(.text.__i686.get_pc_thunk.bx+0x0): In function `__i686.get_pc_thunk.bx':
: multiple definition of `__i686.get_pc_thunk.bx'
/usr/lib/crtbeginS.o(.gnu.linkonce.t.__i686.get_pc_thunk.bx+0x0): first defined here
*** Error code 1
Approved by: portmgr (implicit)
Pyteomics is a collection of lightweight and handy tools for Python
that help to handle various sorts of proteomics data. Pyteomics
provides a growing set of modules to facilitate the most common
tasks in proteomics data analysis, such as:
* calculation of basic physico-chemical properties of polypeptides:
. mass and isotopic distribution
. charge and pI
. chromatographic retention time
* access to common proteomics data:
. MS or LC-MS data
. FASTA databases
. search engines output
* easy manipulation of sequences of modified peptides and proteins
WWW: https://pypi.python.org/pypi/pyteomics
