Commit graph

162407 commits

Author SHA1 Message Date
sno
ad54432e51 Importing package for p5 module PerlIO::via::Bzip2 version 0.02 during
devel/svk update.

PerlIO::via::Bzip2 implements a PerlIO layer which will let you handle
bzip2 compressed files transparently.
2010-09-04 11:27:12 +00:00
sno
631f9e4581 Added devel/p5-SVN-Dump version 0.04 2010-09-04 11:16:05 +00:00
sno
151b5e5256 Importing package for p5 module SVN::Dump version 0.04 during the update
of devel/svk as feature dependency.

This module lets you manage SVN dumps with Perl.
An SVN::Dump object represents a Subversion dump.
2010-09-04 11:15:43 +00:00
wiz
df468d0cc9 Added fonts/mothanna-ttf version 0.02 2010-09-04 10:38:57 +00:00
wiz
a23410c6a3 + mothanna-ttf. 2010-09-04 10:38:46 +00:00
wiz
a50c23d1bf Initial import of mothanna-ttf, packaged for wip by Kamel Derouiche.
Mothanna (from Arabic; twisted, bent) is a sans-serif like Arabic
OpenType font, intended mainly for use in software UIs. It is
developed by Arabeyes.org as part of the Khotot project.
2010-09-04 10:38:24 +00:00
obache
5c3ed09bfa Updated lang/python26 to 2.6.6 2010-09-04 05:12:17 +00:00
obache
ef9e71e4a2 Update to python-2.6.6.
What's New in Python 2.6.6?
===========================

*Release date: 2010-08-24*

Core and Builtins
-----------------

Library
-------


What's New in Python 2.6.6 rc 2?
================================

*Release date: 2010-08-16*

Library
-------

- Issue #9600: Don't use relative import for _multiprocessing on Windows.

- Issue #8688: Revert regression introduced in 2.6.6rc1 (making Distutils
  recalculate MANIFEST every time).

- Issue #5798: Handle select.poll flag oddities properly on OS X.
  This fixes test_asynchat and test_smtplib failures on OS X.

- Issue #9543: Fix regression in socket.py introduced in Python 2.6.6 rc 1
  in r83624.

Extension Modules
-----------------

- Issue #7567: Don't call `setupterm' twice.

Tests
-----

- Issue #9568: Fix test_urllib2_localnet on OS X 10.3.

- Issue #9145: Fix test_coercion failure in refleak runs.

- Issue #8433: Fix test_curses failure caused by newer versions of
  ncurses returning ERR from getmouse() when there are no mouse
  events available.


What's New in Python 2.6.6 rc 1?
================================

*Release date: 2010-08-03*

Core and Builtins
-----------------

- Issue #6213: Implement getstate() and setstate() methods of utf-8-sig and
  utf-16 incremental encoders.

- Issue #8271: during the decoding of an invalid UTF-8 byte sequence, only the
  start byte and the continuation byte(s) are now considered invalid, instead
  of the number of bytes specified by the start byte.
  E.g.: '\xf1\x80AB'.decode('utf-8', 'replace') now returns u'\ufffdAB' and
  replaces with U+FFFD only the start byte ('\xf1') and the continuation byte
  ('\x80') even if '\xf1' is the start byte of a 4-bytes sequence.
  Previous versions returned a single u'\ufffd'.

- Issue #9058: Remove assertions about INT_MAX in UnicodeDecodeError.

- Issue #8941: decoding big endian UTF-32 data in UCS-2 builds could crash
  the interpreter with characters outside the Basic Multilingual Plane
  (higher than 0x10000).

- Issue #8627: Remove bogus "Overriding __cmp__ blocks inheritance of
  __hash__ in 3.x" warning.  Also fix "XXX undetected error" that
  arises from the "Overriding __eq__ blocks inheritance ..." warning
  when turned into an exception: in this case the exception simply
  gets ignored.

- Issue #4108: In urllib.robotparser, if there are multiple 'User-agent: *'
  entries, consider the first one.

- Issue #9354: Provide getsockopt() in asyncore's file_wrapper.

- In the unicode/str.format(), raise a ValueError when indexes to arguments are
  too large.

- Issue #3798: Write sys.exit() message to sys.stderr to use stderr encoding
  and error handler, instead of writing to the C stderr file in utf-8

- Issue #7902: When using explicit relative import syntax, don't try
  implicit relative import semantics.

- Issue #7079: Fix a possible crash when closing a file object while using
  it from another thread.  Patch by Daniel Stutzbach.

- Issue #1533: fix inconsistency in range function argument
  processing: any non-float non-integer argument is now converted to
  an integer (if possible) using its __int__ method.  Previously, only
  small arguments were treated this way; larger arguments (those whose
  __int__ was outside the range of a C long) would produce a TypeError.

- Issue #8417: Raise an OverflowError when an integer larger than sys.maxsize
  is passed to bytearray.

- Issue #8329: Don't return the same lists from select.select when no fds are
  changed.

- Raise a TypeError when trying to delete a T_STRING_INPLACE struct member.

- Issue #1583863: An unicode subclass can now override the __unicode__ method.

- Issue #7507: Quote "!" in pipes.quote(); it is special to some shells.

- Issue #7544: Preallocate thread memory before creating the thread to avoid
  a fatal error in low memory condition.

- Issue #7820: The parser tokenizer restores all bytes in the right if
  the BOM check fails.

- Issue #7072: isspace(0xa0) is true on Mac OS X

C-API
-----

- Issue #5753: A new C API function, :cfunc:`PySys_SetArgvEx`, allows
  embedders of the interpreter to set sys.argv without also modifying
  sys.path.  This helps fix `CVE-2008-5983
  <http://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2008-5983>`_.

Library
-------

- Issue #8447: Make distutils.sysconfig follow symlinks in the path to
  the interpreter executable.  This fixes a failure of test_httpservers
  on OS X.

- Issue #7092: Fix the DeprecationWarnings emitted by the standard library
  when using the -3 flag.  Patch by Florent Xicluna.

- Issue #7395: Fix tracebacks in pstats interactive browser.

- Issue #1713: Fix os.path.ismount(), which returned true for symbolic links
  across devices.

- Issue #8826: Properly load old-style "expires" attribute in http.cookies.

- Issue #1690103: Fix initial namespace for code run with trace.main().

- Issue #5294: Fix the behavior of pdb's "continue" command when called
  in the top-level debugged frame.

- Issue #5727: Restore the ability to use readline when calling into pdb
  in doctests.

- Issue #6719: In pdb, do not stop somewhere in the encodings machinery
  if the source file to be debugged is in a non-builtin encoding.

- Issue #8048: Prevent doctests from failing when sys.displayhook has
  been reassigned.

- Issue #8015: In pdb, do not crash when an empty line is entered as
  a breakpoint command.

- Issue #7909: Do not touch paths with the special prefixes ``\\.\``
  or ``\\?\`` in ntpath.normpath().

- Issue #5146: Handle UID THREAD command correctly in imaplib.

- Issue #5147: Fix the header generated for cookie files written by
  http.cookiejar.MozillaCookieJar.

- Issue #8198: In pydoc, output all help text to the correct stream
  when sys.stdout is reassigned.

- Issue #1019882: Fix IndexError when loading certain hotshot stats.

- Issue #8471: In doctest, properly reset the output stream to an empty
  string when Unicode was previously output.

- Issue #8397: Raise an error when attempting to mix iteration and regular
  reads on a BZ2File object, rather than returning incorrect results.

- Issue #8620: when a Cmd is fed input that reaches EOF without a final
  newline, it no longer truncates the last character of the last command line.

- Issue #7066: archive_util.make_archive now restores the cwd if an error is
  raised. Initial patch by Ezio Melotti.

- Issue #5006: Better handling of unicode byte-order marks (BOM) in the io
  library. This means, for example, that opening an UTF-16 text file in append
  mode doesn't add a BOM at the end of the file if the file isn't empty.

- Issue #3704: cookielib was not properly handling URLs with a / in the
  parameters.

- Issue #4629: getopt raises an error if an argument ends with = whereas getopt
  doesn't except a value (eg. --help= is rejected if getopt uses ['help='] long
  options).

- Issue #7895: platform.mac_ver() no longer crashes after calling os.fork()

- Issue #5395: array.fromfile() would raise a spurious EOFError when an
  I/O error occurred.  Now an IOError is raised instead.  Patch by chuck
  (Jan Hosang).

- Issue #1555570: email no longer inserts extra blank lines when a \r\n
  combo crosses an 8192 byte boundary.

- Issue #9164: Ensure sysconfig handles dupblice archs while building on OSX

- Issue #7646: The fnmatch pattern cache no longer grows without bound.

- Issue #9136: Fix 'dictionary changed size during iteration'
  RuntimeError produced when profiling the decimal module.  This was
  due to a dangerous iteration over 'locals()' in Context.__init__.

- Fix extreme speed issue in Decimal.pow when the base is an exact
  power of 10 and the exponent is tiny (for example,
  Decimal(10) ** Decimal('1e-999999999')).

- Issue #9130: Fix validation of relative imports in parser module.

- Issue #9128: Fix validation of class decorators in parser module.

- Issue #7673: Fix security vulnerability (CVE-2010-2089) in the audioop
  module, ensure that the input string length is a multiple of the frame size

- Issue #6589: cleanup asyncore.socket_map in case smtpd.SMTPServer constructor
  raises an exception.

- Issue #9125: Add recognition of 'except ... as ...' syntax to parser module.

- Issue #9085: email package version number bumped to its correct
  value of 4.0.2 (same as it was in 2.5).

- Issue #9075: In the ssl module, remove the setting of a ``debug`` flag
  on an OpenSSL structure.

- Issue #5610: feedparser no longer eats extra characters at the end of
  a body part if the body part ends with a \r\n.

- Issue #8924: logging: Improved error handling for Unicode in exception text.

- Fix codecs.escape_encode to return the correct consumed size.

- Issue #6470: Drop UNC prefix in FixTk.

- Issue #8833: tarfile created hard link entries with a size field != 0 by
  mistake.

- Issue #1368247: set_charset (and therefore MIMEText) now automatically
  encodes a unicode _payload to the output_charset.

- Issue #7150: Raise OverflowError if the result of adding or subtracting
  timedelta from date or datetime falls outside of the MINYEAR:MAXYEAR range.

- Issue #6662: Fix parsing of malformatted charref (&#bad;), patch written by
  Fredrik Håård

- Issue #1628205: Socket file objects returned by socket.socket.makefile() now
  properly handles EINTR within the read, readline, write & flush methods.
  The socket.sendall() method now properly handles interrupted system calls.

- Issue #3924: Ignore cookies with invalid "version" field in cookielib.

- Issue #6268: Fix seek() method of codecs.open(), don't read or write the BOM
  twice after seek(0). Fix also reset() method of codecs, UTF-16, UTF-32 and
  StreamWriter classes.

- Issue #5640: Fix Shift-JIS incremental encoder for error handlers different
  than strict

- Issue #8782: Add a trailing newline in linecache.updatecache to the last line
  of files without one.

- Issue #8729: Return NotImplemented from collections.Mapping.__eq__ when
  comparing to a non-mapping.

- Issue #5918: Fix a crash in the parser module.

- Issue #8688: Distutils now recalculates MANIFEST everytime.

- Issue #7640: In the new `io` module, fix relative seek() for buffered
  readable streams when the internal buffer isn't empty.  Patch by Pascal
  Chambon.

- Issue #5099: subprocess.Popen.__del__ no longer references global objects,
  leading to issues during interpreter shutdown.

- Issue #8681: Make the zlib module's error messages more informative when
  the zlib itself doesn't give any detailed explanation.

- Issue #8674: Fixed a number of incorrect or undefined-behaviour-inducing
  overflow checks in the audioop module.

- Issue #8571: Fix an internal error when compressing or decompressing a
  chunk larger than 1GB with the zlib module's compressor and decompressor
  objects.

- Issue #8573: asyncore _strerror() function might throw ValueError.

- Issue #8483: asyncore.dispatcher's __getattr__ method produced confusing
  error messages when accessing undefined class attributes because of the cheap
  inheritance with the underlying socket object.

- Issue #4265: shutil.copyfile() was leaking file descriptors when disk fills.
  Patch by Tres Seaver.

- Issue #8621: uuid.uuid4() returned the same sequence of values in the
  parent and any children created using ``os.fork`` on MacOS X 10.6.

- Issue #8313: traceback.format_exception_only() encodes unicode message to
  ASCII with backslashreplace error handler if str(value) failed

- Issue #8567: Fix precedence of signals in Decimal module: when a
  Decimal operation raises multiple signals and more than one of those
  signals is trapped, the specification determines the order in which
  the signals should be handled.  In many cases this order wasn't
  being followed, leading to the wrong Python exception being raised.

- Issue #7865: The close() method of :mod:`io` objects should not swallow
  exceptions raised by the implicit flush().  Also ensure that calling
  close() several times is supported.  Initial patch by Pascal Chambon.

- Issue #8581: logging: removed errors raised when closing handlers twice.

- Issue #4687: Fix accuracy of garbage collection runtimes displayed with
  gc.DEBUG_STATS.

- Issue #8354: The siginterrupt setting is now preserved for all signals,
  not just SIGCHLD.

- Issue #8577: distutils.sysconfig.get_python_inc() now makes a difference
  between the build dir and the source dir when looking for "python.h" or
  "Include".

- Issue #8464: tarfile no longer creates files with execute permissions set
  when mode="w|" is used.

- Issue #7834: Fix connect() of Bluetooth L2CAP sockets with recent versions
  of the Linux kernel.  Patch by Yaniv Aknin.

- Issue #6312: Fixed http HEAD request when the transfer encoding is chunked.
  It should correctly return an empty response now.

- Issue #8086: In :func:`ssl.DER_cert_to_PEM_cert()`, fix missing newline
  before the certificate footer.  Patch by Kyle VanderBeek.

- Issue #8549: Fix compiling the _ssl extension under AIX.  Patch by
  Sridhar Ratnakumar.

- Issue #2302: Fix a race condition in SocketServer.BaseServer.shutdown,
  where the method could block indefinitely if called just before the
  event loop started running.  This also fixes the occasional freezes
  witnessed in test_httpservers.

- Issue #5103: SSL handshake would ignore the socket timeout and block
  indefinitely if the other end didn't respond.

- The do_handshake() method of SSL objects now adjusts the blocking mode of
  the SSL structure if necessary (as other methods already do).

- Issue #5238: Calling makefile() on an SSL object would prevent the
  underlying socket from being closed until all objects get truely destroyed.

- Issue #7943: Fix circular reference created when instantiating an SSL
  socket.  Initial patch by Péter Szabó.

- Issue #8108: Fix the unwrap() method of SSL objects when the socket has
  a non-infinite timeout.  Also make that method friendlier with applications
  wanting to continue using the socket in clear-text mode, by disabling
  OpenSSL's internal readahead.  Thanks to Darryl Miles for guidance.

- Issue #8484: Load all ciphers and digest algorithms when initializing
  the _ssl extension, such that verification of some SSL certificates
  doesn't fail because of an "unknown algorithm".

- Issue #4814: timeout parameter is now applied also for connections resulting
  from PORT/EPRT commands.

- Issue #3817: ftplib.FTP.abort() method now considers 225 a valid response
  code as stated in RFC-959 at chapter 5.4.

- Issue #5277: Fix quote counting when parsing RFC 2231 encoded parameters.

- Issue #8179: Fix macpath.realpath() on a non-existing path.

- Issue #8310: Allow dis to examine new style classes.

- Issue #7667: Fix doctest failures with non-ASCII paths.

- Issue #7624: Fix isinstance(foo(), collections.Callable) for old-style
  classes.

- Issue #7512: shutil.copystat() could raise an OSError when the filesystem
  didn't support chflags() (for example ZFS under FreeBSD).  The error is
  now silenced.

- Issue #3890, #8222: Fix recv() and recv_into() on non-blocking SSL sockets.
  Also, enable the SSL_MODE_AUTO_RETRY flag on SSL sockets, so that blocking
  reads and writes are always retried by OpenSSL itself.

- Issue #6544: fix a reference leak in the kqueue implementation's error
  handling.

- Issue #7774: Set sys.executable to an empty string if argv[0] has been
  set to an non existent program name and Python is unable to retrieve the real
  program name

- Issue #6906: Tk should not set Unicode environment variables on Windows.

- Issue #1054943: Fix unicodedata.normalize('NFC', text) for the Public Review
  Issue #29

- Issue #7494: fix a crash in _lsprof (cProfile) after clearing the profiler,
  reset also the pointer to the current pointer context.

- Issue #4961: Inconsistent/wrong result of askyesno function in tkMessageBox
  with Tcl/Tk-8.5.

- Issue #7356: ctypes.util: Make parsing of ldconfig output independent of
  the locale.

Extension Modules
-----------------

- Fix memory leak in ssl._ssl._test_decode_cert.

- Issue #9422: Fix memory leak when re-initializing a struct.Struct object.

- Issue #7900: The getgroups(2) system call on MacOSX behaves rather oddly
  compared to other unix systems. In particular, os.getgroups() does
  not reflect any changes made using os.setgroups() but basicly always
  returns the same information as the id command.

  os.getgroups() can now return more than 16 groups on MacOSX.

- Issue #9277: Fix bug in struct.pack for bools in standard mode
  (e.g., struct.pack('>?')):  if conversion to bool raised an exception
  then that exception wasn't properly propagated on machines where
  char is unsigned.

- Issue #7384: If the system readline library is linked against
  ncurses, do not link the readline module against ncursesw. The
  additional restriction of linking the readline and curses modules
  against the same curses library is currently not enabled.

- Issue #2810: Fix cases where the Windows registry API returns
  ERROR_MORE_DATA, requiring a re-try in order to get the complete result.

Build
-----

- Issue #8854: Fix finding Visual Studio 2008 on Windows x64.

- Issue #3928: os.mknod() now available in Solaris, also.

- Issue #8175: --with-universal-archs=all works correctly on OSX 10.5

- Issue #6716: Quote -x arguments of compileall in MSI installer.

- Issue #1628484: The Makefile doesn't ignore the CFLAGS environment
  variable anymore.  It also forwards the LDFLAGS settings to the linker
  when building a shared library.

Tests
-----

- Issue #7849: Now the utility ``check_warnings`` verifies if the warnings are
  effectively raised.  A new private utility ``_check_py3k_warnings`` has been
  backported to help silencing py3k warnings.

- Issue #8672: Add a zlib test ensuring that an incomplete stream can be
  handled by a decompressor object without errors (it returns incomplete
  uncompressed data).

- Issue #8629: Disable some test_ssl tests, since they give different
  results with OpenSSL 1.0.0 and higher.

- Issue #8576: Remove use of find_unused_port() in test_smtplib and
  test_multiprocessing.  Patch by Paul Moore.

- Issue #7027: regrtest.py keeps a reference to the encodings.ascii module as a
  workaround to #7140 bug

- Issue #3864: Skip three test_signal tests on freebsd6 because they fail
  if any thread was previously started, most likely due to a platform bug.

- Issue #8193: Fix test_zlib failure with zlib 1.2.4.

Documentation
-------------

- Issue #9255: Document that the 'test' package is for internal Python use
  only.

- Issue #8909: Added the size of the bitmap used in the installer created by
  distutils' bdist_wininst. Patch by Anatoly Techtonik.
2010-09-04 05:12:00 +00:00
obache
3593815b0b exactly pass localedir to configure. 2010-09-04 05:04:57 +00:00
obache
87758ddcb9 Update HOMEPAGE and MASTER_SITES. 2010-09-04 01:51:52 +00:00
wiz
e311f9df71 Set LICENSE. 2010-09-03 23:04:02 +00:00
wiz
4edafc6077 Added devel/bullet version 2.76 2010-09-03 23:02:23 +00:00
wiz
dc89cafcf7 + bullet. 2010-09-03 23:02:13 +00:00
wiz
4954a2ca21 Initial import of bullet-2.76:
Bullet is a 3D Collision Detection and Rigid Body Dynamics Library
for games and animation.  Free for commercial use, including
Playstation 3, open source under the ZLib License.  Discrete and
continuous collision detection, integrated into Blender 3D, and
COLLADA 1.4 Physics import.
2010-09-03 23:01:47 +00:00
wiz
d69d1deff5 Added x11/unicode-screensaver version 0.3 2010-09-03 22:50:51 +00:00
wiz
52f2c8e059 + unicode-screensaver. 2010-09-03 22:50:39 +00:00
wiz
9f1ea3fb45 Initial import of unicode-screensaver-0.3:
unicode-screensaver is a simple screensaver application that
repeatedly randomly picks an unicode character and displays it in
a very large font size together with its unicode code point and
the character name.
2010-09-03 22:50:09 +00:00
wiz
918427449d Updated meta-pkgs/p5-gnome-bindings to 2.30.2 2010-09-03 22:41:25 +00:00
wiz
4db68460df All packaged and up-to-date -- update patterns and add missing dependencies.
Welcome to 2.30.2!
2010-09-03 22:41:15 +00:00
wiz
44fe9748c9 Added devel/p5-Gnome2 version 1.042 2010-09-03 22:40:34 +00:00
wiz
80d69f7eb4 + p5-Gnome2, p5-Gnome2-GConf. 2010-09-03 22:40:23 +00:00
wiz
ea0239a966 Initial import of p5-Gnome2-1.042:
The Gnome2 module allows a perl developer to use the Gnome libraries.

The perl bindings follow the C API very closely, and the C reference
documentation should be considered the canonical source.
2010-09-03 22:39:38 +00:00
wiz
5eaca8785a Added graphics/p5-Gnome2-Canvas version 1.002 2010-09-03 22:39:02 +00:00
wiz
98c55c3da2 + p5-Gnome2-Canvas. 2010-09-03 22:38:52 +00:00
wiz
102b105a45 Initial import of p5-Gnome2-Canvas-1.002:
The Gnome2::Canvas module allows a perl developer to use the
GnomeCanvas widget with Gtk2-Perl.

Like the Gtk2 module on which it depends, Gnome2::Canvas follows
the C API of libgnomecanvas-2.0 as closely as possible while still
being perlish.  Thus, the C API reference remains the canonical
documentation.
2010-09-03 22:38:19 +00:00
wiz
fe5c8b20f9 Added devel/p5-Gnome2-GConf version 1.044 2010-09-03 22:37:47 +00:00
wiz
8ba76acef5 Initial import of p5-Gnome-GConf-1.044:
This module allows you to use the GConf configuration system in
order to store/retrieve the configuration of an application.  GConf
is a powerful configuration manager based on a user daemon that
handles a set of key and value pairs, and notifies any changes of
the value to every program that monitors those keys.  GConf is used
by GNOME 2.x.
2010-09-03 22:36:38 +00:00
wiz
6b45b325e8 Added sysutils/p5-Gnome2-VFS version 1.081 2010-09-03 22:35:49 +00:00
wiz
e26324fd52 + p5-Gnome2-VFS. 2010-09-03 22:35:38 +00:00
wiz
fe3d36925c Initial import of p5-Gnome2-VFS-1.081:
This module allows you to use the GNOME Virtual File System library
(libgnomevfs for short) from Perl.
2010-09-03 22:34:58 +00:00
wiz
0b1e76a2f5 Updated x11/p5-gtk2 to 1.221 2010-09-03 22:33:42 +00:00
wiz
90883b45c4 Update to 1.221:
Overview of changes in Gtk2 1.221
=================================

* Properly wrap the binding for gtk_binding_entry_skip in version guards.
* Fix some build and test failures.
2010-09-03 22:33:32 +00:00
wiz
b89f933680 Updated devel/p5-pango to 1.221 2010-09-03 22:33:22 +00:00
wiz
dae402e0f0 Update to 1.221:
Overview of changes in Pango 1.221
==================================

* Properly export all our public symbols so that linking against us works on
  MSWin32.  (GNOME #576373)
2010-09-03 22:33:13 +00:00
asau
b388750a48 Updated biology/gromacs to 4.5.1 2010-09-03 20:53:35 +00:00
asau
e46ce0136a Update to GROMACS 4.5.1
GROMACS 4.5.1 is bug fix release.


Release notes for 4.5

New features

  * Pencil decomposition of the reciprocal space PME grid to
    improve scaling. This reduces the amount of communication
    for high parallelization and improves load balancing with up
    to 40% overall performance improvement for large systems.
  * Memory usage is improved for very large systems, allowing
    simulations of >100 million atoms.
  * Running on a multi-core node now uses thread-based
    parallelization to automatically spawn the optimum number of
    threads in the default build. MPI is now only required for
    parallelization over the network.
  * Domain decomposition can now also be used without periodic
    boundary conditions
  * GPU acceleration support on NVIDIA cards. This first release
    with GPU support based on OpenMM provides up to an order of
    magnitude faster performance for implicit solvent simulations,
    but PME simulations are about as fast as on a high-end CPU.
  * Check-pointing is made more secure:MD5sum are used to verify
    that all files are correctly in-place before a simulation is
    appended. Output file appending at continuation is turned on
    by default.
  * Increased tolerance for networked file system failures and
    cluster node crashes: checkpoint handling is safer and mdrun
    forces file system cache flushes during checkpoints.
  * Full CMake support. After the 4.5 release we will be
    switching the default build tool from autoconf to cmake,
    and possibly deprecate autoconf in the future.
  * Full support for seven AMBER force fields in the standard
    distribution, with default Amber names. We also include the
    recent Amber99sb-ildn in the distribution.
  * Support for CHARMM27, including cmap for dihedrals
  * Efficient Generalized-Born implicit solvent support
    including the Still/HCT/OBC-models to compute the Born radii,
    a novel way of tabulating the generalized Born-interaction
    formula for greater speed, and optimized SSE-routines in both
    single and double precision.
  * Highly efficient all-vs-all assembly kernels for both vanilla
    and generalized born interactions, in both single and double
    precision.
  * Much better support for nucleic acid simulations, including
    automatic handling by pdb2gmx.
  * Support for Velocity-Verlet integrators for reversible T-
    and P-coupling; MTTK pressure control integrators;
    Nose-Hoover chains.
  * Symplectic Trotter Leap-Frog integrator for twin-range
    non-bonded interactions.
  * Support for Bennet acceptance ratio calculations through
    direct calculation of Hamiltonian differences during the
    simulation.
  * File formats: All GROMACS tools can now read any VMD
    supported trajectory format, without converting trajectory
    first. (VMD libraries are required).
  * pdb2gmx now retains the residue numbers from the input,
    mdrun and all tools use these original numbers.

New tools

  * g_bar: Bennett acceptance ratio (BAR) free energy calculations,
    including automatic error estimates and phase space overlap
    measures.
  * g_rdf was a little bit enhanced that structure factors can
    be calculated for any system, by supplying the necessary data
    via sfactor.dat. Most of the common atomtypes are already
    contained, but everybody who needs more freedom can enhance
    the table
  * g_select: Library support for "dynamic index groups" based
    on textual selections (experimental feature).
    See the tool g_select, the included template.c, or Doxygen
    documentation for information on how to write analysis tools
    using the library. Existing tools have not (yet) been
    converted.
  * g_tune_pme: For a given number of processes or threads this
    tool systematically times mdrun with various numbers of
    PME-only nodes and determines which setting is fastest. It
    also checks whether performance can be enhanced by shifting
    load between the real and the reciprocal space part of the
    Ewald sum.
  * g_membed: a very convenient utility for rapidly embedding
    membrane proteins into equilibrated lipid bilayers
  * g_pme_error: estimates the error of the electrostatic forces
    if using the SPME algorithm. TO be incorporated in g_tune_pme

Changes that might affect your results

  * grompp by default sets the new nstcalcenergy parameter equal
    to nstlist, this has no effect on the integration, only on
    the energy averages stored in ener.edr
  * grompp by default sets the new nsttcouple parameter equal to
    nstlist, this means T-coupling is done less frequently;
    grompp checks if tau_t is large enough
  * grompp by default sets the new nstpcouple parameter equal to
    nstlist, this means P-coupling is done less frequently;
    grompp checks if tau_p is large enough
  * mdrun results with old tpr files with twin-range non-bonded
    interactions will be different, because of the new symplectic
    integrator
  * for free-energy calculations sc-sigma now also sets the minimum
    soft-core sigma (old tpr files retain the old  behavior,
    which can be enforced by setting the env.var. GMX_SCSIGMA_MIN to 0)
2010-09-03 20:52:39 +00:00
wiz
637ac41057 Added fonts/AnonymousPro version 1.001 2010-09-03 18:25:27 +00:00
wiz
8ac3c15d7e + AnonymousPro. 2010-09-03 18:25:17 +00:00
wiz
57ed47dfa3 Initial import of AnonymousPro-1.001:
Anonymous Pro (2009) is a family of four fixed-width fonts designed
especially with coding in mind. Characters that could be mistaken
for one another (O, 0, I, l, 1, etc.) have distinct shapes to make
them easier to tell apart in the context of source code.

Anonymous Pro also features an international, Unicode-based character
set, with support for most Western and European Latin-based languages,
Greek, and Cyrillic. It also includes special for those who need them.
2010-09-03 18:24:47 +00:00
drochner
3edb1ca7bc make that the "silent" qmake feature flag is silently ignored, it is
incompatible with the way libtool support was hacked in (we were getting
something like "libtool --mode=compile echo compiling foo && cc foo.c ...")
bump PKGREVISION
2010-09-03 13:47:12 +00:00
drochner
5a722a067e remove entries for recent updates 2010-09-03 10:46:10 +00:00
fhajny
98d7a1924e ejabberd updated to 2.1.5 2010-09-03 10:32:12 +00:00
fhajny
484c53b603 Updated chat/ejabberd to 2.1.5.
Short list of changes:
* Erlang/OTP R12 support fixed
* Erlang/OTP R14A support added
* OpenSSL 0.9.8 or higher is required
* BOSH: New optional connection attribute process-delay
* C2S: Don't ask for client certificate when using tls
* C2S: Inform client that SSL session caching is disabled
* CTL: Fix problem when FIREWALL_WINDOW options for erl kernel were used
* CTL: Some systems delete the lock dir; in such case don't use Flock at all
* Caps: Support all the hash functions required by XEP-0115
* Config: Fix typo in --enable-transient_supervisors
* Config: New configure option: --enable-nif
* Extauth: Support parallel script running
* MUC: Allow admins to see private rooms in disco
* ODBC: Correct handling of SQL boolean types
* ODBC: Discard too old queued requests (the caller has already got a timeout)
* ODBC: Fixes wrong SQL escaping when --enable-full-xml is set
* ODBC: Use ets insead of asking supervisor in ejabberd_odbc_sup:get_pids/1
* Pubsub: Enforce disco features results
* S2S: When logging s2s out connection attempt or success, log if TLS is used
* Shared Rosters: When account is deleted, delete also member
  of stored rosters
2010-09-03 10:31:43 +00:00
wiz
e6f6f8e259 Updated devel/m4 to 1.4.15 2010-09-03 07:39:55 +00:00
wiz
82910c29a5 Update to 1.4.15:
* Noteworthy changes in release 1.4.15 (2010-08-31) [stable]

** Fix regression introduced in 1.4.9b where the `format' builtin could
   crash on an invalid format string.

** Fix compilation against newer glibc, and on AIX 7.1BETA.

** A number of portability improvements inherited from gnulib.
2010-09-03 07:39:45 +00:00
agc
323f973e90 Note the addition of liboauth-0.8.9 2010-09-03 07:16:33 +00:00
agc
794908d417 Add and enable liboauth 2010-09-03 07:15:09 +00:00
agc
68beccdcbb Import liboauth-0.8.9 into the Packages Collection.
This is an updated version of the liboauth package in pkgsrc-wip by
Kamel Derouiche, modified by myself not to have nss, doxygen, perl and
graphviz pre-requisites.

        OAuth (Open Authorization) is an open standard that allows users to
        share their private resources (e.g.  photos, videos, contact lists)
        stored on one site with another site without having to hand out their
        username and password.

        OAuth allows users to hand out tokens instead of usernames and
        passwords to their data hosted by a given service provider.  Each
        token grants access to a specific site (e.g.  a video editing site)
        for specific resources (e.g.  just videos from a specific album) and
        for a defined duration (e.g.  the next 2 hours).

        Thus OAuth allows a user to grant a third party site access to their
        information stored with another service provider, without sharing
        their access permissions or the full extent of their data.

        OAuth is a service that is complementary to but distinct from OpenID.

        liboauth is a collection of C functions implementing the OAuth
        Core 1.0 standard API.  liboauth provides basic functions to
        escape and encode parameters according to OAuth specs and
        offers high-level functions to sign requests or verify
        signatures.

Necessary these days for twitter applications; useful for flickr and many
others...
2010-09-03 07:14:12 +00:00
sno
51e924d7ed Updated devel/p5-Getopt-Simple to 1.52 2010-09-03 06:11:27 +00:00
sno
ddf028aa7c Updating devel/p5-Getopt-Simple from 1.49nb2 to 1.52
pkgsrc changes:
- add license definition
- tidy

Upstream changes:
1.52  Sun Feb 21 12:55:13 2010
	- Remove text 'All rights reserved' (for Debian licensing).
	- Remove POD heads 'Required Modules' and 'Changes'.

1.51  Wed Feb 10 14:02:06 2010
	- MANIFEST.SKIP updated to exclude MYMETA.yml. Add MYMETA.yml.

1.50  Fri Nov 13 13:20:00 2009
	- Run dos2unix
	- Rename Changes.txt to CHANGES
2010-09-03 06:10:43 +00:00