Age | Commit message (Collapse) | Author | Files | Lines |
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Too many changes and bug fixes since 5.21. See
http://www.complang.org/ragel/ChangeLog for the complete list.
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many bug fixes
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Changes unknown
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A package that provides classes and methods for spatial data. The classes document
where the spatial location information resides, for 2D or 3D data. Utility functions
are provided, e.g. for plotting data as maps, spatial selection, as well as methods
for retrieving coordinates, for subsetting, print, summary, etc.
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genetics 1.3.4 - 2008-08-20
---------------------------
- Fix bug in makeGenotypes that caused it to ignore the 'sep' argument
when determining which columns contain genotypes & add a corresponing
regression test
genetics 1.3.3 - 2007-04-29
---------------------------
- Correct 'obsolete' use of '$'. R no longer permits '$' to be used
to extract named elements from vectors (just lists).
- Remove the power.casectl() function, which was based on invalid
assumpations. It has been marked depreciated. Please use the
functions in the Bioconductor package 'GeneticsDesign' instead.
genetics 1.3.2 - 2007-11-20
---------------------------
- Fix bug in handling of assignment of NA value(s) to elements of an
existing genotype object.
- Fix warning messages from R CMD CHECK
- Correct documentation error by swapping definitions of kp and alpha
arguments of power.casectl().
genetics 1.3.1
--------------
- fixes in genotypeOrder to ensure all genotype/haplotype combinations
are used.
- genotypeOrder<- is now exported
genetics 1.3.0
--------------
- A note is now displayed on startup:
The R-Genetics project has developed an set of enhanced genetics
packages that will shortly replace 'genetics'. Please visit the
project homepage at http://rgenetics.org for more information.
- binsearch() has been moved to the gtools package
- New function groupGenotype to create groups/levels based on genotype
names
- Added some internal utility functions
(.genotype2Haplotype, .genotype2Allele, and .matchGenotype)
- Genotype class gets additional slot genotypeOrder (and genotype()
function gets additional argument with the same name) in order to enable
predefined order of genotypes in other functions e.g. summary
- Added order, sort and %in% methods for genotype and haplotype classes.
- Fixed genotype() with allow.partial.missing=FALSE when 'alleles' argument
is passed
- There is no more warning in genotype() if 'a1' or 'a2' have NA value(s)
and 'alleles'' argument is specified, since NA is NA anyway
- Fixed documentation of power.casectrl()
- added gtools to Depends as needed by expectedGenotypes(); the latter now
gives sorted genotypes according to order of given alleles
- print.HWE.test() wasn't displaying the observed vs expected genotype
frequency table. Fixed.
genetics 1.2.1
--------------
- Update Greg's email address
- Fixed a bug in function allele.number, as pointed out by Chris
Wallace
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CHANGES IN 2.4.2 (2008-05-11)
-----------------------------
- Enhancements and bug fixes for read.xls() and xls2csv():
- More informative log messages when verbose=TRUE
- File paths containing spaces or other non-traditional characters
are now properly handled
- Better error messages, particularly when perl fails to generate
an output .csv file.
- The 'shortcut' character "~" (meaning user's home directory) is
now properly handled in file paths.
- XLS files created by OpenOffice are now properly handled. Thanks to
Robert Burns for pointing out the patch
(http://rt.cpan.org/Public/Bug/Display.html?id=7206)
CHANGES IN 2.4.1 (2008-03-24)
-----------------------------
- Update perl libraries needed by xls2csv() and read.xls()
to latest available versions on CRAN.
- Add read.xls() to exported function list
- Correct iris.xls example file. It didn't contain the complete
& properly formatted iris data set. Fixed.
- Fix typo in win32 example for read.xls()
CHANGES IN 2.4.0 (2008-01-30)
-----------------------------
- The keep() function now includes an 'all' argument to specify how
objects with names starting with '.' are handled.
- keep() now shows an informative warning message when a requested
object does not exist
- New vignette "Mapping Levels of a Factor" describing the use of
mapLevels().
- New vignette "Working with Unknown Values" describing the use of
isUnknown() and unknownToNA().
- Several enhancements to read.xls() (thanks to Gabor Grothendieck):
- New function xls2csv(), which handles converting an xls file
to a csv file and returns a connection to the
temporary csv file
- xls2csv() and read.xls() both allow a file or a url to be specified
- read.xls() has a new 'pattern' argument which, if supplied,
will ignore everything prior to the first line in th csv file
that matches the pattern. This is typically used if there
are a variable number of comment lines prior to the header
in which case one can specify one of the column
headings as the pattern. read.xls should
be compatible with the old read.xls.
- Minor fixes to drop.levels(), is.what().
- Implementation of unit tests for most functions.
CHANGES IN 2.3.1 (2006-10-29)
-----------------------------
- Arguments as well as their position of reorder.factor have been changed
to conform with reorder.factor method in stats package, due to collision
bug. Argument 'make.ordered' is now 'order' and old argument 'order' is
now 'new.order'! Therefore, you have to implicitly specify new.order i.e.
reorder(trt, new.order=c("PLACEBO", "300 MG", "600 MG", "1200 MG"))
- trim() gains ... argument.
- Added "unknown" methods for matrices.
- Added c() method for factors based on mapLevels() functions.
- Added write.fwf, which writes file in *F*ixed *W*idth *F*ormat.
CHANGES FROM 2.1.X to 2.3.0 (2006-09-19)
---------------------------------------
- Added mapLevels(), which produces a map with information on levels and/or
internal integer codes. Contributed by Gregor Gorjanc.
- Extended dropLevels() to work on the factors contained in a data
frame, as well as individual factors.
- Add unknown(), which changes given unknown value to NA and vice
versa. Contributed by Gregor Gorjanc.
- Extended trim() to handle a variety of data types data.frames,
lists, factors, etc. Code changes contributed by Gregor Gorjanc.
- Added resample() command that acts like sample() except that it
_always_ samples from the arguments provided, even if only a single
argument is present. This differs from sample() which behaves
differently in this case.
- Updated my email address.
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Circular Statistics, from "Topics in circular Statistics".
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gtools 2.5.0
------------
New features:
- Add checkRVersion() function to determin if a newer version of R is
available.
- Deprecated assert() in favor of base::stopifnot
Bug fixes:
- Fix bug in binsearch() identified by 2.6.0 R CMD CHECK
Other changes:
- Improve text explanation of how defmacro() and strmacro() differ from
function().
- Update definitions of odd() and even() to use modulus operator
instead of division.
gtools 2.4.0
------------
- Add binsearch() function, previously in the genetics() package.
gtools 2.3.1
------------
- Add ask() function to prompt the user and collect a single response.
gtools 2.3.0
------------
- Update email address for Greg
- Add new 'smartbind' function, which combines data frames
efficiently, even if they have different column names.
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Changes unknown
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Changes unknown
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(10 Oct 2008, from /branches/1.5.x)
http://svn.collab.net/repos/svn/tags/1.5.3
User-visible changes:
* Allow switch to continue after deleting locally modified dirs (issue #2505)
* Update bash_completion to be compatible with 1.5 (r32900, -11, -12)
* Improve 'svn merge' execution time by 30% on Windows (r33447)
* Reuse network sessions during 'svn merge', improving performance (r33476)
* Improve temp file creation time on Windows (r33464)
* Greatly improve merge performance (r29969, r32463, r33013, -016, -022, -112)
* Improve file IO performance on Windows (r33178, -85)
* fixed: merging files with spaces in name (r33109, -121, -369)
* fixed: incorrect relative externals expansion (r33109, -121, -369)
* fixed: 'svn mv' hangs and consumes infinite memory (r33201, -12)
* fixed: correctness regression in 'svn log -g' (issue #3285)
* fixed: current early bailout of 'svn log -g' (r32977)
Developer-visible changes:
* Allow the tests to run as non-administrator on Windows Vista (r31203)
* Allow out-of-tree build of bindings on BSD (r32409)
* Translate messages in svn_fs_util.h (r32771)
* fixed: bindings test for Perl 5.10 (r31546)
* fixed: building bindings and C API tests with VS2008 (r32012)
* fixed: svn_ra_replay API over ra_serf (r33173)
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Changes unknown
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Changes unknown.
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Changes in pixmap version 0.4-9
o Fixed a minor glitch in write.pnm.
Changes in pixmap version 0.4-8
o Fixed a bug that prevented plotting images with only 1 row (bug
report by Robert Esswein).
Changes in pixmap version 0.4-7
o Use LazyLoad instead of SaveImage.
Changes in pixmap version 0.4-6
o Modified one of the regression tests for changes in R 2.4:
terrain.colors() now return transparency information
-> do not use it in example.
Changes in pixmap version 0.4-5
o standardized license filed in DESCRIPTION file.
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devel/coccinelle package.
Menhir is a LR(1) parser generator for the Objective Caml programming
language. That is, Menhir compiles LR(1) grammar specifications down
to Objective Caml code. It is mostly compatible with ocamlyacc(1).
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Need to BUILDLINK_ABI_DEPENDS on the 2.2.11 versions of the libraries.
Bump PKGREVISION wholesale to disambiguate the fixed packages from the botched
ones and depend on them.
Use GPLed version of the plugins instead of the non-free version.
While here fix permissions of PKG_SYSCONFDIR in nessus-core/Makefile.
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the dependencies on aspell and hunspell); added a MESSAGE file mentioning
the need for dictionaries.
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Pkgsrc changes:
- does not support Module::Build anymore.
Changes since version 1.01:
===========================
1.03 2008-08-07
Forgot the Changelog for 1.02. Oops.
1.02 2008-08-07
Added support for strict HTML output. Fixes #34378. Thanks JUERD
and SIGZERO for the report and VRK for the patch that fixes it.
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Pkgsrc changes:
- none
Changes since version 0.28:
===========================
0.32 Wed Oct 01 12:19:22 MDT 2008
- Added width and height accessors
0.31 Thu Aug 14 08:16:37 MDT 2008
- removed GD version requirement
- fixed _distill_gdSpecial when using non-numeric colors (from srezic)
- fixed partically incomplete lines with square caps (jettero)
- Correctly handle the case where a rectangle's bottomright and topleft
are flipped. This is arguably a caller bug, but GD handles it.
0.30 Thu Aug 7 14:37:25 EDT 2008
- Added grouping features.
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Changes unknown
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Changes unknown.
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minor bugfixes.
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Official changelog:
Changes between 0.9.3 and 0.9.4:
------------------------------------
Various bugfixes:
* Crashes fixed in ogg, vobsub, dvdread
* Fixes several memory leaks.
Mac OS X port:
* Apple machines without Quartz Extreme are no longer supported (use 0.9.2 or earlier )
* Fixed a crash with deletion of old preferences.
* Fixed targetname for downloaded updates
Windows port:
* Stability fix for the video output.
Changes between 0.9.2 and 0.9.3:
------------------------------------
Various bugfixes:
* Fixed DTS channel order on 5.1 systems
* Fixed pausing behavior for subtitles and for Audio-CD
* Multiple subtitles and podcast fixes
* Various crashes fixed in PS, SSA, mkv, xspf, freetype
* Fixed update system bugs
* Other bug fixes (dvd language selection, subtitle colours, HTTP keep-alive...)
Mac OS X port:
* Fixed ffmpeg slowness on PowerPC-based Macs
* Fixed crash on startup when installed on old preferences
* Fixed bug in directory opening on Mac OS X
* Fixed font selection in the Simple Preferences
* Thicker border to the subtitle renderer
* Fixed the appearance of playlist items in the Streaming/Transcoding Wizard
* Fixed AC3 passthrough on Mac OS X
* Fixed behavior of the Volume Normalizer settings on Mac OS X
* Removed the deprecated QuickDraw video output module to avoid crashes on
modern Mac OS X versions
Windows port:
* Fixed sensitivity of Fullscreen Controller
* Fixed error messages on startup when VLC wasn't correctly uninstalled
before installation
* Fix showing of controller when returning from fullscreen playback
* Multiple directory and path location fixes.
Qt4 interface:
* Added Faster/Slower icons to the controller panel
* Fixed lost playlist columns when switching the playlist view
* Added needed options to Simple preferences (to avoid NVIDIA drivers issues)
* Fullscreen controller: added time label, remembering of last position
* Fixed drag'n drop behaviour on the playlist
* Multiple other fixes (Enter hotkey in preferences, Skins selection...)
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needed by at least p5-DBD-postgresql.
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doesn't seem to have lock/unlock primitives, this looks like the right thing
to do.
Fixes audio/tcd's eject function too.
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going to be returned. This fixes some issues with automatic installation
of dependencies.
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- If the idle timeout is not configured, it is now set to 20 minutes
after qmail exits to prevent never-ending spamdyke processing.
Thanks to Matthew Kettlewell for reporting this one.
- Fixed the AUTH advertisements to display correctly when
"smtp-auth-level" is "always" or "always-encrypted". Thanks
to Youri Kravatsky for reporting this one.
- Fixed a sequencing error that would cause qmail to exit prematurely,
even if valid recipients could still possibly be given. Thanks
to David Stiller for reporting this one.
- Fixed the handling of unencoded null characters in messages
(technically not legal) so spamdyke does become confused and
timeout. Thanks to Arthur Girardi for reporting this one.
- Fixed an issue in the DNS query code that was setting array indexes
beyond the end of the array, resulting in garbage log messages
and segmentation faults. Thanks to Arthur Girardi for reporting
this one.
- Fixed verbose logging in the RHSBL filter to print the correct
log message. Thanks to Arthur Girardi for reporting this one.
- Rewrote the address parser to correctly handle strange/invalid
email addresses. Thanks to Erald Troja for reporting this one.
- Fixed a serious error in the code that loads array values from
files that was returning pointers to unallocated memory, causing
segmentation faults. Many, many thanks to David Stiller for
reporting this one and providing tons of help to nail it down.
- Fixed a serious error that was attempting to move data by
dereferencing the NULL address when the remote server disconnected
unexpectedly, causing segmentation faults. Many, many thanks
to David Stiller for reporting this one and providing tons of
help to nail it down.
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