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2008-10-14Yet more R package updates.markd1-1/+18
2008-10-14Note update of ragel.minskim1-1/+2
2008-10-14Update ragel to 6.3. Patches provided by Matthias-Christian Ott.minskim3-8/+9
Too many changes and bug fixes since 5.21. See http://www.complang.org/ragel/ChangeLog for the complete list.
2008-10-14Update R-gstat to 0.9.51markd2-8/+9
many bug fixes
2008-10-14Update R-geoR to 0.9.26markd2-8/+9
Changes unknown
2008-10-14Initial import of R-sp version 0.9.26markd3-0/+24
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.
2008-10-14Update R-clim.pact to 2.2.15markd2-7/+7
Changes unknown
2008-10-14Update R-genetics to 1.3.4markd2-7/+7
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
2008-10-14Update R-gdata to 2.4.2markd2-8/+7
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.
2008-10-14Update R-Rcmdr to 1.4.2markd2-8/+7
Changes unknown
2008-10-14Update R-wle to 0.9.3markd2-8/+10
Changes unknown
2008-10-14Initial import of R-circular version 0.3.8markd3-0/+23
Circular Statistics, from "Topics in circular Statistics".
2008-10-14Update R-gtools to 2.5.0markd2-7/+7
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.
2008-10-14Update R-httpRequest to 0.0.6markd2-8/+7
Changes unknown
2008-10-14Update R-hwde to 0.5markd2-8/+7
Changes unknown
2008-10-14Update R-lmm to 0.3.5markd3-9/+22
Changes unknown
2008-10-14Put commented out LICENSE line (gnu-gpl-v3).uebayasi1-1/+2
2008-10-14Updated devel/subversion to 1.5.3epg2-3/+3
2008-10-14Version 1.5.3epg8-18/+18
(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)
2008-10-14Update R-mapproj to 1.1.7.2markd2-8/+9
Changes unknown
2008-10-14Update to R-maps 2.0.40markd2-8/+7
Changes unknown
2008-10-14Update R-mvtnorm to 0.9.2markd2-7/+7
Changes unknown.
2008-10-14Fix homepage.markd1-2/+2
2008-10-14Update R-pixmap to 0.4.9markd2-7/+7
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.
2008-10-14Accept emacs22nox too.uebayasi1-2/+2
2008-10-13correct forgotten CTYPE=Added for devel/menhirbjs1-2/+2
2008-10-13Updated devel/menhir to 20080912bjs1-1/+2
2008-10-13Add menhir to devel/Makefile.bjs1-1/+2
2008-10-13Import menhir-20080912. This is the parser used by the upcomingbjs5-0/+141
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).
2008-10-13Fix botched update of nessus.bad10-26/+40
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.
2008-10-13No need to depend on Python at runtime. Bump revision.joerg2-2/+5
2008-10-13updated MASTER_SITES urlschwarz1-2/+2
2008-10-13Mention the need for dictionariessmb1-0/+6
2008-10-13Add a dependency on ispell-base if ispell is enabled (parallel tosmb2-2/+4
the dependencies on aspell and hunspell); added a MESSAGE file mentioning the need for dictionaries.
2008-10-13Updated to version 1.03.heinz2-7/+7
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.
2008-10-13Updated to version 0.32.heinz2-6/+6
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.
2008-10-13Few more R package updates.markd1-1/+4
2008-10-13Update R-statmod to 1.3.6markd2-8/+7
Changes unknown
2008-10-13Update R-shapefiles to 0.6markd2-8/+7
Changes unknown.
2008-10-13Update R-sgeostat to 1.0.21markd2-8/+7
minor bugfixes.
2008-10-13Updated multimedia/vlc to 0.9.4.ahoka1-1/+2
2008-10-13Update to version 0.9.4, plus a lot of PLIST adjustmentsahoka4-19/+35
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...)
2008-10-13Bump BUILDLINK_API_DEPENDS to p5-DBI>=1.52 as that's the minimum versionerh1-2/+2
needed by at least p5-DBD-postgresql.
2008-10-13Apply patch to first unlock the CD before trying to eject it. Since SDLreinoud4-4/+18
doesn't seem to have lock/unlock primitives, this looks like the right thing to do. Fixes audio/tcd's eject function too.
2008-10-13Fix strip_txz() so it actually works even when the extension found isn'terh2-5/+5
going to be returned. This fixes some issues with automatic installation of dependencies.
2008-10-13Updated mail/spamdyke to 4.0.5schmonz1-1/+2
2008-10-13Update to 4.0.5. From the changelog:schmonz2-6/+6
- 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.
2008-10-13${NOTFOR_emacs22}hoge -> ${NOTFOR_emacs22}${NOTFOR_emacs22nox}hogeuebayasi1-2/+2
2008-10-13Correct copy&paste error.uebayasi1-4/+4
2008-10-13Updated lang/ocamlduce to 3.10.2obache1-1/+2
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