[release-notes] Populated Scientific and Technical section
John J. McDonough
jjmcd at fedoraproject.org
Fri May 10 15:07:15 UTC 2013
commit 0cb697638972d790375e9d07b12d6a038773cbc9
Author: John J. McDonough <jjmcd at fedoraproject.org>
Date: Fri May 10 11:07:04 2013 -0400
Populated Scientific and Technical section
en-US/Scientific_and_Technical.xml | 1075 +++++++++++++++++++++++++++++++++++-
1 files changed, 1072 insertions(+), 3 deletions(-)
---
diff --git a/en-US/Scientific_and_Technical.xml b/en-US/Scientific_and_Technical.xml
index 9f130ef..846450d 100644
--- a/en-US/Scientific_and_Technical.xml
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@@ -4,9 +4,1078 @@
<?xml-stylesheet href="http://www.informatik.fh-wiesbaden.de/~werntges/home_t/proj/dbkcss102/wysiwygdocbook1.02/driver.css" type="text/css"?>
-<section>
-
+
+<section id="sect-Release_Notes-EngineeringGroup">
<title>Scientific and Technical</title>
- <para />
+
+ <section>
+ <title>E</title>
+ <indexterm><primary>E</primary></indexterm>
+ <para>
+ The <package>E</package> theorem prover version 1.7 is now
+ included in Fedora 19. Improvements include:
+ <itemizedlist spacing="compact">
+ <listitem>
+ <para>
+ Improved automatic mode
+ </para>
+ </listitem>
+ <listitem>
+ <para>
+ Interactive querying against large specifications
+ </para>
+ </listitem>
+ <listitem>
+ <para>
+ Various minor bugfixes
+ </para>
+ </listitem>
+ </itemizedlist>
+ </para>
+ </section>
+
+ <section>
+ <title>gabedit</title>
+ <indexterm><primary>gabedit</primary></indexterm>
+ <para>
+ <package>gabedit</package> has been upgraded to 2.4.6.
+ Improvements include:
+ <itemizedlist spacing="compact">
+ <indexterm><primary>GENNBO</primary>
+ <secondary>gabedit</secondary></indexterm>
+ <indexterm><primary>Orbitals</primary>
+ <secondary>gabedit</secondary></indexterm>
+ <indexterm><primary>Gaussian filter</primary>
+ <secondary>gabedit</secondary></indexterm>
+ <indexterm><primary>Blackman filter</primary>
+ <secondary>gabedit</secondary></indexterm>
+ <indexterm><primary>Blackman-Harris filter</primary>
+ <secondary>gabedit</secondary></indexterm>
+ <indexterm><primary>Psi4</primary>
+ <secondary>gabedit</secondary></indexterm>
+ <indexterm><primary>NCI</primary>
+ <secondary>gabedit</secondary></indexterm>
+ <indexterm><primary>non-covalent interactions index</primary>
+ <secondary>gabedit</secondary></indexterm>
+ <indexterm><primary>Analysis of Spatial Extent</primary>
+ <secondary>gabedit</secondary></indexterm>
+ <indexterm><primary>Charge-Transfer Excitations</primary>
+ <secondary>gabedit</secondary></indexterm>
+ <indexterm><primary>Spatial Extent</primary>
+ <secondary>gabedit</secondary></indexterm>
+ <listitem>
+ <para>
+ Gabedit can now read orbitals from GENNBO files
+ </para>
+ </listitem>
+ <listitem>
+ <para>
+ Several filters (Gaussian, Blackman, Blackman-Harris,...)
+ implemented in the GabexitXYPlot window
+ </para>
+ </listitem>
+ <listitem>
+ <para>
+ Psi4 is partially supported : input file, geometries,
+ frequencies, UV Spectrum
+ </para>
+ </listitem>
+ <listitem>
+ <para>
+ NCI (non-covalent interactions index) analysis implemented
+ (see Johnson et al., J. Am. Chem. Soc. 132, 6498 (2010))
+ </para>
+ </listitem>
+ <listitem>
+ <para>
+ Analysis of Spatial Extent in Charge-Transfer Excitations
+ implemented (See Le Bahers et al., J. Chem. Theory
+ Comput. 2011, 7, 2498-2506)
+ </para>
+ </listitem>
+ </itemizedlist>
+ </para>
+ </section>
+
+ <section>
+ <title>gdl</title>
+ <indexterm><primary>gdl</primary></indexterm>
+ <para>
+ The Gnu Data Language, <package>gdl</package>, has been updated
+ to 0.9.3. New features include:
+ <itemizedlist spacing="compact">
+ <indexterm><primary>FOR loop</primary>
+ <secondary>gdl</secondary></indexterm>
+ <indexterm><primary>SCOPE_VARFETCH</primary>
+ <secondary>gdl</secondary></indexterm>
+ <indexterm><primary>LEVEL</primary>
+ <secondary>gdl</secondary></indexterm>
+ <indexterm><primary>.SKIP</primary>
+ <secondary>gdl</secondary></indexterm>
+ <indexterm><primary>DIM</primary>
+ <secondary>gdl</secondary></indexterm>
+ <indexterm><primary>MOMENT()</primary>
+ <secondary>gdl</secondary></indexterm>
+ <indexterm><primary>MEAN()</primary>
+ <secondary>gdl</secondary></indexterm>
+ <indexterm><primary>STDDEV()</primary>
+ <secondary>gdl</secondary></indexterm>
+ <indexterm><primary>VARIANCE()</primary>
+ <secondary>gdl</secondary></indexterm>
+ <indexterm><primary>SKEWNESS()</primary>
+ <secondary>gdl</secondary></indexterm>
+ <indexterm><primary>KURTOSIS()</primary>
+ <secondary>gdl</secondary></indexterm>
+ <indexterm><primary>SIGN</primary>
+ <secondary>gdl</secondary></indexterm>
+ <indexterm><primary>FINITE</primary>
+ <secondary>gdl</secondary></indexterm>
+ <indexterm><primary>READ_JPEG</primary>
+ <secondary>gdl</secondary></indexterm>
+ <indexterm><primary>READ_PNG</primary>
+ <secondary>gdl</secondary></indexterm>
+ <indexterm><primary>WRITE_JPEG</primary>
+ <secondary>gdl</secondary></indexterm>
+ <indexterm><primary>WRITE_PNG</primary>
+ <secondary>gdl</secondary></indexterm>
+ <indexterm><primary>ICONIC</primary>
+ <secondary>gdl</secondary></indexterm>
+ <indexterm><primary>WSHOW</primary>
+ <secondary>gdl</secondary></indexterm>
+ <indexterm><primary>ISOTROPIC</primary>
+ <secondary>gdl</secondary></indexterm>
+ <indexterm><primary>PLOT</primary>
+ <secondary>gdl</secondary></indexterm>
+ <indexterm><primary>CONTOUR</primary>
+ <secondary>gdl</secondary></indexterm>
+ <indexterm><primary> WIDGET_LIST</primary>
+ <secondary>gdl</secondary></indexterm>
+ <indexterm><primary>CW_GROUP</primary>
+ <secondary>gdl</secondary></indexterm>
+ <indexterm><primary>_overloadIsTrue</primary>
+ <secondary>gdl</secondary></indexterm>
+ <indexterm><primary>_overloadPlus</primary>
+ <secondary>gdl</secondary></indexterm>
+ <indexterm><primary>_overloadMinus</primary>
+ <secondary>gdl</secondary></indexterm>
+ <indexterm><primary>_overloadBracketsLeftSide</primary>
+ <secondary>gdl</secondary></indexterm>
+ <indexterm><primary>_overloadBracketsRightSide</primary>
+ <secondary>gdl</secondary></indexterm>
+ <indexterm><primary>_overloadEQ</primary>
+ <secondary>gdl</secondary></indexterm>
+ <indexterm><primary> _overloadNE</primary>
+ <secondary>gdl</secondary></indexterm>
+ <listitem>
+ <para>
+ support for empty arrays and <code>!NULL</code> system variable
+ </para>
+ </listitem>
+ <listitem>
+ <para>
+ promotion of <code>FOR</code> loop index variable type
+ </para>
+ </listitem>
+ <listitem>
+ <para>
+ <code>SCOPE_VARFETCH</code> (only <code>LEVEL</code>
+ keyword supported)
+ </para>
+ </listitem>
+ <listitem>
+ <para>
+ support for <code>.SKIP [NSteps]</code> command
+ </para>
+ </listitem>
+ <listitem>
+ <para>
+ keyword <code>DIM</code> in <code>MOMENT()</code>,
+ <code>MEAN()</code>, <code>STDDEV()</code>,
+ <code>VARIANCE()</code>, <code>SKEWNESS()</code>,
+ <code>KURTOSIS()</code>
+ </para>
+ </listitem>
+ <listitem>
+ <para>
+ keyword <code>SIGN</code> in <code>FINITE</code>
+ </para>
+ </listitem>
+ <listitem>
+ <para>
+ various improvments on <code>READ_JPEG</code>,
+ <code>READ_PNG</code>, <code>WRITE_JPEG</code>,
+ <code>WRITE_PNG</code>
+ </para>
+ </listitem>
+ <listitem>
+ <para>
+ keyword <code>ICONIC</code> in <code>WSHOW</code>
+ </para>
+ </listitem>
+ <listitem>
+ <para>
+ keyword <code>ISOTROPIC</code> in <code>PLOT</code>,
+ <code> CONTOUR</code>
+ </para>
+ </listitem>
+ <listitem>
+ <para>
+ new widget features incl. <code>WIDGET_LIST</code>
+ and <code>CW_GROUP</code>
+ </para>
+ </listitem>
+ <listitem>
+ <para>
+ support for some overloaded operators
+ (<code>_overloadIsTrue</code>,
+ <code>_overloadPlus</code>, <code>_overloadMinus</code>,
+ <code>_overloadBracketsLeftSide</code>,
+ <code>_overloadBracketsRightSide</code>,
+ <code>_overloadEQ</code>, <code>_overloadNE</code>)
+ </para>
+ </listitem>
+ </itemizedlist>
+ </para>
+ <para>
+ There are also some newly implemented routines:
+ <itemizedlist spacing="compact">
+ <indexterm><primary>STRMATCH()</primary>
+ <secondary>gdl</secondary></indexterm>
+ <indexterm><primary>USERSYM</primary>
+ <secondary>gdl</secondary></indexterm>
+ <indexterm><primary>LUDC</primary>
+ <secondary>gdl</secondary></indexterm>
+ <indexterm><primary>LUSOL</primary>
+ <secondary>gdl</secondary></indexterm>
+ <indexterm><primary>DETERM</primary>
+ <secondary>gdl</secondary></indexterm>
+ <indexterm><primary>ROT</primary>
+ <secondary>gdl</secondary></indexterm>
+ <indexterm><primary>CONGRID</primary>
+ <secondary>gdl</secondary></indexterm>
+ <indexterm><primary>BILINEAR</primary>
+ <secondary>gdl</secondary></indexterm>
+ <indexterm><primary>QROMB()</primary>
+ <secondary>gdl</secondary></indexterm>
+ <indexterm><primary>QSIMP()</primary>
+ <secondary>gdl</secondary></indexterm>
+ <indexterm><primary>QROMO()</primary>
+ <secondary>gdl</secondary></indexterm>
+ <indexterm><primary>TRISOL()</primary>
+ <secondary>gdl</secondary></indexterm>
+ <indexterm><primary>STANDARDIZE</primary>
+ <secondary>gdl</secondary></indexterm>
+ <indexterm><primary>HIST_EQUAL</primary>
+ <secondary>gdl</secondary></indexterm>
+ <indexterm><primary>FX_ROOT</primary>
+ <secondary>gdl</secondary></indexterm>
+ <indexterm><primary>FZ_ROOTS</primary>
+ <secondary>gdl</secondary></indexterm>
+ <listitem>
+ <para>
+ STRMATCH(), USERSYM
+ </para>
+ </listitem>
+ <listitem>
+ <para>
+ LUDC, LUSOL and DETERM
+ </para>
+ </listitem>
+ <listitem>
+ <para>
+ ROT, CONGRID and BILINEAR
+ </para>
+ </listitem>
+ <listitem>
+ <para>
+ TV for PS output
+ </para>
+ </listitem>
+ <listitem>
+ <para>
+ QROMB(), QSIMP() and QROMO()
+ </para>
+ </listitem>
+ <listitem>
+ <para>
+ TRISOL()
+ </para>
+ </listitem>
+ <listitem>
+ <para>
+ STANDARDIZE and HIST_EQUAL
+ </para>
+ </listitem>
+ <listitem>
+ <para>
+ FX_ROOT
+ </para>
+ </listitem>
+ <listitem>
+ <para>
+ FZ_ROOTS
+ </para>
+ </listitem>
+ </itemizedlist>
+ </para>
+ </section>
+
+ <section>
+ <title>genius</title>
+ <para>
+ <indexterm><primary>genius</primary></indexterm>
+
+ <package>genius</package> has been updated from version 1.0.14
+ to 1.0.16. Changes include:
+ <itemizedlist spacing="compact">
+ <indexterm><primary>CurrentTime</primary>
+ <secondary>genius</secondary></indexterm>
+ <indexterm><primary>MacaulayRep</primary>
+ <secondary>genius</secondary></indexterm>
+ <indexterm><primary>MacaulayLowerOperator</primary>
+ <secondary>genius</secondary></indexterm>
+ <indexterm><primary>MacaulayBound</primary>
+ <secondary>genius</secondary></indexterm>
+ <indexterm><primary>SurfacePlotData</primary>
+ <secondary>genius</secondary></indexterm>
+ <indexterm><primary>SurfacePlotDataGrid</primary>
+ <secondary>genius</secondary></indexterm>
+ <indexterm><primary>LinePlotDrawAxisLabels</primary>
+ <secondary>genius</secondary></indexterm>
+ <indexterm><primary>SurfacePlotDrawLegends</primary>
+ <secondary>genius</secondary></indexterm>
+ <indexterm><primary>ExportPlot</primary>
+ <secondary>genius</secondary></indexterm>
+ <indexterm><primary>sinc</primary>
+ <secondary>genius</secondary></indexterm>
+ <indexterm><primary>BesselJ0</primary>
+ <secondary>genius</secondary></indexterm>
+ <indexterm><primary>BesselJ1</primary>
+ <secondary>genius</secondary></indexterm>
+ <indexterm><primary>BesselJn</primary>
+ <secondary>genius</secondary></indexterm>
+ <indexterm><primary>BesselY0</primary>
+ <secondary>genius</secondary></indexterm>
+ <indexterm><primary>BesselY1</primary>
+ <secondary>genius</secondary></indexterm>
+ <indexterm><primary>BesselYn</primary>
+ <secondary>genius</secondary></indexterm>
+ <listitem>
+ <para>
+ New functions CurrentTime, MacaulayRep,
+ MacaulayLowerOperator, MacaulayBound
+ </para>
+ </listitem>
+ <listitem>
+ <para>
+ Fix rational powers of negative numbers, and exact
+ negative rational powers
+ </para>
+ </listitem>
+ <listitem>
+ <para>
+ Fix zooming in graphs using the mouse when the functions
+ take long to run
+ </para>
+ </listitem>
+ <listitem>
+ <para>
+ Accept log instead of ln for symbolic derivative when used
+ with only one parameter
+ </para>
+ </listitem>
+ <listitem>
+ <para>
+ Add SurfacePlotData and SurfacePlotDataGrid functions to
+ draw arbitrary surface data, to allow more complicated 3d
+ plots and 3d plots from data
+ </para>
+ </listitem>
+ <listitem>
+ <para>
+ Add LinePlotDrawAxisLabels and SurfacePlotDrawLegends
+ parameters and add corresponding UI checkboxes
+ </para>
+ </listitem>
+ <listitem>
+ <para>
+ Add ExportPlot function to export the current contents of
+ the plot window to a file from GEL
+ </para>
+ </listitem>
+ <listitem>
+ <para>
+ Surface plot now allows "fit dependent axis" automatically
+ when z limits are unspecified. And this is the default in
+ the UI
+ </para>
+ </listitem>
+ <listitem>
+ <para>
+ Add sinc, BesselJ0, BesselJ1, BesselJn, BesselY0,
+ BesselY1, BesselYn function
+ </para>
+ </listitem>
+ <listitem>
+ <para>
+ Plot window slightly bigger (700x500 now) and there are
+ wider side margins in the lineplot (2D) version to make
+ tick labels always fit
+ </para>
+ </listitem>
+ <listitem>
+ <para>
+ In both 2D and 3D plots, tick labels now use scientific
+ notation when needed to avoid ugly labels
+ </para>
+ </listitem>
+ <listitem>
+ <para>
+ In surface plot the gradient always shows only the range
+ of the function, so color is more useful when zoomed out
+ </para>
+ </listitem>
+ <listitem>
+ <para>
+ Simpler output when typing "help foo" when foo is neither
+ defined nor documented
+ </para>
+ </listitem>
+ <listitem>
+ <para>
+ When for/sum/prod loops are in terms of floating point
+ numbers and the final number is within 2^-20 times the step
+ size of the goal, assume there were roundoff errors and
+ still execute the body
+ </para>
+ </listitem>
+ <listitem>
+ <para>
+ Handle wider matrices than 2^15 columns in expansion
+ </para>
+ </listitem>
+ <listitem>
+ <para>
+ Fix flicker when plotting surfaces to allow animations
+ with 3d plots
+ </para>
+ </listitem>
+ <listitem>
+ <para>
+ Fix possible uninitialized crash when reading badly formed
+ standard library
+ </para>
+ </listitem>
+ <listitem>
+ <para>
+ Fix LinearRecursiveSequence and allow it to take vector for n
+ </para>
+ </listitem>
+ <listitem>
+ <para>
+ Fix crash on uninitialized variables in conjugate transpose
+ </para>
+ </listitem>
+ <listitem>
+ <para>
+ Fix crash on extreme zoom out or zoom in of a graph
+ </para>
+ </listitem>
+ <listitem>
+ <para>
+ Fix derivatives of Im and Re
+ </para>
+ </listitem>
+ <listitem>
+ <para>
+ Fix file chooser dialogs not starting in current directory
+ </para>
+ </listitem>
+ <listitem>
+ <para>
+ Avoid double error about uninitialized variables
+ </para>
+ </listitem>
+ <listitem>
+ <para>
+ Spelling fixes and documentation fixes
+ </para>
+ </listitem>
+ <listitem>
+ <para>
+ Require MPFR at least 2.3.0
+ </para>
+ </listitem>
+ </itemizedlist>
+ </para>
+ </section>
+
+ <section>
+ <title>gnome-chemistry-utils</title>
+ <indexterm><primary>gnome-chemistry-utils</primary></indexterm>
+ <para>
+ Fedora 19 includes the latest 0.14.2 version of
+ <package>gnome-chemistry-utils</package>. Compared to 0.13.99
+ there are some changes to <application>GChemPaint</application>:
+ <itemizedlist spacing="compact">
+ <listitem>
+ <para>
+ Fix reaction construction
+ </para>
+ </listitem>
+ <listitem>
+ <para>
+ Fix non bonding electron pairs
+ </para>
+ </listitem>
+ <listitem>
+ <para>
+ Do not allow a mesomery destruction when inside a reaction
+ </para>
+ </listitem>
+ </itemizedlist>
+ </para>
+ </section>
+
+ <section>
+ <title>gromacs</title>
+ <indexterm><primary>gromacs</primary></indexterm>
+ <para>
+ <package>gromacs</package> 4.6.1 is included in Fedora 19. In
+ addition to the <package>gromacs</package> package itself, the
+ following related packages have also been changed:
+ <simplelist>
+ <member><package>gromacs-bash</package></member>
+ <member><package>gromacs-common</package></member>
+ <member><package>gromacs-csh</package></member>
+ <member><package>gromacs-devel</package></member>
+ <member><package>gromacs-libs</package></member>
+ <member><package>gromacs-tutor</package> (dropped)</member>
+ <member><package>gromacs-zsh</package></member>
+ </simplelist>
+ </para>
+ <para>
+ In addition to various bug fixes, 4.6.1 includes the following
+ changes:
+ <itemizedlist spacing="compact">
+ <listitem>
+ <para>
+ increased shared object major version to 8
+ </para>
+ </listitem>
+ <listitem>
+ <para>
+ updates to HTML manual, install guide, PDF manual, shell
+ completions
+ </para>
+ </listitem>
+ <listitem>
+ <para>
+ new and enhanced error messages
+ </para>
+ </listitem>
+ <listitem>
+ <para>
+ various GPU performance enhancements
+ </para>
+ </listitem>
+ <listitem>
+ <para>
+ more checks for system support for setting thread affinities
+ </para>
+ </listitem>
+ <listitem>
+ <para>
+ removed inter-flag dependency in g_order
+ </para>
+ </listitem>
+ <listitem>
+ <para>
+ incorporated new changes from release 4.5.x branch
+ </para>
+ </listitem>
+ <listitem>
+ <para>
+ adding warning about not building with icc version < 12
+ </para>
+ </listitem>
+ </itemizedlist>
+ </para>
+ </section>
+
+ <section>
+ <title>HippoDraw</title>
+ <indexterm><primary>HippoDraw</primary></indexterm>
+ <para>
+ <package>HippoDraw</package> has been dropped from Fedora.
+ </para>
+ </section>
+
+ <section>
+ <title>kst</title>
+ <indexterm><primary>kst</primary></indexterm>
+ <para>
+ <package>kst</package> has been upgraded to 2.0.6. New features
+ include:
+ <itemizedlist spacing="compact">
+ <listitem>
+ <para>
+ user-visible string changes
+ </para>
+ </listitem>
+ <listitem>
+ <para>
+ finish UI revamp (esp. context menus + connect plot dialog
+ pages to the way the dialog is opened, e.g. double click
+ on axes opens plot dialog in the right place)
+ </para>
+ </listitem>
+ <listitem>
+ <para>
+ scientific notation for extreme axis numbers
+ </para>
+ </listitem>
+ <listitem>
+ <para>
+ change scalar value directly in the scalar selection combobox
+ </para>
+ </listitem>
+ <listitem>
+ <para>
+ as-you-type search in comboboxes (vector selection)
+ </para>
+ </listitem>
+ <listitem>
+ <para>
+ view items have an option to scroll/zoom with the contents
+ of the plot
+ </para>
+ </listitem>
+ <listitem>
+ <para>
+ improve automatic plot layout algorithm
+ </para>
+ </listitem>
+ <listitem>
+ <para>
+ option to have anti-aliased plots
+ </para>
+ </listitem>
+ <listitem>
+ <para>
+ mouse wheel scrolls and zooms
+ </para>
+ </listitem>
+ <listitem>
+ <para>
+ Adding a drag and drop capability
+ </para>
+ </listitem>
+ <listitem>
+ <para>
+ data source text box handles ~/ as shortcut to $HOME
+ </para>
+ </listitem>
+ <listitem>
+ <para>
+ legends wrapped to always fit inside their plot
+ </para>
+ </listitem>
+ <listitem>
+ <para>
+ new datasource: Matlab .mat file reader (Matlab pretty
+ much sucks at plotting, that'd be a pretty interesting
+ move and there's a spec at
+ <ulink type="http"
+ url="http://www.mathworks.com/access/helpdesk/help/pdf_doc/matlab/matfile_format.pdf"
+ />)
+ </para>
+ </listitem>
+ <listitem>
+ <para>
+ beta of python-based, mathplotlib-alike scripting (Linux
+ only for now)
+ </para>
+ </listitem>
+ </itemizedlist>
+ </para>
+ </section>
+
+ <section>
+ <title>Octave</title>
+ <indexterm><primary>Octave</primary></indexterm>
+ <para>
+ <package>octave</package> has been updated to 3.6.4.
+ </para>
+ </section>
+
+ <section>
+ <title>qcad</title>
+ <indexterm><primary>qcad</primary></indexterm>
+ <para>
+ <package>qcad</package> has been dropped from Fedora.
+ </para>
+ </section>
+
+ <section>
+ <title>R</title>
+ <indexterm><primary>R</primary></indexterm>
+ <indexterm><primary>Statistics</primary><secondary>R</secondary></indexterm>
+ <indexterm><primary>R-devel</primary></indexterm>
+ <indexterm><primary>R-core</primary></indexterm>
+
+ <para>
+ <package>R</package> is a language and environment for
+ statistical computing and graphics. Fedora 19 includes the
+ latest 3.0.0 release of <package>R</package>, which is a major
+ upgrade.
+ </para>
+ <para>
+ <note>
+ <title>Must re-install packages</title>
+ <para>
+ There are many add-on packages for <package>R</package> which
+ must be re-installed for this release.
+ </para>
+ </note>
+ </para>
+ <para>
+ A major thrust of release 3.0.0 is to better exploit 64-bit
+ platforms, however there are many, many improvements to a number
+ of functions. Perhaps obviously, support for long vectors has
+ been greatly improved, but there are dozens of improvements to
+ other functions as well.
+ </para>
+ <para>
+ For full details on this new release of <package>R</package>,
+ the reader is referred to the NEWS page at <ulink type="http"
+ url="http://cran.r-project.org/src/base/NEWS.html" />.
+ </para>
+ <para>
+ In addition to updates to <package>R</package> itself, a number
+ of R packages have also been enhanced. The table below lists
+ those packages and the upstream web sites to obtain additional
+ information:
+ <indexterm><primary>R-qtl</primary></indexterm>
+ <indexterm><primary>R-mvtnorm</primary></indexterm>
+ <indexterm><primary>R-multcomp</primary></indexterm>
+ <indexterm><primary>R-lmtest</primary></indexterm>
+ <indexterm><primary>R-java-devel</primary></indexterm>
+ <indexterm><primary>R-java</primary></indexterm>
+ <indexterm><primary>R-IRanges</primary></indexterm>
+ <indexterm><primary>R-hgu95av2probe</primary></indexterm>
+ <indexterm><primary>R-car</primary></indexterm>
+ <indexterm><primary>R-BufferedMatrix</primary></indexterm>
+ <indexterm><primary>R-BSgenome.Celegans.UCSC.ce2</primary></indexterm>
+ <indexterm><primary>R-Biobase</primary></indexterm>
+ <indexterm><primary>R-affyio</primary></indexterm>
+ <table frame="all" id="tabl-R-Package-changes">
+ <title>Updated R Packages</title>
+ <tgroup cols="4">
+ <colspec colnum="1" colname="c1" colwidth="2*" />
+ <colspec colnum="2" colname="c2" colwidth="1*" />
+ <colspec colnum="3" colname="c3" colwidth="1*" />
+ <colspec colnum="4" colname="c4" colwidth="4*" />
+ <thead>
+ <row>
+ <entry>
+ Package
+ </entry>
+ <entry>
+ Old Version
+ </entry>
+ <entry>
+ New Version
+ </entry>
+ <entry>
+ Upstream URL
+ </entry>
+ </row>
+ </thead>
+ <tbody>
+ <row>
+ <entry>
+ <package>R-affyio</package>
+ </entry>
+ <entry>
+ 1.22.0
+ </entry>
+ <entry>
+ 1.28.0
+ </entry>
+ <entry>
+ <ulink type="http" url="http://bioconductor.org/packages/release/bioc/html/affyio.html" />
+ </entry>
+ </row>
+ <row>
+ <entry>
+ <package>R-Biobase</package>
+ </entry>
+ <entry>
+ 2.14.0
+ </entry>
+ <entry>
+ 2.20.0
+ </entry>
+ <entry>
+ <ulink type="http" url="http://bioconductor.org/packages/release/bioc/html/Biobase.html" />
+ </entry>
+ </row>
+ <row>
+ <entry>
+ <package>R-BSgenome. Celegans.UCSC.ce2</package>
+ </entry>
+ <entry>
+ 1.3.17
+ </entry>
+ <entry>
+ 1.3.19
+ </entry>
+ <entry>
+ <ulink type="http" url="http://www.bioconductor.org/packages/release/data/annotation/html/BSgenome.Celegans.UCSC.ce2.html" />
+ </entry>
+ </row>
+ <row>
+ <entry>
+ <package>R-BufferedMatrix</package>
+ </entry>
+ <entry>
+ 1.20.0
+ </entry>
+ <entry>
+ 1.24.0
+ </entry>
+ <entry>
+ <ulink type="http" url="http://bioconductor.org/packages/release/bioc/html/BufferedMatrix.html" />
+ </entry>
+ </row>
+ <row>
+ <entry>
+ <package>R-car</package>
+ </entry>
+ <entry>
+ 2.0
+ </entry>
+ <entry>
+ 2.0.16
+ </entry>
+ <entry>
+ <ulink type="http" url="http://cran.r-project.org/web/packages/car/index.html" />
+ </entry>
+ </row>
+ <row>
+ <entry>
+ <package>R-hgu95av2probe</package>
+ </entry>
+ <entry>
+ 2.9.0
+ </entry>
+ <entry>
+ 2.12.0
+ </entry>
+ <entry>
+ <ulink type="http" url="http://www.bioconductor.org/packages/release/data/annotation/html/hgu95av2probe.html" />
+ </entry>
+ </row>
+ <row>
+ <entry>
+ <package>R-IRanges</package>
+ </entry>
+ <entry>
+ 1.14.4
+ </entry>
+ <entry>
+ 1.18.0
+ </entry>
+ <entry>
+ <ulink type="http" url="http://bioconductor.org/packages/release/bioc/html/IRanges.html" />
+ </entry>
+ </row>
+ <row>
+ <entry>
+ <package>R-java</package>
+ </entry>
+ <entry>
+ 2.15.2
+ </entry>
+ <entry>
+ 3.0.0
+ </entry>
+ <entry>
+ <ulink type="http" url="http://www.r-project.org" />
+ </entry>
+ </row>
+ <row>
+ <entry>
+ <package>R-java-devel</package>
+ </entry>
+ <entry>
+ 2.15.2
+ </entry>
+ <entry>
+ 3.0.0
+ </entry>
+ <entry>
+ <ulink type="http" url="http://www.r-project.org" />
+ </entry>
+ </row>
+ <row>
+ <entry>
+ <package>R-lmtest</package>
+ </entry>
+ <entry>
+ 0.9.29
+ </entry>
+ <entry>
+ 0.9.30
+ </entry>
+ <entry>
+ <ulink type="http" url="http://cran.r-project.org/web/packages/lmtest/index.html" />
+ </entry>
+ </row>
+ <row>
+ <entry>
+ <package>R-multcomp</package>
+ </entry>
+ <entry>
+ 1.2
+ </entry>
+ <entry>
+ 1.2.17
+ </entry>
+ <entry>
+ <ulink type="http" url="http://cran.r-project.org/web/packages/multcomp/index.html" />
+ </entry>
+ </row>
+ <row>
+ <entry>
+ <package>R-mvtnorm</package>
+ </entry>
+ <entry>
+ 0.9.9991
+ </entry>
+ <entry>
+ 0.9.9994
+ </entry>
+ <entry>
+ <ulink type="http" url="http://cran.r-project.org/web/packages/mvtnorm/index.html" />
+ </entry>
+ </row>
+ <row>
+ <entry>
+ <package>R-qtl</package>
+ </entry>
+ <entry>
+ 1.25.15
+ </entry>
+ <entry>
+ 1.27.10
+ </entry>
+ <entry>
+ <ulink type="http" url="http://www.rqtl.org/" />
+ </entry>
+ </row>
+ <row>
+ <entry>
+ <package>R-qvalue</package>
+ </entry>
+ <entry>
+ 1.30.0
+ </entry>
+ <entry>
+ 1.34.0
+ </entry>
+ <entry>
+ <ulink type="http" url="http://bioconductor.org/packages/release/bioc/html/qvalue.html" />
+ </entry>
+ </row>
+ <row>
+ <entry>
+ <package>R-rlecuyer</package>
+ </entry>
+ <entry>
+ 0.3.1
+ </entry>
+ <entry>
+ 0.3.3
+ </entry>
+ <entry>
+ <ulink type="http" url="http://cran.r-project.org/web/packages/rlecuyer/index.html" />
+ </entry>
+ </row>
+ </tbody>
+ </tgroup>
+ </table>
+ </para>
+ </section>
+
+ <section>
+ <title>Veusz</title>
+ <para>
+ <package>veusz</package> has been updated to 1.17.1. Some new
+ features include:
+ <itemizedlist spacing="compact">
+ <listitem>
+ <para>
+ Allow coloured points for non-orthogonal plots (polar, ternary)
+ </para>
+ </listitem>
+ <listitem>
+ <para>
+ Remove unnecessary exception data
+ </para>
+ </listitem>
+ <listitem>
+ <para>
+ Add new broken axis widget with gaps in the numerical sequence
+ </para>
+ </listitem>
+ <listitem>
+ <para>
+ Grid lines are plotted always under (or over) the data
+ </para>
+ </listitem>
+ <listitem>
+ <para>
+ Shift+Scroll wheel scrolls left/right
+ </para>
+ </listitem>
+ <listitem>
+ <para>
+ Polar plots can have a "minimum" radius and log axes
+ </para>
+ </listitem>
+ <listitem>
+ <para>
+ Many more LaTeX symbols added
+ </para>
+ </listitem>
+ <listitem>
+ <para>
+ Add SAMP/VoTable support
+ </para>
+ </listitem>
+ <listitem>
+ <para>
+ New shifted-points xy line mode, which plots a stepped
+ line with the points shifted to lie between the
+ coordinates given
+ </para>
+ </listitem>
+ <listitem>
+ <para>
+ Points can be picked to console and/or clipboard
+ </para>
+ </listitem>
+ <listitem>
+ <para>
+ Allow reversed ternary plot
+ </para>
+ </listitem>
+ </itemizedlist>
+ </para>
+ </section>
+
</section>
+
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