Documentation Scientific and Technical Beat

archimedes

archimedes is a 2D Quantum Monte Carlo simulator for semiconductor devices. New features for Fedora 17 include:

• Quantum Effective Potential modified
• Bohm Potential Model implemented
• Calibrated Bohm Model implemented
• Density Gradient corrected and tested
• Full effective potential model implemented
• New tests created
• Parabolic, Kane and Full band checked
• Full band Parameters for all materials
• Scattering phonons can be set to ON and OFF
• Support to Full Band approach

gnome-chemistry-utils

gnome-chemistry-utils has been updated to the latest development release.

Changes include:

• GChem3d:
  • Import from InChI or SMILES.
  • Export to GChemPaint and GChemCalc.
  • Generates InChI, InChiKey and SMILES.
  • Add access to databases.
• GChemPaint:
  • Brackets inside a molecule accept a stoichiometry coefficient.
• GCrystal:
  • Use multiple selection in atoms and lines dialogs.
• GSpectrum:
  • Allow markup in combo boxes and axes titles.
• Goffice component:
  • Add support for crystal structures.

gnuplot

In addition to a number of bug fixes, gnuplot 4.4.4 includes:

• boxxyerrors plot style now allows variable color
• splot with pm3d now allows variable rgb color
• "nonuniform matrix" indicates ascii data with explicit x, y
• columnhead(N) is a string-valued function, not a keyword
• Demarcate plots in svg output using <g id="Plot_#"><title>...
• xticlabels() works for binary data files as well as ascii
• "set key maxrows" now applies to 3D plots as well as 2D

lapack

lapack has been updated to 3.4.0,

• xGEQRT: QR factorization (improved interface). xGEQRT is analogous to xGEQRF with a modified interface which enables better performance when the blocked reflectors need to be reused. The companion subroutines xGEMQRT apply the reflectors.
• xGEQRT3: recursive QR factorization. The recursive QR factorization enables cache-oblivious and enables high performance on tall and skinny matrices.
• xTPQRT: Communication-Avoiding QR sequential kernels. These subroutines are useful for updating a QR factorization and are used in sequential and parallel Communication Avoiding QR. These subroutines support the general case Triangle on top of Pentagon which includes as special cases so-called Triangle on top of Triangle and Triangle on top of Square. This is the right-looking version of the subroutines and the subroutines are blocked. The T matrices and the block size are part of the interface. The companion subroutines xTPMQRT apply the reflectors.
• LAPACKE - Standard C language APIs for LAPACK. Since LAPACK 3.3.0, LAPACK includes new C interfaces. With the LAPACK 3.4.0 release, LAPACKE is directly integrated within the LAPACK library and has been enriched by the full set of LAPACK subroutines.

Refer to http://www.netlib.org/lapack/lapack-3.4.0.html for more details.

mapnik

Version 2.0.0 of mapnik is a major upgrade with numerous changes. Go to https://github.com/mapnik/mapnik/wiki/Release2.0.0 for complete details.

mathomatic

Refer to http://www.mathomatic.org/NEWS for the complete list of changes in mathomatic 15.7.3.

octave

The numerical computation language octave has been updated to 3.6.0. For details of the many new features please review http://www.gnu.org/software/octave/NEWS-3.6.html

paraview

The parallel visualization application paraview has been updated to version 3.12.0. The release notes for this application may be found at http://www.kitware.com/news/home/browse/367?siteid=12

pspp

Changes for version 0.7.8 of pspp:

• New commands:
  • ADD FILES
  • CORRELATIONS
  • DATAFILE ATTRIBUTES
  • DATASET ACTIVATE
  • DATASET CLOSE
  • DATASET COPY
  • DATASET DECLARE
  • DATASET DISPLAY
  • DATASET NAME
  • MATCH FILES
  • MRSETS
  • PRESERVE and RESTORE
  • QUICK CLUSTER
  • RELIABILITY
  • ROC
  • SAVE TRANSLATE to CSV and tab-delimited files
  • UPDATE
  • VARIABLE ATTRIBUTES
• Changes to existing commands:
  • AUTORECODE has a new GROUP subcommand.
  • CROSSTABS has been re-implemented to fix numerous bugs.
  • DO REPEAT command has been reimplemented. Now, when DO REPEAT contains an INCLUDE or INSERT command, substitutions are not applied to the included file.
  • HOST has been updated to use more modern syntax.
  • INCLUDE and INSERT have a new ENCODING subcommand.
  • MISSING VALUES can now assign missing values to long string variables.
  • NPAR TESTS has new KRUSKAL-WALLIS, SIGN, WILCOXON, and RUNS subcommands.
  • SET and SHOW no longer have ENDCMD, NULLINE, PROMPT, CPROMPT, and DPROMPT subcommands. The defaults are now fixed values.
  • VALUE LABELS can now assign value labels to long string variables.
• Other language changes:
  • The new DATASET commands replace the "scratch file" PSPP extension, which is no longer supported.
  • Strings may now include arbitrary Unicode code points specified in hexadecimal, using the syntax U'hhhh'. For example, Unicode code point U+1D11E, the musical G clef character, may be expressed as U'1D11E'.
  • In previous versions of PSPP, in a string expressed in hexadecimal with X'hh' syntax, the hexadecimal digits expressed bytes in the locale encoding. In this version of PSPP, X'hh' syntax always expresses bytes in UTF-8 encoding.
• PSPPIRE graphical user interface improvements:
  • Added support for non-ASCII characters in strings, labels and variable names.
  • A "Split Window" function is available, which makes it easier to see different parts of a large data file.
  • Data files can now be opened by specifing their name as the first argument. This means that on a properly configured desktop, double clicking on an icon will open the file.
• Output changes:
  • The new "cairo" output driver supports output in PostScript, PDF, and SVG formats. Its functionality is a superset of that of the "postscript" driver, which has been removed. You must have Cairo and Pango installed to build the "cairo" driver.
  • Charts are now produced with Cairo and Pango, instead of libplot. Without them, the new graphing features will not work. If you do not have Cairo and Pango installed, you must run `configure' with --without-cairo.
  • The plain text output driver now properly supports multibyte UTF-8 characters, including double-width characters and combining accents.
• The "pspp" program has a new option --batch (or -b) that selects "batch" syntax mode. In previous versions of PSPP this syntax mode was the default. Now a new "auto" syntax mode is the default. In "auto" mode, PSPP interprets most syntax files correctly regardless of their intended syntax mode.
• The "pspp" program has a new option --syntax-encoding that specifies the encoding for syntax files listed on the command line, as well as the default encoding for syntax files included with INCLUDE or INSERT. The default is to accept the system locale encoding, UTF-8, UTF-16, or UTF-32, automatically detecting which one the system file uses.
• A new Perl module allows Perl programs to read and write PSPP system files.
• A tutorial chapter has been added to the user manual.

python-fiat

Generation of arbitrary order instances of the Lagrange elements

 Old Version: 0.9.9 -> New Version: 1.0.0

Project site: (http://www.fenicsproject.org)

qgis

A user friendly Open Source Geographic Information System

 Old Version: 1.7.1 -> New Version: 1.7.3

Project site: (http://www.qgis.org)

qgis-grass

GRASS Support Libraries for Quantum GIS

 Old Version: 1.7.1 -> New Version: 1.7.3

Project site: (http://www.qgis.org)

qgis-python

Python integration and plug-ins for Quantum GIS

 Old Version: 1.7.1 -> New Version: 1.7.3

Project site: (http://www.qgis.org)

qtgpsc

A client for the gpsd GPS server

 Old Version: 0.2.3 -> New Version: 0.3.1

Project site: (http://www.navlost.eu/survey/gpsd/)

R

The statistics package R has been updated to December Snowflakes. Key changes include:

• NEW FEATURES:
  • Reference classes now keep a record of which fields are locked. $lock() with no arguments returns the names of the locked fields.
  • HoltWinters() reports a warning rather than an error for some optimization failures (where the answer might be a reasonable one).
  • tools::dependsOnPkg() now accepts the shorthand dependencies = "all".
  • parallel::clusterExport() now allows specification of an environment from which to export.
  • tempfile() on a Unix-alike now takes the process ID into account. This is needed with multicore (and as part of parallel) because the parent and all the children share a session temporary directory, and they can share the C random number stream used to produce the uniaue part. Further, two children can call tempfile() simultaneously.
  • Option print in Sweave's RweaveLatex() driver now emulates auto-printing rather than printing (which can differ for an S4 object by calling show() rather than print()).
  • filled.contour() now accepts infinite values: previously it might have generated invalid graphics files (e.g. containing NaN values).
• PACKAGE INSTALLATION:
  • R CMD INSTALL will now do a test load for all sub-architectures for which code was compiled (rather than just the primary sub-architecture).
• UTILITIES:
  • When checking examples under more than one sub-architecture, R CMD check now uses a separate directory examples_arch for each sub-architecture, and leaves the output in file pkgname-Ex_arch.Rout. Some packages expect their examples to be run in a clean directory ....

Refer to https://stat.ethz.ch/pipermail/r-announce/2011/000548.html for the complete list of changes and bug fixes.

R-affyio

Tools for parsing Affymetrix data files

 Old Version: 1.20.0 -> New Version: 1.22.0

Project site: (http://bioconductor.org/packages/release/bioc/html/affyio.html)

R-Biobase

Base functions for Bioconductor

 Old Version: 2.12.2 -> New Version: 2.14.0

Project site: (http://bioconductor.org/packages/release/bioc/html/Biobase.html)

R-BufferedMatrix

A matrix data storage object method from bioconductor

 Old Version: 1.16.0 -> New Version: 1.18.0

Project site: (http://bioconductor.org/packages/release/bioc/html/BufferedMatrix.html)

R-GeneR

R for genes and sequences analysis

 Old Version: 2.22.0 -> New Version: 2.24.0

Project site: (http://bioconductor.org/packages/release/bioc/html/GeneR.html)

R-hgu95av2probe

Probe sequence data for microarrays of type hgu95av2

 Old Version: 2.8.0 -> New Version: 2.9.0

Project site: (http://www.bioconductor.org/packages/release/data/annotation/html/hgu95av2probe.html)

R-IRanges

Low-level containers for storing sets of integer ranges

 Old Version: 1.10.4 -> New Version: 1.12.1

Project site: (http://bioconductor.org/packages/release/bioc/html/IRanges.html)

R-java

R with Fedora provided Java Runtime Environment

 Old Version: 2.13.1 -> New Version: 2.14.1

Project site: (http://www.r-project.org)

R-java-devel

Development package for use with Java enabled R components

 Old Version: 2.13.1 -> New Version: 2.14.1

Project site: (http://www.r-project.org)

R-lmtest

Testing Linear Regression Models for R

 Old Version: 0.9 -> New Version: 0.9.29

Project site: (http://cran.r-project.org/web/packages/lmtest/index.html)

R-mvtnorm

Multivariate normal and T distribution R Package

 Old Version: 0.9 -> New Version: 0.9.9991

Project site: (http://cran.r-project.org/web/packages/mvtnorm/index.html)

roundup

Simple and flexible issue-tracking system

 Old Version: 1.4.15 -> New Version: 1.4.18

Project site: (http://roundup.sourceforge.net/)

R-qcc

R-qcc is new to Fedora. R-qcc is an R package which provides a rich set of quality control and statistical process control tools, including:

• Plot Shewhart quality control charts
• Plot Cusum and EMWA charts for continuous data
• Draw operating characteristic curves
• Perform process capability analysis
• Draw Pareto charts and Ishikawa diagrams

R-qtl

Tools for analyzing QTL experiments

 Old Version: 1.21.2 -> New Version: 1.22.21

Project site: (http://www.rqtl.org/)

R-qvalue

Q-value estimation for false discovery rate control

 Old Version: 1.26.0 -> New Version: 1.28.0

Project site: (http://bioconductor.org/packages/release/bioc/html/qvalue.html)

R-RSQLite

SQLite database interface for R

 Old Version: 0.9.1 -> New Version: 0.10.0

Project site: (http://cran.r-project.org/web/packages/RSQLite/index.html)

R-systemfit

Simultaneous Equation Estimation R Package

 Old Version: 1.1 -> New Version: 1.1.11

Project site: (http://r-forge.r-project.org/projects/systemfit/)

R-zoo

Z's ordered observations for irregular time series

 Old Version: 1.6 -> New Version: 1.7.6

Project site: (http://cran.r-project.org/web/packages/zoo/index.html)

seaview

Graphical multiple sequence alignment editor

 Old Version: 4.2.12 -> New Version: 4.3.2

Project site: (http://pbil.univ-lyon1.fr/software/seaview.html)

tcd-utils

TCD (Tide Constituent Database) Utils

 Old Version: 20080820 -> New Version: 20120115

Project site: (http://www.flaterco.com/xtide/)

veusz

GUI scientific plotting package

 Old Version: 1.12 -> New Version: 1.14

Project site: (http://home.gna.org/veusz/)

vtk-examples

Examples for VTK

 Old Version: 5.6.1 -> New Version: 5.8.0

Project site: (http://vtk.org/)

vtk-testing

Testing programs for VTK

 Old Version: 5.6.1 -> New Version: 5.8.0

Project site: (http://vtk.org/)

wgrib

Manipulate, inventory and decode GRIB files

 Old Version: 1.8.1.0h -> New Version: 1.8.1.2a

Project site: (http://www.cpc.ncep.noaa.gov/products/wesley/wgrib.html)

wgrib2

Manipulate, inventory and decode GRIB2 files

 Old Version: 1.9.4 -> New Version: 1.9.5.1

Project site: (http://www.cpc.ncep.noaa.gov/products/wesley/wgrib2/)

why

Software verification platform

 Old Version: 2.29 -> New Version: 2.30

Project site: (http://why.lri.fr/)

why-coq

Libraries for interfacing Coq with Why

 Old Version: 2.29 -> New Version: 2.30

Project site: (http://why.lri.fr/)

why-gwhy

IDE for Why software verification platform

 Old Version: 2.29 -> New Version: 2.30

Project site: (http://why.lri.fr/)

xtide

Calculate tide all over the world

 Old Version: 2.12 -> New Version: 2.12.1

Project site: (http://www.flaterco.com/xtide/)

xtide-common

Xtide common files

 Old Version: 2.12 -> New Version: 2.12.1

Project site: (http://www.flaterco.com/xtide/)