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

A high-level language for numerical computations

 Old Version: 3.4.2 -> New Version: 3.6.0

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

paraview

Parallel visualization application

 Old Version: 3.10.1 -> New Version: 3.12.0

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

paraview-data

Data files for ParaView

 Old Version: 3.10.1 -> New Version: 3.12.0

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

paraview-devel

 Old Version:  -> New Version: 3.12.0

Project site: ()

pspp

A program for statistical analysis of sampled data

 Old Version: 0.6.2 -> New Version: 0.7.8

Project site: (http://www.gnu.org/software/pspp/)

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-devel

Files for development of R packages

 Old Version: 2.13.1 -> New Version: 2.14.1

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

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/)