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5. Changes in Fedora for Specific Audiences

5.1. Scientific and Technical

5.1.1. E

The E theorem prover version 1.7 is now included in Fedora 19. Improvements include:
  • Improved automatic mode
  • Interactive querying against large specifications
  • Various minor bugfixes

5.1.2. gabedit

gabedit has been upgraded to 2.4.6. Improvements include:
  • Gabedit can now read orbitals from GENNBO files
  • Several filters (Gaussian, Blackman, Blackman-Harris,...) implemented in the GabexitXYPlot window
  • Psi4 is partially supported : input file, geometries, frequencies, UV Spectrum
  • NCI (non-covalent interactions index) analysis implemented (see Johnson et al., J. Am. Chem. Soc. 132, 6498 (2010))
  • Analysis of Spatial Extent in Charge-Transfer Excitations implemented (See Le Bahers et al., J. Chem. Theory Comput. 2011, 7, 2498-2506)

5.1.3. gdl

The Gnu Data Language, gdl, has been updated to 0.9.3. New features include:
  • support for empty arrays and !NULL system variable
  • promotion of FOR loop index variable type
  • SCOPE_VARFETCH (only LEVEL keyword supported)
  • support for .SKIP [NSteps] command
  • keyword SIGN in FINITE
  • various improvements on READ_JPEG, READ_PNG, WRITE_JPEG, WRITE_PNG
  • keyword ICONIC in WSHOW
  • new widget features incl. WIDGET_LIST and CW_GROUP
  • support for some overloaded operators (_overloadIsTrue, _overloadPlus, _overloadMinus, _overloadBracketsLeftSide, _overloadBracketsRightSide, _overloadEQ, _overloadNE)
There are also some newly implemented routines:
  • TV for PS output
  • QROMB(), QSIMP() and QROMO()
  • TRISOL()

5.1.4. genius

genius has been updated from version 1.0.14 to 1.0.16. Changes include:
  • New functions CurrentTime, MacaulayRep, MacaulayLowerOperator, MacaulayBound
  • Fix rational powers of negative numbers, and exact negative rational powers
  • Fix zooming in graphs using the mouse when the functions take long to run
  • Accept log instead of ln for symbolic derivative when used with only one parameter
  • Add SurfacePlotData and SurfacePlotDataGrid functions to draw arbitrary surface data, to allow more complicated 3d plots and 3d plots from data
  • Add LinePlotDrawAxisLabels and SurfacePlotDrawLegends parameters and add corresponding UI checkboxes
  • Add ExportPlot function to export the current contents of the plot window to a file from GEL
  • Surface plot now allows "fit dependent axis" automatically when z limits are unspecified. And this is the default in the UI
  • Add sinc, BesselJ0, BesselJ1, BesselJn, BesselY0, BesselY1, BesselYn function
  • Plot window slightly bigger (700x500 now) and there are wider side margins in the lineplot (2D) version to make tick labels always fit
  • In both 2D and 3D plots, tick labels now use scientific notation when needed to avoid ugly labels
  • In surface plot the gradient always shows only the range of the function, so color is more useful when zoomed out
  • Simpler output when typing "help foo" when foo is neither defined nor documented
  • 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
  • Handle wider matrices than 2^15 columns in expansion
  • Fix flicker when plotting surfaces to allow animations with 3d plots
  • Fix possible uninitialized crash when reading badly formed standard library
  • Fix LinearRecursiveSequence and allow it to take vector for n
  • Fix crash on uninitialized variables in conjugate transpose
  • Fix crash on extreme zoom out or zoom in of a graph
  • Fix derivatives of Im and Re
  • Fix file chooser dialogs not starting in current directory
  • Avoid double error about uninitialized variables
  • Spelling fixes and documentation fixes
  • Require MPFR at least 2.3.0

5.1.5. gnome-chemistry-utils

Fedora 19 includes the latest 0.14.2 version of gnome-chemistry-utils. Compared to 0.13.99 there are some changes to GChemPaint:
  • Fix reaction construction
  • Fix non bonding electron pairs
  • Do not allow a mesomery destruction when inside a reaction

5.1.6. gromacs

gromacs 4.6.1 is included in Fedora 19. In addition to the gromacs package itself, the following related packages have also been changed:
gromacs-tutor (dropped)
In addition to various bug fixes, 4.6.1 includes the following changes:
  • increased shared object major version to 8
  • updates to HTML manual, install guide, PDF manual, shell completions
  • new and enhanced error messages
  • various GPU performance enhancements
  • more checks for system support for setting thread affinities
  • removed inter-flag dependency in g_order
  • incorporated new changes from release 4.5.x branch
  • adding warning about not building with icc version < 12

5.1.7. HippoDraw

HippoDraw has been dropped from Fedora.

5.1.8. kst

kst has been upgraded to 2.0.6. New features include:
  • user-visible string changes
  • 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)
  • scientific notation for extreme axis numbers
  • change scalar value directly in the scalar selection combobox
  • as-you-type search in comboboxes (vector selection)
  • view items have an option to scroll/zoom with the contents of the plot
  • improve automatic plot layout algorithm
  • option to have anti-aliased plots
  • mouse wheel scrolls and zooms
  • Adding a drag and drop capability
  • data source text box handles ~/ as shortcut to $HOME
  • legends wrapped to always fit inside their plot
  • 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
  • beta of python-based, mathplotlib-alike scripting (Linux only for now)

5.1.9. Octave

octave has been updated to 3.6.4.

5.1.10. qcad

qcad has been dropped from Fedora.

5.1.11. R

R is a language and environment for statistical computing and graphics. Fedora 19 includes the latest 3.0.0 release of R, which is a major upgrade.

Must re-install packages

There are many add-on packages for R which must be re-installed for this release.
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.
For full details on this new release of R, the reader is referred to the NEWS page at
In addition to updates to R 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:

5.1.12. Veusz

veusz has been updated to 1.17.1. Some new features include:
  • Allow coloured points for non-orthogonal plots (polar, ternary)
  • Remove unnecessary exception data
  • Add new broken axis widget with gaps in the numerical sequence
  • Grid lines are plotted always under (or over) the data
  • Shift+Scroll wheel scrolls left/right
  • Polar plots can have a "minimum" radius and log axes
  • Many more LaTeX symbols added
  • Add SAMP/VoTable support
  • New shifted-points xy line mode, which plots a stepped line with the points shifted to lie between the coordinates given
  • Points can be picked to console and/or clipboard
  • Allow reversed ternary plot

5.1.13. Sailcut

Fedora 19 adds sailcut, CAD software for designing and visualizing sails.

5.2. Circuit Design

5.2.1. gtkwave

gtkwave has been updated from 3.3.41 to 3.3.46.

5.2.2. XCircuit

xcircuit has been updated to 3.7.44. Version 3.7 has a modified selection mechanism that considers both points and segments of elements as well as entire elements. This allows the "edit" function to work as a stretch function to many elements at once.
Also added linewidth invariance on objects. Object instances (such as circuit symbols) can be made linewidth-invariant, such that an instance of the object can be scaled without changing the linewidth. This allows some circuit symbols to be resized relative to others on the same schematic without a discontinuity in wire width at the pins.
A number of other useful additions including:
  • Tracking spline control points for adjoining splines in paths
  • Clipmasks (shapes can be used to clip the view of other elements)
  • polygon-to-curve conversion routine
  • undo/redo on raise/lower elements
  • single-step raise and lower elements
  • gradient field generator---color graded fields are made from graphic image types

5.3. Embedded Development

5.3.1. avr-gcc

avr-gcc and avr-gcc-c++ have been updated to 4.7.3. Changes include:
  • The -fconserve-space flag has been deprecated. The flag had no effect for most targets: only targets without a global .bss section and without support for switchable sections. Furthermore, the flag only had an effect for G++, where it could result in wrong semantics (please refer to the GCC manual for further details). The flag will be removed in GCC 4.8
  • The AVR port's libgcc has been improved and its multilib structure has been enhanced. As a result, all objects contributing to an application must either be compiled with GCC versions up to 4.6.x or with GCC versions 4.7.1 or later. If the compiler is used with AVR Libc, you need a version that supports the new layout, i.e. implements #35407.
  • The AVR port's -mshort-calls command-line option has been deprecated. It will be removed in the GCC 4.8 release. See -mrelax for a replacement.
  • The AVR port only references startup code that clears .bss and the common section resp. initializes the .data and .rodata section provided respective sections (or subsections thereof) are not empty, see PR18145. Applications that put all static storage objects into non-standard sections or define all static storage objects in assembler modules, must reference __do_clear_bss resp. __do_copy_data by hand or undefine the symbol(s) by means of -Wl,-u,__do_clear_bss resp. -Wl,-u,__do_copy_data.
  • GCC versions 4.7.0 and 4.7.1 had changes to the C++ standard library which affected the ABI in C++11 mode: a data member was added to std::list changing its size and altering the definitions of some member functions, and std::pair's move constructor was non-trivial which altered the calling convention for functions with std::pair arguments or return types. The ABI incompatibilities have been fixed for GCC version 4.7.2 but as a result C++11 code compiled with GCC 4.7.0 or 4.7.1 may be incompatible with C++11 code compiled with different GCC versions and with C++98/C++03 code compiled with any version.
In addition, there are a number of improvements to the optimizer. The reader is referred to for additional details.

5.3.2. gputils

gputils has been upgraded to version 1.1.0 from 0.14.3. Changes in 1.1.0 include:
  • added -P (--preprocess) command line option to emit preprocessed asm file
  • added support for undocumented HALT, TRAP and TRET opcodes
  • .inc and .lkr files are synced with MPLABX 1.70
  • fixed support for 12 bit extended instruction set, devices PIC12F529T48A, PIC12F529T39A, PIC16F527 and PIC16F570

5.3.3. z88dk

z88dk has been upgraded from 1.10 to 1.10.1. This slightly modified release includes a bugfix in CPP preventing the inline assembler to work correctly plus few minor target specific corrections (ZX81 and MTX among the others)

5.4. Amateur Radio

5.4.1. chirp

chirp has been upgraded to 0.3.0. Some new features:
  • Automatic split->offset conversion during import when odd-split is not supported
  • Per-memory extra settings and detailed editing
  • TravelPlus importing
  • RadioReference importing
In addition, the following new radios are supported:
  • Baofeng UV-5R
  • Icom IC-208H
  • Icom IC-T7H
  • Icom IC-T8A
  • Icom IC-746
  • Kenwood TM-G707
  • Yaesu FT-1802M
  • Wouxun KG-UV6D/UV6X

5.4.2. demorse

demorse has been updated to 1.1. This is primarily a maintenance release and no changes should be user visible.

5.4.3. fldigi

fldigi 3.21.68 is now included in Fedora 19. This is primarily a maintenance/bugfix release.

5.4.4. gnuradio

There are quite a number of changes to get gnuradio to version, including:
  • Addition of the ability to add and connect formally defined asynchronous message ports to signal processing blocks and hierarchical blocks
  • the concept of PDUs (Protocol Data Units) as a convention for passing data+metadata using the new messaging ports
  • A few new general purpose blocks supporting these capabilities are in gnuradio-core:
    • gr_message_debug
    • gr_message_strobe
    • gr_tagged_stream_to_pdu
    • gr_pdu_to_tagged_stream
  • Two new blocks for interfacing with networking stacks using the new PDU semantics:
    • gr_socket_pdu
    • gr_tuntap_pdu
  • Addition of new Python-based signal processing blocks
  • Addition of gr-analog top-level component
  • Addition of gr-blocks top-level component
  • Metadata file source and sink blocks
  • GNU Radio buffer latency control
  • Ability to set processor affinity for GNU Radio blocks
  • Inclusion of gr_modtool
  • Use of GNU Radio preferences in native C++ applications
  • Addition of GNU Radio block performance counters
  • dozens of other features considered minor

5.4.5. linsmith

Fedora 19 includes version 0.99.24 of linsmith. Improvements include:
  • Slight improvements to the vector plot.
  • Better default values for colors of plot.
  • Modified the confmgr to accept hex and octal values in the configuration file.
  • Removed the (deprecated) gnomeprint dependency. Now the complete print route relies on Pango/Cairo to generate the plot, and the GtkPrint interface to do the actual printing.
  • Change papersize_combo to combobox, and load the list from the available papersizes.
  • Adapted confmgr to accept char * from comboboxes.
  • Moving elements up implemented.
  • Converted the strange negative default values for the color definitions to their (easier to understand?) hex values.
  • The 'standard cable' code mostly re-written, and a few more cable types added.

5.4.6. soundmodem

soundmodem has been updated to 0.16, primarily to interoperate with systemd.

5.4.7. xnec2c

xnec2c 2.1 includes a number of improvements:
  • Modify the xnec2c user interface so that it will, as far as possible, allow the user to save and re-open NEC2 files in the Editor window, without closing the Radiation Pattern and/or the Frequency Plots windows
  • replaced all the (deprecated) GDK drawing primitives with equivalent Cairo graphics equivalents (e.g. replaced gdk_draw_line() with cairo_line_to()) since Cairo provides for nicer anti-aliased drawing.
  • added code to save data of the structure display, radiation patterns and frequency plots into file, in a format suitable for the "gnuplot" plotting program