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Recent Package Updates

2019-10-13: tcoffee-12.00.7fb08c2-102 (T-Coffee Multiple Sequence Alignment Program)
T-Coffee computes multiple sequence alignments for protein or dna/rna
sequences. It is considerably slower than ClustalW but does a better
job aligning more distantly related sequences (<30% identity).  There
are also some enhancements for cDNA alignments.

commit log from Daniel Macks (dmacks@netspace.org):

    Backport new version to 10.9 (retain rev-separation for system-perl)
2019-10-13: raster3d-3.0-4-1 (Tools for generating images of molecules)
Raster3D is a set of tools for generating high quality raster images of
proteins or other molecules. The core program renders spheres, triangles,
cylinders, and quadric surfaces with specular highlighting, Phong shading,
and shadowing. It uses an efficient software Z-buffer algorithm which is
independent of any graphics hardware. Ancillary programs process atomic
coordinates from PDB files into rendering descriptions for pictures
composed of ribbons, space-filling atoms, bonds, ball+stick, etc. Raster3D
can also be used to render pictures composed in other programs such as
Molscript in glorious 3D with highlights, shadowing, etc. Output is to
pixel image files with 24 bits of color information per pixel.

commit log from Daniel Macks (dmacks@netspace.org):

    new version and gcc bump
2019-10-13: xfoil-699-3 (Design and analyze subsonic isolated airfoils)
XFOIL is an interactive program for the design and analysis of subsonic 
  isolated  airfoils. 
  It consists of a collection of menu-driven routines which perform various 
  useful functions such as:
  
    -Viscous (or inviscid) analysis of an existing airfoil, allowing
      -forced or free transition
      -transitional separation bubbles
      -limited trailing edge separation
      -lift and drag predictions just beyond CLmax
      -Karman-Tsien compressibility correction
      -fixed or varying Reynolds and/or Mach numbers
  
    -Airfoil design and redesign by interactive modification of surface speed 
     distributions, in two methods:
      -Full-Inverse method, based on a complex-mapping formulation
      -Mixed-Inverse method, an extension of XFOIL's basic panel method
  
    -Airfoil redesign by interactive modification of geometric parameters such 
     as
      -max thickness and camber, highpoint position
      -LE radius, TE thickness
      -camber line via geometry specification
      -camber line via loading change specification
      -flap deflection
      -explicit contour geometry (via screen cursor)
  
    -Blending of airfoils
    -Writing and reading of airfoil coordinates and polar save files
    -Plotting of geometry, pressure distributions, and multiple polars
    
  Set environment variable OSMAP to "%p/share/xfoil/osmap.dat" if it is 
  desired to use the option to see individual-frequency plotting on the
  A/Ao plot.c
  
  This package compiles xfoil with double precision arithmetic.

commit log from Daniel Macks (dmacks@netspace.org):

    Migrate off gcc5
2019-10-12: gcc9-9.2.0-1 (GNU Compiler Collection Version 9)
GCC, the GNU Compiler Collection, includes front ends for
 C, C++, Objective-C, Objective-C++, Fortran and Ada.
 .
 C, C++, Objective C and Fortran are included in this package.
 .
 The C and C++ compilers are named gcc-9 and g++-9 to avoid
 conflicts with gcc and g++ installed by the Apple Developer Tools

commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):

    gcc 9.2.0
2019-10-12: gd3-2.2.5-3 (Graphics generation library)
The GD library is useful for creating graphics like hit counters on
 the fly. This version supports the PNG, JPEG and WBMP formats and lets
 you use TrueType fonts rendered via freetype2.

commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):

    update debian patches to cover new CVE.