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Commits on Oct 8, 2012
  1. Revbump after updating graphics/pango

    adam authored
Commits on Oct 4, 2012
Commits on Oct 3, 2012
  1. CONFLICTS between python modules

    cheusov authored
  2. Bump all packages that use perl, or depend on a p5-* package, or

    wiz authored
    are called p5-*.
    I hope that's all of them.
Commits on Oct 2, 2012
  1. Mass recursive bump after the dependence fix of the "cairo" package

    tron authored
    requested by Thomas Klausner.
Commits on Sep 16, 2012
  1. CONFLICTS with generate-[0-9]*; ++pkgrevision

    cheusov authored
Commits on Sep 15, 2012
  1. recursive bump from libffi shlib major bump

    obache authored
    (additionaly, reset PKGREVISION of qt4-* sub packages from base qt4 update)
Commits on Sep 14, 2012
  1. Fix PKGNAME.

    asau authored
  2. + plink

    asau authored
  3. Import PLINK 1.07 as biology/plink

    asau authored
    From Jason Bacon via pkgsrc-wip.
    PLINK is a free, open-source whole genome association analysis
    toolset, designed to perform a range of basic, large-scale
    analyses in a computationally efficient manner.
    The focus of PLINK is purely on analysis of genotype/phenotype
    data, so there is no support for steps prior to this (e.g. study
    design and planning, generating genotype or CNV calls from raw
    data). Through integration with gPLINK and Haploview, there is
    some support for the subsequent visualization, annotation and
    storage of results.
Commits on Sep 11, 2012
  1. "user-destdir" is default these days

    asau authored
Commits on Sep 7, 2012
  1. Revbump after updating graphics/cairo

    adam authored
Commits on Aug 30, 2012
  1. more omf-scrollkeeper missing

    drochner authored
Commits on Aug 16, 2012
  1. Update to 0.12.13

    ryoon authored
    Version 0.12.13
                    * Fix View::BuildSVG() and View::BuildEPS() which were missing the
                    trailing 0.
                    * Fix loading of arrows inside a group. [#27032]
Commits on Jul 3, 2012
  1. Update to 0.12.12

    ryoon authored
    Version 0.12.12
                    * Fix atoms loading.
                    * Fix infinite loop condition. [#36583]
    Version 0.12.11
                    * fixed text position serialization. [#34947]
                    * fixed crash when selecting the alignment item inside a mechanism
                    step. [#35626]
Commits on Jun 14, 2012
Commits on Apr 8, 2012
  1. All supported python versions in pkgsrc support eggs, so remove

    wiz authored
    ${PLIST.eggfile} from PLISTs and support code from lang/python.
  2. Remove python24 and all traces of it from pkgsrc.

    wiz authored
    Remove devel/py-ctypes (only needed by and supporting python24).
    lines that just mirror defaults now.
    Miscellaneous cleanup while editing all these files.
Commits on Mar 3, 2012
  1. More pcre PKGREVISION bumps.

    wiz authored
Commits on Feb 7, 2012
  1. Add csh scripts to REPLACE_CSH and add USE_TOOLS+=csh:run

    sbd authored
Commits on Feb 6, 2012
  1. Revbump for

    wiz authored
    a) tiff update to 4.0 (shlib major change)
    b) glib2 update 2.30.2 (adds libffi dependency to
Commits on Jan 14, 2012
  1. Update to Gromacs 4.5.5

    asau authored
    Notable changes in Gromacs 4.5.5:
      * Improved pdb2gmx -chainsep option and reintroduced the -merge option.
      * Fixed mdrun file appending truncating files to 0 bytes when
        continuation runs stopped before writing new output.
      * Fixed COM pulling with multiple constraints checking the
        convergence of one constraint instead of all.
      * Fixed some dihedrals in sugars in Gromos53a5/6 working on the wrong atoms.
      * AmberGS force field is now based on Amber94 instead of Amber96.
      * Moved hydrogens in Charmm27 protein termini to separate
        charge groups and added ACE and CT3 residue types.
      * Many small fixes which avoid termination with fatal errors
        or crashes in mdrun and tools.
      * Many small updates to the manual pages of programs.
Commits on Jan 8, 2012
  1. Update to 1.6.13.

    ryoon authored
    Fixes and enhancements in chemtool 1.6.13
    - New export option "ASY" for Asymptote files (
    - Added support for Unicode symbol characters inserted e.g. by cut-and-paste from LibreOffice
    - Fixed build with newer linkers that do not resolve indirect requirements automatically
    - Rewritten logic for choosing to include national language support during build
    - Fixed crash on startup due to errors in menu icon setup
    - Batch mode could crash due to incomplete initialisation of color arrays
    - Undo/redo in "move fragment"-mode did not work as intended
    - Default extension is now appended to the save filename as needed
    - Fixed exporting to files or directories containing spaces in their names
Commits on Dec 9, 2011
  1. PKGREV bump for libXp-less openmotif

    drochner authored
Commits on Nov 25, 2011
  1. Remove concurrently created patch.

    joerg authored
Commits on Nov 24, 2011
  1. Fix build with GCC 4.5

    joerg authored
Commits on Nov 23, 2011
  1. biology/mummer: Put sort function in scope

    marino authored
    Add <algorithm> header for sort, DragonFly's compiler needs it.
    No PKGREVISION bump required.
Commits on Nov 22, 2011
  1. Update to 0.12.10

    ryoon authored
    Version 0.12.10
                    * show only atoms from the first crystal when loading a CIF file
                    with several structures.
                    * don't crash when loading a file with invalid atoms.
                    * don't display two atoms at the same position.
                    * don't loose the radius ratio on serialization.
                    * fix build with most recent glib-2.0 and xulrunner.
                    * enhanced translation: de.
Commits on Nov 1, 2011
Commits on Oct 31, 2011
  1. Initial import of primer3.

    brook authored
    Primer3 is a widely used program for designing PCR primers (PCR =
    "Polymerase Chain Reaction").  PCR is an essential and ubiquitous tool
    in genetics and molecular biology.  Primer3 can also design
    hybridization probes and sequencing primers.
Commits on Oct 28, 2011
  1. python24 is not acceptable.

    obache authored
Commits on Oct 27, 2011
  1. Update py-mol to 1.4.1.

    obache authored
    many improvements and bug fixes.
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