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2012-10-21Add CONFLICTS between "azara" and "connect"cheusov1-2/+4
2012-10-21Fix pkglint warnings; Clean-upscheusov1-16/+8
2012-10-20Don't return without value in non-void function.joerg2-1/+15
2012-10-16Recursive bump for new gtkglext pangox-compat dependency.wiz1-2/+2
2012-10-08Revbump after updating graphics/pangoadam3-6/+6
2012-10-04Bump revision for packages with changed CONFLICTS (PYTHON_SELF_CONFLICT)cheusov1-2/+2
2012-10-03CONFLICTS between python modulescheusov1-2/+3
2012-10-03Bump all packages that use perl, or depend on a p5-* package, orwiz5-9/+10
are called p5-*. I hope that's all of them.
2012-10-02Mass recursive bump after the dependence fix of the "cairo" packagetron3-6/+6
requested by Thomas Klausner.
2012-09-16CONFLICTS with generate-[0-9]*; ++pkgrevisioncheusov1-1/+4
2012-09-15recursive bump from libffi shlib major bumpobache3-6/+6
(additionaly, reset PKGREVISION of qt4-* sub packages from base qt4 update)
2012-09-14Fix PKGNAME.asau1-1/+2
2012-09-14+ plinkasau1-1/+2
2012-09-14Remove errorneously imported backup file. (Why was it not ignored??)asau1-1/+0
2012-09-14Import PLINK 1.07 as biology/plinkasau6-0/+134
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.
2012-09-11"user-destdir" is default these daysasau31-88/+31
2012-09-07Revbump after updating graphics/cairoadam3-5/+6
2012-08-30more omf-scrollkeeper missingdrochner1-1/+2
2012-08-16Update to 0.12.13ryoon2-6/+6
Changelog: Version 0.12.13 GChemPaint: * Fix View::BuildSVG() and View::BuildEPS() which were missing the trailing 0. * Fix loading of arrows inside a group. [#27032]
2012-07-03Update to 0.12.12ryoon3-9/+9
Changelog: Version 0.12.12 GCrystal: * Fix atoms loading. * Fix infinite loop condition. [#36583] Version 0.12.11 GChemPaint: * fixed text position serialization. [#34947] * fixed crash when selecting the alignment item inside a mechanism step. [#35626]
2012-06-14Recursive PKGREVISION bump for libxml2 buildlink addition.sbd5-7/+10
2012-04-08All supported python versions in pkgsrc support eggs, so removewiz1-2/+2
${PLIST.eggfile} from PLISTs and support code from lang/python.
2012-04-08Remove python24 and all traces of it from pkgsrc.wiz1-3/+1
Remove devel/py-ctypes (only needed by and supporting python24). Remove PYTHON_VERSIONS_ACCEPTED and PYTHON_VERSIONS_INCOMPATIBLE lines that just mirror defaults now. Miscellaneous cleanup while editing all these files.
2012-03-03More pcre PKGREVISION bumps.wiz1-2/+2
2012-03-03Recursive bump for pcre-8.30* (shlib major change)wiz2-4/+4
2012-02-07Add csh scripts to REPLACE_CSH and add USE_TOOLS+=csh:runsbd1-2/+5
Bump PKGREVISION
2012-02-06Revbump forwiz3-4/+6
a) tiff update to 4.0 (shlib major change) b) glib2 update 2.30.2 (adds libffi dependency to buildlink3.mk) Enjoy.
2012-01-14Update to Gromacs 4.5.5asau3-8/+25
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.
2012-01-08Update to 1.6.13.ryoon2-8/+7
Changelog: Fixes and enhancements in chemtool 1.6.13 - New export option "ASY" for Asymptote files (http://asymptote.sourceforge.net) - 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
2011-12-09PKGREV bump for libXp-less openmotifdrochner1-2/+2
2011-11-25Remove concurrently created patch.joerg2-14/+1
2011-11-24Fix build with GCC 4.5joerg2-1/+14
2011-11-23biology/mummer: Put sort function in scopemarino2-1/+14
Add <algorithm> header for sort, DragonFly's compiler needs it. No PKGREVISION bump required.
2011-11-22Update to 0.12.10ryoon2-7/+6
Changelog: Version 0.12.10 GCrystal: * 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. Other: * fix build with most recent glib-2.0 and xulrunner. * enhanced translation: de.
2011-11-01Recursive bump for graphics/freetype2 buildlink addition.sbd1-1/+2
2011-11-01Recursive bump for graphics/freetype2 buildlink addition.sbd2-2/+4
2011-10-31Initial import of primer3.brook6-1/+96
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.
2011-10-28python24 is not acceptable.obache1-1/+3
2011-10-27Update py-mol to 1.4.1.obache3-39/+238
many improvements and bug fixes.
2011-10-07Fix impossible depends.dholland1-2/+2
2011-10-05Add bodr, chemical-mime-data, gnome-chemistry-utils, and openbabel.ryoon1-1/+5
2011-10-05Reset MAINTAINER, because no response.ryoon2-4/+4
2011-10-05Initial import of gnome-chemistry-utils-0.12.9 from wip/gnome-chemistry-utilsryoon4-0/+365
GChemPaint, a 2D chemical editor and some other programs related to chemistry suitable for the GNOME desktop. The Gnome Chemistry Utils include three utilities: - a 2D chemical editor (GChemPaint). - a chemical calculator (computes raw formule, molar weight, mass composition, etc..) and isotopic pattern). - a molecule 3d viewer using OpenGL to display molecular models. - a crystal structues viewer and editor. - a periodic table of the elements. - a spectrum viewer. These programs are based on an included C++ library which provides a few widgets and various classes, some related to chemistry and some utility classes.
2011-10-05Initial import of openbabel-2.3.0 from wip/openbabelryoon7-0/+338
Open Babel is a chemical toolbox designed to speak the many languages of chemical data. It's an open, collaborative project allowing anyone to search, convert, analyze, or store data from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas.
2011-10-05Import of chemical-mime-data-0.1.94 as biology/chemical-mime-dataryoon5-0/+115
from wip/chemical-mime-data The chemical-mime-data package is a collection of data files to add support for various chemical MIME types on Linux/UNIX desktops, such as KDE and GNOME. Chemical MIMEs were proposed in 1995, though it seems they have never been registered with IANA. But they are widely used and the project's aim is, to support these important, but unofficial MIME types.
2011-10-05Initial import of bodr-9 from wip/bodrryoon5-0/+60
The Blue Obelisk Data Repository lists many important chemoinformatics data such as element and isotope properties, atomic radii, etc. including references to original literature. Developers can use this repository to make their software interoperable.
2011-08-14Revision bump after updating perl5 to 5.14.1.obache1-2/+2
2011-04-22recursive bump from gettext-lib shlib bump.obache2-3/+4
2011-03-23Update to Gromacs 4.5.4:asau3-7/+8
* Fixed pdb2gmx picking up force field from local instead of library directory * Made pdb2gmx vsite generation work again for certain His namings. * Fixed incorrect virial and pressure averages with certain nst... values (instantaneous values correct) * Fixed incorrect cosine viscosity output * New -multidir alternative for mdrun -multi option * Several minor fixes in analysis tools * Several updates to the program documentation
2011-01-13png shlib name changed for png>=1.5.0, so bump PKGREVISIONs.wiz1-2/+2
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