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2004-02-01In the new compiler selection framework, GCC_REQD is appended to, notjlam1-2/+2
overridden.
2004-01-29call ${MAKE} with the right environment and arguments, override CC.grant1-4/+9
fixes build with non-gcc. minor style fixes.
2004-01-29make sure we use ${CC}.grant1-1/+3
2004-01-24Use GCC_REQD instead of USE_PKGSRC_GCC when overriding the compilerkristerw1-2/+2
for arm, so that we don't need to install the gcc package(s) on machines that already have a working compiler in their /usr/bin.
2004-01-22replace deprecated USE_GMAKE with USE_GNU_TOOLS+=make.grant2-4/+4
2004-01-20Move WRKSRC definition away from the first paragraph in a Makefile.agc15-30/+33
2003-12-30Add trailing / on HOMEPAGEscjep1-2/+2
2003-12-25Update to 9.5:wiz2-5/+5
9.5: The last release introduced a bug when adding customary meals to regular meals. The program now adds the foods without the additional prompt screen. 9.4: This release changes the method of searching for foods to a substring search. The narrowing-down of food categories to a unique food is the same as in prior releases.
2003-12-13Update to 9.3:wiz2-5/+5
This release fixes a bug in the graphs where the "Daily Value" was such a small percentage of the values graphed that the DV line indicator exceeded the graph width.
2003-10-07Apply patches from Tyler Retzlaff in PR pkg/23083 to make this behave withjschauma4-10/+38
gcc3. While here, update to version 2.12 (previous version was erraneously named 2.1, when it should have been 2.10) which is the only distfile available on the ftp site. Changelog seems to say: - Fix bug on long-orfs.cc to avoid occasional array out-of-bounds error (detected on Mac OS X).
2003-10-05Update to 9.2:wiz2-5/+5
9.2: The upper limit of the polyunsaturated reference value for linoleic acid has been reduced to 4% of calories, while that for alpha linolenic acid has been raised to 2%. An internal constant for the percentage of total fat that is fatty acids has been replaced by a function that figures it for each analysis. 9.1: The program is no longer limited to three meals a day, and can now be set for 1 to 19 meals per day. A list of the meals not yet recorded for a selected day is displayed as a mnemonic during the "Record Meals" function.
2003-10-04Add/enable xylemjschauma1-1/+2
2003-10-04Initial import of xylem, one of the many packages provided byjschauma6-0/+322
brook at biology dot nmsu dot edu and his team at NMSU. XYLEM is a package of tools designed to exploit the Unix environment to enable the user to identify, extract and manipulate data from major databases such as GenBank, EMBL and PIR.
2003-09-30Add/enable glimmer.jschauma1-1/+2
2003-09-30Initial import of glimmer, one of the many packages provided byjschauma5-0/+78
brook at biology dot nmsu dot edu and his team at NMSU. Glimmer (Gene Locator and Interpolated Markov Modeler) is a system for finding genes in microbial DNA, especially the genomes of bacteria and archaea. Glimmer uses interpolated Markov models (IMMs) to identify the coding regions and distinguish them from noncoding DNA. The IMM approach uses a combination of Markov models from 1st through 8th-order, weighting each model according to its predictive power.
2003-09-30Add/enable genesplicer.jschauma1-1/+2
2003-09-30Initial import of genesplicer, one of the many packages provided byjschauma5-0/+208
brook at biology dot nmsu dot edu and his team at NMSU. GeneSplicer is a fast, flexible system for detecting splice sites in the genomic DNA of various eukaryotes. The system has been trained and tested successfully on Plasmodium falciparum (malaria), Arabidopsis thaliana, human, Drosophila, and rice.
2003-09-30Add/enable fluctuate.jschauma1-1/+2
2003-09-30Initial import of fluctuate, one of the many packages provided byjschauma6-0/+106
brook at biology dot nmsu dot edu and his team at NMSU. FLUCTUATE fits the model which has a single population which has been growing (or shrinking) according to an exponential growth law. It estimates 4Nu and g, where N is the effective population size, u is the neutral mutation rate per site, and g is the growth rate of the population.
2003-09-30Add/enable coalesce.jschauma1-1/+2
2003-09-30Initial import of coalesce, one of the many packages provided byjschauma5-0/+85
brook at biology dot nmsu dot edu and his team at NMSU. COALESCE fits the model which has a single population of constant size, and estimates 4Nu, where N is the effective population size and u is the neutral mutation rate per site.
2003-09-27Add/enable stridejschauma1-1/+2
2003-09-27Initial import of stride, one of the many packages provided byjschauma5-0/+55
brook at biology dot nmsu dot edu and his team at NMSU. Knowledge-based protein secondary structure assignment from atomic coordinates.
2003-09-27Add/enable sewerjschauma1-1/+2
2003-09-27Initial import of sewer, one of the many packages provided byjschauma5-0/+116
brook at biology dot nmsu dot edu and his team at NMSU. SeWeR is SEquence Analysis using WEb Resources. It has web based Sequence Analysis. SeWeR is an integrated portal to common web-based services in bioinformatics.
2003-09-27Add/enable profitjschauma1-1/+2
2003-09-27Initial import of profit, one of the many packages provided byjschauma5-0/+119
brook at biology dot nmsu dot edu and his team at NMSU. ProFit (pronounced Pro-Fit, not profit!) is designed to be the ultimate program for performing least squares fits of two protein structures. It performs a very simple and basic function, but allows as much flexibility as possible in performing this procedure. Thus one can specify subsets of atoms to be considered, specify zones to be fitted by number, sequence, or by sequence alignment.
2003-09-27Add/enable mummerjschauma1-1/+2
2003-09-27Initial import of mummer, one of the many packages provided byjschauma5-0/+137
brook at biology dot nmsu dot edu and his team at NMSU. Mummer is a system for aligning whole genome sequences. Using an efficient data structure called a suffix tree, the system is able rapidly to align sequences containing millions of nucleotides whether in complete or draft form. MUMmer can also align incomplete genomes; it handles the 100s or 1000s of contigs from a shotgun sequencing project with ease, and will align them to another set of contigs or a genome using the NUCmer program included with the system.
2003-09-26Add trailing slash to HOMEPAGE to placate pkglint.wiz1-2/+2
2003-09-26Remove autogenerated file.wiz1-95/+0
2003-09-26Add/enable hmmer.jschauma1-1/+2
2003-09-26Initial import of hmmer, one of the many packages provided byjschauma5-0/+74
brook at biology dot nmsu dot edu and his team at NMSU. HMMER is an implementation of profile HMM methods for sensitive database searches using multiple sequence alignments as queries. HMMER takes multiple sequence alignement as input and builds statistical model called "Hidden Markov Model" which can be used as a query into a sequence database to find and/or align additional homologues of the sequence family.
2003-09-26Add/enable gp.jschauma1-1/+2
2003-09-26Initial import of gp, one of the many packages provided byjschauma7-0/+227
brook at biology dot nmsu dot edu and his team at NMSU. GP is a set of small utilities written in ANSI C to manipulate DNA sequences in a Unix fashion, fit for combining within shell and cgi scripts.
2003-09-26Add/enable pdbalign.jschauma1-1/+2
2003-09-26Remove align after reimporting it as pdbalign. Sorry 'bout that.jschauma8-117/+0
2003-09-26Rats. Re-import ``align'' as ``pdbalign'', as that's the package's name.jschauma8-0/+117
Given a GCG multiple sequence alignment file (a GCG MSF file), which a includes a sequence of known structure, the program pdbalign maps the sequence variability onto the known structure. The central premise is of course, that for a closely related family of proteins (sequence ID > 40%) the 3-D structures will not be significantly different.pdbdist calculates the distance from each atom in the pdb file to each atom in the ligand and records the minimum in the temperature field for that atom record.distalign reads the output from pdbdist and also the original GCG MSF file and produces an MSF file annotated with a measure of sequence variability and the distance of the residue at that position (of the sequence of known structure) from the ligand.
2003-09-26Initial import of pdbalign-20030812, one of the many packages provided byjschauma8-0/+117
brook at biology dot nmsu dot edu and his team at NMSU. Given a GCG multiple sequence alignment file (a GCG MSF file), which a includes a sequence of known structure, the program pdbalign maps the sequence variability onto the known structure. The central premise is of course, that for a closely related family of proteins (sequence ID > 40%) the 3-D structures will not be significantly different.pdbdist calculates the distance from each atom in the pdb file to each atom in the ligand and records the minimum in the temperature field for that atom record.distalign reads the output from pdbdist and also the original GCG MSF file and produces an MSF file annotated with a measure of sequence variability and the distance of the residue at that position (of the sequence of known structure) from the ligand.
2003-09-17get rid of USE_GCC2/3 in pkg Makefiles, and set GCC_REQD orgrant1-2/+2
USE_PKGSRC_GCC as appropriate, as this is handled by compiler.mk now.
2003-09-12kill all references to gcc.buildlink2.mk and compiler.mk, and definegrant1-2/+2
USE_GCC2 or USE_GCC3 where appropriate. the functionality of the old gcc.buildlink2.mk has been rolled into compiler.mk now, which is automatically used. more changes to come later...
2003-08-30Update to version 1.6.jtb7-102/+44
New features in chemtool 1.6 - universal import mode based on BABEL (both openbabel and babel supported) - Formula weight calculator now handles all main group elements and the first row of transition elements, and accepts greek phi as phenyl substituent. - Movable hexagonal or square grid backdrop - Improved SVG export, optional preview bitmaps in EPS export, optional EMF export - Cursor key support for pixel-precise drawing and moving - The cleanup function now corrects bonds that deviate from ideal horizontal or vertical orientation by a single pixel - Color support (bonds and text can be red,green,blue,cyan,magenta or yellow). - Default bond length now configurable, additional grid positions at two and three times this length added - Added a brief help text to accompany the 'About' window in the 'Help' menu. - Added alternate text font (Times Roman) - An attachment site can be marked before saving a molecule or fragment, which act as reference point for adding this fragment to other molecules (previously, this had to be the first atom in a file). Attachment sites are marked in the preview window by a small x. - Background color can now be chosen for screen display and EPS export, and drawing whiteout boxes under labels is now an option ( off by default !). - Text at 8,10,12,14,17,20 and 24pt can now coexist in a drawing. - Increased allowed label length to 100. - Improved rendering of dashed wedge and dotted lines - Improved text kerning in xfig-based print and export. - It is now possible to place an auto-incrementing counter at the cursor position for numbering sites. - Changed double bond drawing code to no longer switch sides depending on drawing (or rotation) angle. (As a result of this, some older drawings will need fixing) - Rescaling a molecule now also scales its labels. Downscaling beyond zero size (causing strange inversions) is no longer possible. - Renamed the "Orbitals" template menu to "Symbols" and added "plus", "minus" and a rearrangement arrow to it. - Added two new bond types, a triple bond with all three lines equal, and a quadruple bond.
2003-08-11Update to 9.0.wiz4-12/+12
Changes: This release introduces the new USDA Nutrient Database, SR16, which has 6,661 foods and 125 nutrients, and includes an automatic conversion feature so that NUT 8.x installations can preserve existing meal records and have them interpreted with the latest USDA database.
2003-07-21COMMENT should start with a capital letter.martti1-2/+2
2003-07-17s/netbsd.org/NetBSD.org/grant3-6/+6
2003-07-13PKGREVISION bump for libiconv update.wiz1-2/+2
2003-07-12Update to 8.10. Not sure what has changed since 4.x, but I'd guess ratherwiz6-80/+51
much.
2003-06-11Update for the fact that 'arm' ports have been called NetBSD-*-arm for a whileabs1-2/+2
now and not NetBSD-*-arm32. Changes include one or more of: - Change MACHINE_ARCH == arm32 to also match arm - Where ONLY_FOR_PLATFORM includes NetBSD-*-arm32, add NetBSD-*-arm - Where BROKEN or worked around for arm gcc bugs, set USE_GCC3 The last may shake out a few more broken packages the next bulk build.
2003-06-02Use mk/gcc.buildlink2.mk rather than gcc/buildlink2.mk so lang/gcc3abs1-2/+2
is accepted. Suggested by Grant.
2003-06-02Use tech-pkg@ in favor of packages@ as MAINTAINER for orphaned packages.jschauma3-6/+6
Should anybody feel like they could be the maintainer for any of thewe packages, please adjust.
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