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2005-02-22Add RMD160 digests in addition to the SHA1 ones.agc20-20/+40
2004-12-30Update to 10.14:wiz2-5/+5
This release changes some computations to make the nutrient values for packaged foods added from food labels more accurate.
2004-12-26Update to 10.13.wiz2-5/+5
New in 10.13: This release fixes the incorrect "Analyze Meals" screen header that says "Record Meals". It fixes the function that guesses recipes of packaged foods, which worked properly but had a variable and a constant of the same value reversed so that user modifications to increase the precision would fail. New in 10.12: The function that guesses the recipes of packaged foods based on the nutrition and ingredient statements has been rewritten. A much faster implementation is achieved by quantizing all the values. This algorithm is a search through all possible recipes because simultaneous equations do not work for this problem. New in 10.11: This release contains a fix for bad Pumpkin Pie values, specifically, null "carb/prot/fat" values for foods for which the USDA does not supply this data. New in 10.10: This release fixes a bug in the function that allows foods to be added from food labels. The carb/protein/fat field was not correct because calories-per-gram fields were not explicitly set. New in 10.9: This release contains a fix for wrong calories-per-gram values when the program starts because it read a float as an integer from the options file. New in 10.8: This release contains many small changes, among them an update of the fatty acid reference values, a removal of the hard-to-obtain "Alaska Native" foods as food suggestions, and a closer approximation when protein or carbs are expressed as a percentage of calories. New in 10.7: This release changes how personal options are saved to disk so that personal options will never be lost across program upgrades. Changes have also been made to how the program upgrades itself on dual-boot systems, and levels of the Omega-3 reference values have been modified. New in 10.6: This release fixes minor bugs related to the "Carb/Prot/Fat" field. Values for alcoholic beverages have been corrected. Also, an error was fixed that led to different fat values based on whether the user input changes to the protein and carb "Daily Values" in percentages or grams. If the two operations led to the same number of grams of protein and carbs, there should have been no difference in the fat value. New in 10.5: This release adjusts the Omega-3 default reference values, for which there are no U.S.A. Daily Values, so that EPA and DHA will be higher and alpha-linolenic acid a little lower. New in 10.4: This release contains two minor design changes to the new feature of the last release, which automatically chooses a meal analysis period. Always choosing integer days, the new version picks the day closest to the target rather than the day before; and allows no period shorter than five days, instead of four. New in 10.3: don't know.
2004-12-05Update to version 3.15. From David Price in PR#28305.cube4-13/+12
3.05 - Added -k option to show-coords to only display the best frame for overlapping PROmer alignments. Added --[no]optimize option to nucmer and promer to allow alignment score optimization to be turned off, i.e allow alignments to extend to the ends of sequences rather than backtracking to optimize the alignment score. Updated docs. 3.06 - Added -F and -h option to mummer. Changed -mumcand option to -mumreference, but left deprecated -mumcand option available. Added -maxmatch option to mummer, and changed default behavior of all applicable programs to -mumreference (nucmer, promer and mummer). Added -w (screen width) option to show-aligns. Updated documentation with all of these changes. 3.07 - Added the 'mapview' plotting utility and appropriate documentation. Fixed origin wrap shadowing bug in show-tiling when using the -c option. NUCmer and PROmer now convert to absolute paths to avoid ambiguity. 3.08 - Added MUMmer examples web docs which gives brief walkthroughs 3.10 - Now Mac OSX compatible. Added -R option to show-tiling. 3.11 - Fixed bug show-tiling -R option. Added some mapview changes. Fixed the issue with mummerplot being to faint. 3.12 - Added the --nosimplify option to nucmer for repeat searching. Fixed a bug in nucmer and promer. Fixed rounding issue in show-coords. Updated citations. 3.13 - Added -d, -g, -G and -o options to show-coords and updated documentation. Fixed bug in show-tiling -R 3.14 - Fixed gcc3 compilation bug 3.15 - Fixed --nooptimize in nuc/promer.
2004-12-03Rename ALL_TARGET to BUILD_TARGET for consistency with other *_TARGETs.wiz5-10/+10
Suggested by Roland Illig, ok'd by various.
2004-12-01Update hmmer to 2.3.2. Patch provided by David Price in PR pkg/28483.minskim2-7/+8
While here, enable pkgviews installation. Changes: -:- hmmsearch intermittently failed on Swissprot searches, on some platforms (reports on AMD/Linux; Mac OS/X). (#h25) -:- hmmpfam memory allocation strategy did not guarantee RAMLIMIT, and could explode to very large allocations when searching with large sequences. (#h26) -:- technical improvements in handing dsq's (digitized sequences); "bug" has no visible effects, except when compiling on different platforms. (#h27) -:- typo fix in P7Forward() recursion; typo may have had minor effect on calculated scores. (#h28) -:- hmmalign now includes --outformat and --oneline option for specifying different output alignment formats than the default Stockholm.
2004-10-03Libtool fix for PR pkg/26633, and other issues. Update libtool to 1.5.10tv1-1/+2
in the process. (More information on tech-pkg.) Bump PKGREVISION and BUILDLINK_DEPENDS of all packages using libtool and installing .la files. Bump PKGREVISION (only) of all packages depending directly on the above via a buildlink3 include.
2004-08-23Modify patch-aa to replace -e tests with -d tests, so install will workben2-7/+11
on IRIX. Addresses PR#26647.
2004-08-23Remove unnecessary -p following MKDIR commands.ben2-6/+6
2004-08-19Fix patch-aa so gp installs under IRIX. Addresses PR#26647.ben2-4/+73
Patch supplied by Georg Schwarz.
2004-08-19Update to glimmer-2.13, thanks to cngo@nmsu.edu.ben2-7/+7
CHANGELOG, 12 October 2003 add -X option to glimmer2, to allow orfs extending off ends of sequence to be scored. Also fix bug affecting -p and -o options when user chose zero overlap.
2004-08-18Update to 10.2:wiz2-5/+5
This release fixes a computation error in the value for monounsaturated fat when the user sets a fat level higher than the Daily Value.
2004-08-17Add DIST_SUBDIR because contents changed while archive filename did not.ben2-4/+5
2004-08-16Update phylip to version 3.61. No ChangeLog included. However there is aben5-71/+104
very long list of bux fixes since 3.57 at: http://evolution.genetics.washington.edu/phylip/bugs.html
2004-08-16Update fastDNAml to version 1.2.2. Notable changes include:ben2-22/+13
* Now under GPL * Convert to function definitions with parameter type lists * General code clean-up
2004-08-16Update to clustalw 1.83. Changes since 1.8 include:ben3-9/+9
* The FASTA format has been added to the list of alignment output options. * It is now possible to save the residue ranges (appended after the sequence names) when saving a specified range of the alignment. * The efficiency of the neighour-joining algorithm has been improved. This work was done by Tadashi Koike at the Center for Information Biology and DNA Data Bank of Japan and FUJITSU Limited. Some example speedups are given below : (timings on a SPARC64 CPU) No. of sequences original NJ new NJ 200 0' 12" 0.1" 500 9' 19" 1.4" 1000 XXXX 0' 31" * ClustalW now returns error codes for some common errors when exiting. This may be useful for people who run clustalw automatically from within a script. Error codes are: 1 bad command line option 2 cannot open sequence file 3 wrong format in sequence file 4 sequence file contains only 1 sequence (for multiple alignments) * Alignments can now be saved in Nexus format, for compatibility with PAUP, MacClade etc. For a description of the Nexus format, see: Maddison, D. R., D. L. Swofford and W. P. Maddison. 1997. NEXUS: an extensible file format for systematic information. Systematic Biology 46:590-621. * Phylogenetic trees can also be saved in nexus format. * A ClustalW icon has been designed for MAC and PC systems.
2004-08-16Make hmmer honor $MKDIR for cross-platform install.ben3-10/+44
Addresses pr#26650 from Georg Schwarz.
2004-08-15Update HOMEPAGE, addresses PR#26667 from Georg Schwarz.ben1-2/+2
2004-08-15Update to 10.1:wiz4-30/+35
10.1: This release adds a fix for zero values that display as no data. 10.0: This release updates the USDA Nutrient Database to version SR17, and allows current NUT installations to have their existing meal records reinterpreted with the new database. 9.20: This release optimizes the new code of the last release, the focus of which was distinguishing no data from zero in the USDA database. 9.19: The program now distinguishes between zero values and no data in the USDA database, and uses this information to produce a new screen that lists foods high in some nutrient while minimizing some other nutrient. 9.18: This release contains revisions to the polyunsaturated fatty acid reference values and how they scale up as fats increase and carbs decrease. 9.17: This release provides what may be more reasonable or optimal default settings for fat percentages when the user sets the program for low carb. 9.16: This release contains bugfixes for a segmentation fault which occurred when entering a control-D and a monounsaturated fat reference value that was too high. 9.15: This release makes serving sizes more consistent among food groups. It adds functions to change the default serving size, and to sort foods by nutrients per serving. 9.14: This release adds support for an optional database subdirectory, allowing the user to easily maintain multiple databases, for multiple family members, for instance. It also adds display of non-fiber carbohydrate grams ("net carbs") on the main analysis screen. 9.13: The program now allows commercial foods that have a nutrition label and an ordered ingredients statement to be added to the food database. An approximation to a food's recipe is found that best fits the criteria and the recipe is analyzed to provide information about the additional nutrients not stated on the nutrition label. 9.12: [unknown]
2004-08-14Update HOMEPAGE and MASTER_SITES to new locations.ben2-6/+6
Update distinfo for new archive. Only minor bug fixes, no version change. For a detailed diff, see: ftp://ftp.netbsd.org/pub/NetBSD/misc/ben/profit-2004-08-14.txt This addresses PR#26656 from Georg Schwarz.
2004-08-14Use buildlink3. Requested by Georg Schwarz in PR pkg/26654.snj1-1/+2
2004-06-11don't call "install -d" with multiple directory arguments.grant2-6/+16
2004-04-11Convert to buildlink3.snj5-11/+11
2004-04-11Convert to buildlink3 and correct a spelling error in DESCR.snj2-3/+3
2004-04-11Convert to buildlink3.snj6-12/+12
2004-04-10bl3ify and enable pkgviews installation.minskim1-3/+5
2004-04-10Disable gnome support explicitly. Otherwise this package installsminskim1-1/+3
more files on platforms where /usr/share/mime-info exists.
2004-03-10Update to 9.11:wiz3-10/+16
New in 9.11: Because the program uses the approximation of 4 calories per gram for carbohydrate and protein to analyze meals according to the "Daily Value" -- although real food has various values for calories per gram -- the program now refigures fat percentage values at each analysis so that when calories, carbs, and protein are each at exactly 100%, fat will be also. New in 9.10: This release fixes a buffer overflow in the food selection function which caused the program to not find certain foods even though they existed in the database. New in 9.9: A bug has been fixed in which during food selection, the program lost the value of the food name key. Also, some of the program's reference values for the essential fatty acids have been modified. New in 9.8: The program now defaults to either grams or ounces, depending on the weight unit the user enters to specify servings. A bug in handling customary meal names that are too long has been fixed. New in 9.7: The program computes essential fatty acid reference values based on the user's diet. Prior releases aimed toward a particular balance of Omega-6 and Omega-3. This release allows the user to specify the balance between Omega-6 and Omega-3 without having to determine the amount of the individual fatty acids. New in 9.6: The program is now capable of understanding food names in simple English, such as "fried chicken" and "mashed potatoes." This is accomplished by including the list of abbreviations the USDA uses and by successively searching for each tokenized term, whatever the order in the USDA name.
2004-02-18Do not install files not specified in PLIST.minskim1-5/+6
While here, remove trailing whitespace and enable pkgviews installation.
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.
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