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2005-08-26Changes 1.6.7:adam4-35/+36
- Fixed several serious bugs related to label rendering and printing that occured when chemtool was built with GTK 2 instead of GTK 1.2 (see ChangeLog for details) - SVG export now adds a namespace header as required by current builds of the firefox browser - SVG export now uses color values instead of color names for better SVGT compatibility - The separation between the lines of multiple bonds is configurable - The keys of the numeric keypad now create two dots instead of a line for free electron pairs when the Shift key is pressed - Two new bond types for drawing filled and unfilled p orbital lobes - chemtool now checks for fig2sxd (sourceforge.net) and offers to export to OpenOffice Draw format when it is present. - rpm packages did not install the dutch locale file. Chnges 1.6.6: - Fixed bug in molfile preview that caused an immediate crash in 1.6.5 - Made drawing of wiggly bonds work again
2005-08-06Bump the PKGREVISIONs of all (638) packages that hardcode the locationsjlam1-1/+2
of Perl files to deal with the perl-5.8.7 update that moved all pkgsrc-installed Perl files into the "vendor" directories.
2005-07-16Remove some unnecessarily strong dependencies on perl that resultedjlam1-3/+2
from including perl5/buildlink3.mk. These packages just need the Perl interpreter, and can just add "perl" to USE_TOOLS instead.
2005-07-15Drop distinction between PKGSRC_USE_TOOLS and USE_TOOLS by makingjlam2-4/+4
PKGSRC_USE_TOOLS go away. There is now only a single USE_TOOLS variable that specifies all of the tools we need to build/run the package.
2005-07-13Turn PERL5_PACKLIST into a relative path instead of an absolute path.jlam1-2/+2
These paths are now relative to PERL5_PACKLIST_DIR, which currently defaults to ${PERL5_SITEARCH}. There is no change to the binary packages.
2005-06-19Prevent paths to the build directories from being included in the package.kristerw3-2/+18
Bump PKGREVISION.
2005-06-16Create directories before installing files into them.jlam12-12/+29
2005-06-01Massive cleanup of buildlink3.mk and builtin.mk files in pkgsrc.jlam2-4/+3
Several changes are involved since they are all interrelated. These changes affect about 1000 files. The first major change is rewriting bsd.builtin.mk as well as all of the builtin.mk files to follow the new example in bsd.builtin.mk. The loop to include all of the builtin.mk files needed by the package is moved from bsd.builtin.mk and into bsd.buildlink3.mk. bsd.builtin.mk is now included by each of the individual builtin.mk files and provides some common logic for all of the builtin.mk files. Currently, this includes the computation for whether the native or pkgsrc version of the package is preferred. This causes USE_BUILTIN.* to be correctly set when one builtin.mk file includes another. The second major change is teach the builtin.mk files to consider files under ${LOCALBASE} to be from pkgsrc-controlled packages. Most of the builtin.mk files test for the presence of built-in software by checking for the existence of certain files, e.g. <pthread.h>, and we now assume that if that file is under ${LOCALBASE}, then it must be from pkgsrc. This modification is a nod toward LOCALBASE=/usr. The exceptions to this new check are the X11 distribution packages, which are handled specially as noted below. The third major change is providing builtin.mk and version.mk files for each of the X11 distribution packages in pkgsrc. The builtin.mk file can detect whether the native X11 distribution is the same as the one provided by pkgsrc, and the version.mk file computes the version of the X11 distribution package, whether it's built-in or not. The fourth major change is that the buildlink3.mk files for X11 packages that install parts which are part of X11 distribution packages, e.g. Xpm, Xcursor, etc., now use imake to query the X11 distribution for whether the software is already provided by the X11 distribution. This is more accurate than grepping for a symbol name in the imake config files. Using imake required sprinkling various builtin-imake.mk helper files into pkgsrc directories. These files are used as input to imake since imake can't use stdin for that purpose. The fifth major change is in how packages note that they use X11. Instead of setting USE_X11, package Makefiles should now include x11.buildlink3.mk instead. This causes the X11 package buildlink3 and builtin logic to be executed at the correct place for buildlink3.mk and builtin.mk files that previously set USE_X11, and fixes packages that relied on buildlink3.mk files to implicitly note that X11 is needed. Package buildlink3.mk should also include x11.buildlink3.mk when linking against the package libraries requires also linking against the X11 libraries. Where it was obvious, redundant inclusions of x11.buildlink3.mk have been removed.
2005-05-25Add RMD160 checksum.wiz1-1/+2
2005-05-24Removed an empty line.rillig1-2/+1
2005-05-23Removed trailing empty line.rillig1-2/+1
2005-05-23Removed trailing white-space.rillig7-24/+24
2005-05-22Remove USE_GNU_TOOLS and replace with the correct USE_TOOLS definitions:jlam3-6/+6
USE_GNU_TOOLS -> USE_TOOLS awk -> gawk m4 -> gm4 make -> gmake sed -> gsed yacc -> bison
2005-05-15Note where gzip or gunzip is required by the package since it isn'tjlam2-2/+4
required by default any longer in bsd.pkg.mk under the new tools framework.
2005-05-07Do not add CC to MAKE_FLAGS. This was not quoted correctly, and thekristerw1-3/+1
pkgsrc infrastructures already adds this anyway.
2005-05-07Sort to make pkglint happy.kristerw1-2/+2
2005-05-07Sort file names to fix lint warnings.kristerw1-4/+4
2005-05-07Do not add CC to MAKE_FLAGS. This was not quoted correctly, and thekristerw1-2/+1
pkgsrc infrastructures already adds this anyway.
2005-04-19Enable pkgviews installation.minskim1-1/+5
2005-04-19Update to 10.18. Should fix PR 27404.wiz4-16/+16
10.18: This release contains a fix for the floating point exception on NetBSD-2.0/alpha. 10.17: This release corrects the formatting of the man page and restores the correct alpha-linolenic acid reference value, which was too low in the last release. 10.16: This release fixes a segfault that occurs when analyzing added and subtracted foods that total zero calories. 10.15: This release completes the changing of all calculations to substitute user averages for program constants in the values of calories per gram of carb, fat, and protein, and of the percentage of total fat that is fatty acids. This means that personal options in terms of percentages and ratios will be more precise.
2005-04-11Remove USE_BUILDLINK3 and NO_BUILDLINK; these are no longer used.tv15-30/+15
2005-04-05Convert to bl3, untested.wiz1-3/+2
2005-03-30Add "USE_X11=yes".kristerw1-1/+2
2005-03-27Add and enable arka.jmmv1-1/+2
2005-03-27Initial import of arka, version 0.11:jmmv6-0/+101
Arka is a program that serves as a graphical interface for the programs from the GP package. Furthermore, it has some interesting functions of it's own. The main scope of the program is the manipulation and visualisation of DNA / RNA / protein sequences. This package comes from pkgsrc-wip; created by <hdp at cs.nmsu.edu> with several changes by me.
2005-03-27Fix MASTER_SITES.jmmv1-2/+2
2005-03-26Add and enable lucy.minskim1-1/+2
2005-03-26Import lucy from pkgsrc-wip. Packaged by David Price and modified by me.minskim6-0/+113
A Sequence Cleanup Program. Lucy is a utility that prepares raw DNA sequence fragments for sequence assembly,possibly using the TIGR Assembler. The cleanup process includes quality assessment, confidence reassurance, vector trimming and vector removal. The primary advantage of Lucy over other similar utilities is that it is a fully integrated, stand alone program.
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