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.
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.
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.
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.
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.
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.
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.
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.
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.
* 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.
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]
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.
