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CVS commit: pkgsrc/biology/puzzle
Module Name: pkgsrc
Committed By: obache
Date: Sun Sep 19 08:38:14 UTC 2010
Modified Files:
pkgsrc/biology/puzzle: Makefile PLIST distinfo
Log Message:
Update puzzle to 5.2.
Based on PR#43775 by Kamel Derouiche.
5.2 14.07.2004 - Version 5.2 !!!
NEW RELEASE
===========
5.2.rc17 14.07.2004 - Manual sources moved out of the package
- numerous changes in the manual
5.2.rc16 12.07.2004 - Makefile.am: double distclean rule removed
- fflush added before mygets() - because of Windows
- manual spell-checked
- '-consmrel' fixed
- usage message extended
5.2.rc15 09.07.2004 - many changes to the manual
5.2.rc14 01.07.2004 - test suite checked, notice about results added
5.2.rc13 01.07.2004 - a number of small fixes (alloc and dealloc in epe)
- convergence output for user branches fixed
- G-T rate output precision fixed
- tests checked and fixed
5.2.rc12 30.06.2004 - branch length convergence output corrected for
user set branch lengths (i.e. no estimate)
- avergedist updated: output of min/max/var/std.dev.
- tstvratio and yrtsratio - no output for GTR
- some future cmdline flags added to help
- -prefix, -sub50, -randseed moved to usage output
- -randseed=# added
- release date changed in code
5.2.rc11 18.06.2004 - flags to set epsilon values added for debugging
(dependent on USE_ADJUSTABLE_EPS compiler switch)
19.06.2004 - quartet percent computation fixed:
quartet sums moved qinfomatr[0] -> qinfomatr[8]
qinfomatr[0]=missing qs. (release 5.2.rc9)
- character state output added to R/Q matrix output
- average computation of dist-matrix changed:
mean=average, variance, std deviation
TODO: proper output / use Korbis S.E. method
25.06.2004 - GTR model ready, menu order HKY, TN, GTR, (SH), HKY
29.06.2004 - many changes to the manual
5.2.rc10 11.06.2004 - fixed no quartets in parameter estimtion for <4 seqs
15.06.2004 - computation of Bayesian weights moved into
subroutine loglkl2weight.
- use subroutine loglkl2weight in parallel code
-> fixing division by zero bug
5.2.rc9 11.06.2004 - sequence number check for <4 and >257 added
<4 - no quartet methods available
>257 - no quartet puzzling available
- counting for missing quartets added for parallel
message checking (TODO: handling and checking)
- output of root branch name added for clock analysis
(sequence name or "internal branch")
5.2.rc8 04.05.2004 - tree tests move to treetest.c/treetest.h
- comments added
- typo corrected (suset -> subset)
08.06.2004 - ELW: continue counting p, when significantly worse
- 1sKH/2sKH: restrict tests to 3 digits (0.00)
(test behaviour: seems not to use some trees (KH),
see above - used, but too low variance)
5.2.rc7 12.02.2004 - corrected typos in usage/README
20.02.2004 - cmdline: prefix flag fixed
22.02.2004 - '-wsr/-wsl' flags fixed: output file
and file name output
5.2.rc6 25.11.2003 - 'FPRINTF...' changed to 'fprintf(STDOUT,'
- strcpy added in openfile-routines
5.2.rc5 25.11.2003 - filename length chack added
- typo FILENAMELENTH corrected
5.2.rc4 19.11.2003 - minor corrections: int/uli comparisons
- SPRNG added to src/sprng
- src/sprng autoconf/automake setup
- Parallel Parameter Estimation (JPDC, Ekki 1)
5.2.rc3 07.11.2003 - WAG Matrix code/docu corrected (Goldman)
TODO: remove additional output for printrmat
TODO: make PEPS* smaller to have better accuracy
in parameter estimation.
5.2.rc2 01.09.2003 - bug from 5.1.pl29 found and eliminated
alloc size wrong: worked if Maxsubset<=Maxspc
TODO: remove out-commented debug messages
5.2.rc1 20.08.2003 - first release candidate for tree-puzzle 5.2
CODE FREEZE
===========
5.1.pl30 20.08.2003 - naming convention changed for manual name input to
use FILENAME.puzzle, ...
5.1.pl29 23.07.2003 - new compiler warnings fixed
- index error naming fixed
- debugging of matrix based permutation (not finished)
5.1.pl28 01.07.2003 - cmdline flags to switch off ml branch lengths
(-notreelh), tree tests (-notreetest)
5.1.pl27 24.06.2003 - output quartet support for incorporated split in
report file
5.1.pl26 06.06.2003 - menu order of tree reconstruction methods altered to
QP, user tree, consensus, dist (no tree)
(last two switched)
5.1.pl25 05.06.2003 - small changes to fix compiler warnings
5.1.pl24 04.06.2003 - changes from benchmark-branch merged:
debug output removed
- checktime fixed: sumtodo <-> done for quartets
5.1.pl23 26.05.2003 - puzzle.c: CONSENSUS -> QUARTPUZ,
allocated unnecessary memory
- additional malloc-checks added (if buffer == NULL)
01.06.2003 - mlmode conditions with readable constants (ml2.c,ml.h)
- garbage collection in tree2bipart/subtree2bipart
5.1.pl22 16.05.2003 - fixing Array Bound Read in fputid
(bug had no effect, but was read before check)
- garbage collection completed in p-step algorithms
and node-label (free_tree/internalnode),
trueIDtmp (allpstep),
- small fix in test script and rebuild of check-files
5.1.pl21 14.05.2003 - fixing free of all allocations in puzzling step
(mrca, recur, split, orig)
5.1.pl20 05.05.2003 - small fix in recursive Alg. (recur.c)
- debug output removed
- cross check removed from (recur.c,mrca.c)
5.1.pl19 27.04.2003 - recursive Alg. (recur.c) fixed:
edge cluster has not to be reconstructed after
adding new leaves only updated.
- debug output removed from recur.c, split.c
- MRCA-based (mrca.c) finished
5.1.pl18 26.04.2003 - recursive (recur.c) finished
TODO: remove debug output
- MRCA (mrca.c) startet
5.1.pl17 25.04.2003 - split-based (split.c) finished
TODO: remove debug output
- recursive (recur.c) startet
5.1.pl16 22.04.2003 - orig pstep alg: updating of edgemap outsourced to
updateedgemap_orig
- writeOTU_orig, writetree_orig, resetedgeinfo_orig,
minimumedgeinfo_orig:
_orig removed, since independent of algorithm type
- onepstep: _orig added (onepstep_orig)
- time check/status output moved to checktime routine.
added to ml step of parallel version
- split.c temporarily added to release
5.1.pl15 18.04.2003 - trueID dependent procedures 'de-trueID-ed'
trueID saved in the tips of the tree.
5.1.pl14 10.04.2003 - consensus stuff moved to consensus.h/.c
- unique tree sorting moved to treesort.h/.c
- changes to pstep-split.h/.c
- changed names of procedures using trueID to
*_trueID
5.1.pl13 07.04.2003 - subsetmatr.[hc] added to process missing data
analyses. (old version, functions in puzzle2)
- deglobalized: guessdatatype, readsequencefile,
getsizesites, initid, getseqs
removed obsolete: getdataset
- moved: output of taxa after input
- computation of Maxbrnch moved from readsequencefile
to inputandinit
- readsubsetfile, permutetaxa_ss added, '-rssm' works
- empty quartets fixed in checkquartet
missing data -> OK, HALT error otherwise
5.1.pl12 04.04.2003 - tests: check-qp-clock regenerated, changes in
Makefile.am and template-test
- obsolete stuff removed: global trueID_orig + alloc,
inittree_orig/freetree_orig from PP_SendDoPermutBlock
PP_slave_do_puzzling (ppuzzle), global _orig
variables (pstep), makenewsplitentries (old),
kh_test (old)
- column variable in tree output routines deglobalized
- copyright headers added to pstep.[hc]
- pstep copied to pstep-{split | mrca | recursive}
- implementation of pstep-split.[ch] started
(done: structure/init, todo: remove _orig stuff)
5.1.pl11 03.04.2003 - tests/Makefile.am: 'build-puzzle failed' fixed
- some changes in test script template
- cleanup: removed obsolete routines
- puzzle module: makenewsplitentriesnew
- ppuzzle module: PP_do_puzzling, PP_SendPermut,
PP_RecvPermut, PP_SendSplits, PP_RecvSplits
- deglobalized: makenewsplitentries, makepart,
computebiparts, copysplit
- parallel puzzling step based on allpstep, onepstep
- time check/status output added to parallel version
(inaccurate since current slave progress not known)
- TIMECHECK_INTERVAL for setting time interval
of status output in ML/puzzling step
- Header when printing 1 PAM rate matrix (-printrmat)
- final pstep copied to pstep-{split | mrca | recursive}
5.1.pl10 02.04.2003 - tests/Makefile.am fixed (TODO: build-puzzle.test)
- Dates/Version adjusted: April 2003/TREE-PUZZLE 5.2
- Dates/Version fixed in doc/*.html, doc/*.tex
- number added to outgroup(menu)/sequence(start) output
- Time measurement only done after each completed
intermediate tree to reduce the the number from
O(Numtrial*n^4) to O(Numtrial) -> less overhead,
but 15min met less accurate.
- quartet support output for splits added in
writeoutputfile for later use (TODO: '#if0'ed)
- (sequential) puzzling step moved from puzzle1.c
to pstep.c: allpstep, onepstep
TODO: parallel puzzling step in ppuzzle.c
(works but with old PP_slave_do_puzzling)
5.1.pl9 31.03.2003 - consensus construction added to menu
- support value computation fixed for phylip tree,
wrong divisor used in consensus
- test directory/Makefile.am/tests created
(make check)
5.1.pl8 30.03.2003 - puzzling step proc's: most variables 'deglobalized'
5.1.pl7 26.03.2003 - original puzzling step out-sourced to pstep-orig.c
and pstep-orig.h
pstep.c, pstep.h (and above) added to Makefile.am
5.1.pl6 25.03.2003 - '-usebranch' option added fr later use
- 'SONJA' added for external parameter estimation
5.1.pl5 24.03.2003 - ml branch length estimation added to consensus option
(todo: plausibility check - is tree file available)
- output for reportfile fixed
- output of likelihood to clocklike tree in treefile
added/fixed
5.1.pl4 21.03.2003 - consensus option added to compute usertree consensus
(only consensus is computed and printed to stdin)
- usertreefile PREFIX fixed
5.1.pl3 20.03.2003 - TP_MAX_EXP_DIFF=b-a>0 introduced, such that
(1.0+exp(a-b) == 1.0) to avoid the computation
as well as possible FPE, when a-b gets very small.
- flag '-prefix=XXX' added: use 'XXX' as filename
prefix instead of 'Infilename'
5.1.pl2 05.12.2002 - PP_Finalized before exit in parallel programs.
5.1.pl1 05.12.2002 - FPE in Brent's algorithm fixed: ()/0, when x=w=v.
5.1 05.11.2002 - Version 5.1 !!!
To generate a diff of this commit:
cvs rdiff -u -r1.11 -r1.12 pkgsrc/biology/puzzle/Makefile
cvs rdiff -u -r1.3 -r1.4 pkgsrc/biology/puzzle/PLIST
cvs rdiff -u -r1.5 -r1.6 pkgsrc/biology/puzzle/distinfo
Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.
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