Subject: CVS commit: pkgsrc/biology/puzzle
From: OBATA Akio
Date: 2010-09-19 10:38:14
Message id:

Log Message:
Update puzzle to 5.2.
Based on PR#43775 by Kamel Derouiche.

5.2       14.07.2004    - Version 5.2 !!!


5.2.rc17  14.07.2004    - Manual sources moved out of the package
			- numerous changes in the manual

5.2.rc16  12.07.2004    - 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/
			- 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


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
			- writeOTU_orig, writetree_orig, resetedgeinfo_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

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 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/ '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/ 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/ 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

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

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 !!!