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PR/43775 CVS commit: pkgsrc/biology/puzzle

The following reply was made to PR pkg/43775; it has been noted by GNATS.

From: OBATA Akio <>
Subject: PR/43775 CVS commit: pkgsrc/biology/puzzle
Date: Sun, 19 Sep 2010 08:38:14 +0000

 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 !!!
 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 
                        - 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 !!!
 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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