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PR/43395 CVS commit: pkgsrc/biology/clustalw

The following reply was made to PR pkg/43395; it has been noted by GNATS.

From: "Wen Heping" <>
Subject: PR/43395 CVS commit: pkgsrc/biology/clustalw
Date: Thu, 13 Dec 2012 13:27:13 +0000

 Module Name:   pkgsrc
 Committed By:  wen
 Date:          Thu Dec 13 13:27:13 UTC 2012
 Modified Files:
        pkgsrc/biology/clustalw: Makefile PLIST distinfo
 Removed Files:
        pkgsrc/biology/clustalw: MESSAGE
        pkgsrc/biology/clustalw/patches: patch-aa patch-ab patch-interface.c
 Log Message:
 Update to 2.1, from Wen Heping(myself) in PR 43395
 Remove unneeded MESSAGE file
 Upstream changes:
 Version 2.1
 * Fixed bug 196 "clustalx: user feedback about use of secondary structure
   printed to console" - secondary structure is now used if specified
   in Alignment -> Alignment Parameters -> Secondary Structure Parameters
   UserParameters->getGui() should be used when ClustalW code needs to
   know if a function has been called from ClustalX
 * Fixed bug 204 "Nexus alignment format contain invalid line" - the amino
   acid alphabet line has been removed
 * Missing/corrupted file names in ClustalX status messages have been
 * Fixed bug 175 "msf/pileup files cannot be read if sequences names are
   all numbers" - this happened if a line such as
 528244          .......... .......... .......... .......... ..........
   was present in the first block of the file
 * Fixed bug 192 "Alignment in Phylip Format broken for big Alignments"
 * Fixed bug 198 "Warning about divergent sequences gets printed to
   console in ClustalX"
 * Fixed bug 151 "clustalx doesn't switch to profile alignment mode when
   profile12 is given on cmdline"
 Version 2.0.12
 * Fixed bug 189 "Fixed filename used for iteration":
 Now Creating temporary file and added error check
 * Fixed bug 180 "Pairwise NJ tree: final bracket missing"
 * Fixed bug 178 "Seg-fault on 64bit when -quicktree -upgma for sequences with 
high identity":
   Using relative error now to avoid unsafe comparison which led to
   incorrect branching
 * Fixed Bug 176 "iteration doesn't iterate if -usetree is used as well"
 * Fixed bug 162 "percent identity file option in clustalW not working":
 Added -pim as command line option. See help
 * Fixed bug 155 "upgma trees cannot be read"
 * Fixed bug 147 "report duplicate sequences":
  "ClustalW/X now report offending sequences which are empty, duplicates etc
 * Fixed bug 134 "Exit when encountering unrecognized cmdline params":
 ClustalW now exits when encountering invalid values for command line
 arguments instead of just reverting to default values
 * Fixed bug 185 "clustal alignments differ between interactive and commandline 
 window-gap and ktuple initialisation now fixed and made the same
 between commandline and interactive mode
 * Fixed bug 184 "error messages are send to stdout"
 * Fixed bug when weights are 0, and nseq > INT_SCALE_FACTOR in UPGMA
   code (see RootedGuideTree.cpp)
 * General code cleanup
 - Introduced return values where control reached end of non-void function
 - Removed unused variables
 - Removed comparison between signed and unsigned integer expressions
 - Removed deprecated conversion from string constant to char*
 Version 2.0.11
 * fixed file extension bug 166 in interactive mode
 * Fixed bug 169, memory violation for DNA/RNA k-tuple
 * Cut down distance calculation, symmetric matrix
 Version 2.0.10
 * Fixed g++-4.3 compilation errors
 * Added new -quiet command line flag
 * Added new -stats=<file> command line flag
 * Fixed bug 142: command separator can now be mixed "/" and "-" on all 
 * Fixed bug 141: profile merging and saving failed
 * Fixed bug 139: saving of column quality scores
 * Updated help files (new flags, new colour parameter format)
 Version 2.0.9
 * GUI now responding and giving feedback during alignment
 * automatic automake os detection
 * new OS_ define (set by clustalw/configure clustalx/
 * got rid of qt3 dependencies
 * removed QScrollArea bug workaround (fixed in Qt 4.3)
 * Fixed bug 135: Last sequence and last residue not displayed on MacOSX
 * Fixed bug 123: secondary structure profile alignment in clustalX on Mac
 * Fixed g++-4.3 build error (include climits.h)
 Version 2.0.8
 * Implemented maxseqlen cmdline switch
 * Updated help-file
 * Fixed Bug 123: loading profile using gap penalties (ClustalX, Mac)
 * Fixed bug 133: providing profiles on command line fails (ClustalX)
 * Fixed bug 125: Angle bracket inside sequence
 * Fixed bug 129: Early exit on empty sequence
 * Fixed a couple of possible memory leaks
 Version 2.0.7
 * Fixed bug 121: CRLF  in sequence names (Pearson) are not trimmed
 * Fixed bug 122: convert option broken
 * Fixed reopened bug 114: profile alignment input didn't work with new
   getSeqRange routines
 * Fixed bug 119: build with g++ 4.3
 Version 2.0.6
 * Fixed bug 77: fasta input performance issue
 * Fixed bug 114: segfault while doing profile alignment with secondary
   structure mask
 * Removed unncessary id console output in EMBLFileParser.cpp
 * Fixed Bugs 108 and 109 and allowed mixed-case command line options
 Version 2.0.5
 * Fixed bug 105: Disallowed combination of "Reset Gaps"
   and Iteration in GUI
 * Fixed bug 104 "reset all gaps doesn't work"
 * Changed command line separator for Mac to hyphen instead slash
 * Fixed full command line parsing for ClustalX after help flag
 Version 2.0.4
 * Updated URLs in help files
 * Fixed bug 96: error message when loading alignment with identical
   sequence names
 * Made console output look more like 1.83
 * Fixed bug 100: "Scores in clustalw2.0 don't match clustalw1.83"
   getMatrix was called with wrong scaling factor
 * Fixed bug 99: "stars in input not ignored"
   Asterisks were changed to gaps in alignment
 * New command line option: -fullhelp which dumps the built-in help
   file content.
 * Quickfix for bug 94 "quicktree seqfault"
 <= Version 2.0.3
 * Added LICENSE file to distribution
 This file contains the information about commercial licensing of
 clustal as well as FAQ for licensing issues
 * Added README file to distribution
 This is the file that lists the files and directories on the Clustal
 FTP site.  It also includes acknowledgements of people who have
 contributed binaries
 * Removed .pro Qt file from the distribution
 pro-file should be generated anew using qmake and modified according
 to build requirements, i.e. no need for version control.
 * Fixed bug where ClustalX2 was not processing command line args
 * Fixed Segfault on opening helpfile.  Happened on Linux only with -O2
 and when calling binary directly, not using the wrapper
 * Added debian packaging files
 * Added support for help command line flag GUI/xmenus version
 When requesting help file, graphical version of command line help is
 displayed (1.83 tried to open clustalw help)
 * Added complete automake (configure etc) system according to the
 following websites:
 * clustalw files source files have been moved to subdir
 * Fixed bug #53 change MAXNAMESTODISPLAY back to 10 from 30.
 This fixes problem of large amount of space between sequence name and
 actual alignment in clustal output files
 * This solves bug #72 with long lines (5000+) in fasta files
 changed code to use strings rather than arrays.  Needed to add delim
 parameter to getline in order to read files formatted for different
 OSs on different platforms.
 * Fixed Bug 79:
 "The count of amino acids in the ClustalX Postscript output not correct"
 Off-by-one issue
 * ClustalX and ClustalW version numbers are now the same and defined in
 ClustalW code (automake)
 * Fixed problem with compilation of ClustalX2 with gcc3
 avoiding gcc3 error message: cannot declare member function
 * Target now clustalw2 instead of clustalw
 * Fixed Bug 46
 added in aminoacid code O for pyrrolysine
 * Fixed bug 89
 changed clustalw2.0 to conform to 1.83 behaviour for width of sequence
 ID and alignment
 * Fixed bug 90
 changed clustalw2.0 to conform to 1.83 behaviour leading spaces are
 stripped from FASTA identifiers.
 * Fixed bug 91
 Clustalw2.0 now handles pseudo-FASTA/MoST format files. Strips out
 numbers and spaces.
 To generate a diff of this commit:
 cvs rdiff -u -r1.3 -r0 pkgsrc/biology/clustalw/MESSAGE
 cvs rdiff -u -r1.12 -r1.13 pkgsrc/biology/clustalw/Makefile
 cvs rdiff -u -r1.2 -r1.3 pkgsrc/biology/clustalw/PLIST
 cvs rdiff -u -r1.5 -r1.6 pkgsrc/biology/clustalw/distinfo
 cvs rdiff -u -r1.1.1.1 -r0 pkgsrc/biology/clustalw/patches/patch-aa \
 cvs rdiff -u -r1.1 -r0 pkgsrc/biology/clustalw/patches/patch-interface.c
 Please note that diffs are not public domain; they are subject to the
 copyright notices on the relevant files.

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