[med-svn] r4223 - trunk/packages/clustalx/trunk/debian

Mon Oct 19 13:01:49 UTC 2009

Author: plessy
Date: 2009-10-19 13:01:49 +0000 (Mon, 19 Oct 2009)
New Revision: 4223

Added:
   trunk/packages/clustalx/trunk/debian/CHANGELOG.upstream
   trunk/packages/clustalx/trunk/debian/README.source
Modified:
   trunk/packages/clustalx/trunk/debian/changelog
   trunk/packages/clustalx/trunk/debian/rules
Log:
Added upstream changelog and patch meta-documentation.


Added: trunk/packages/clustalx/trunk/debian/CHANGELOG.upstream
===================================================================

--- trunk/packages/clustalx/trunk/debian/CHANGELOG.upstream	                        (rev 0)
+++ trunk/packages/clustalx/trunk/debian/CHANGELOG.upstream	2009-10-19 13:01:49 UTC (rev 4223)
@@ -0,0 +1,249 @@
+----------------------------------------------------------------------
+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 mode"
+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 platforms
+
+* 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/clustalx.pro)
+
+* 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:
+- http://www.openismus.com/documents/linux/automake/automake.shtml
+- http://www.bioinf.uni-freiburg.de/~mmann/HowTo/automake.html
+
+* 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
+QDir::currentPath'
+
+* 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.

Added: trunk/packages/clustalx/trunk/debian/README.source
===================================================================
--- trunk/packages/clustalx/trunk/debian/README.source	                        (rev 0)
+++ trunk/packages/clustalx/trunk/debian/README.source	2009-10-19 13:01:49 UTC (rev 4223)
@@ -0,0 +1,2 @@
+This package uses the ‘quilt’ program to patch the original upstream sources.
+This is documented in ‘/usr/share/doc/quilt/README.source’.

Modified: trunk/packages/clustalx/trunk/debian/changelog
===================================================================
--- trunk/packages/clustalx/trunk/debian/changelog	2009-10-19 05:15:16 UTC (rev 4222)
+++ trunk/packages/clustalx/trunk/debian/changelog	2009-10-19 13:01:49 UTC (rev 4223)
@@ -26,6 +26,10 @@
   * Updated package description.
   * Hardcoded the localisation of accessory files in /usr/share/clustalx.
     (debian/patches/hardcode-accessory-file-locations.patch)
+  * Documented in debian/README.source that the documentation for quilt
+    is in /usr/share/doc/quilt.
+  * Added upstream changelog downloaded from upstream website
+    (debian/rules, debian/CHANGELOG.upstream).
 
  -- Charles Plessy <plessy at debian.org>  Mon, 19 Oct 2009 13:19:51 +0900
 

Modified: trunk/packages/clustalx/trunk/debian/rules
===================================================================
--- trunk/packages/clustalx/trunk/debian/rules	2009-10-19 05:15:16 UTC (rev 4222)
+++ trunk/packages/clustalx/trunk/debian/rules	2009-10-19 13:01:49 UTC (rev 4223)
@@ -21,4 +21,8 @@
 
 binary: binary-arch
 binary-indep: # does nothing
+
+override_dh_installchangelogs:
+	dh_installchangelogs debian/CHANGELOG.upstream
+
 .PHONY: build clean binary-arch binary install


