[med-svn] r3823 - in trunk/packages/emboss/trunk/debian: . patches
Charles Plessy
plessy at alioth.debian.org
Tue Aug 25 14:45:51 UTC 2009
Author: plessy
Date: 2009-08-25 14:45:51 +0000 (Tue, 25 Aug 2009)
New Revision: 3823
Modified:
trunk/packages/emboss/trunk/debian/changelog
trunk/packages/emboss/trunk/debian/control
trunk/packages/emboss/trunk/debian/patches/official-upstream-patch.patch
trunk/packages/emboss/trunk/debian/rules
Log:
New upstream patch (patch-1-2):
In addition:
* Incremented Standards-Version in debian/control to reflect conformance
with Policy 3.8.3 (no changes needed).
* Removed the libtool archive files from the development packages (debian/rules).
Modified: trunk/packages/emboss/trunk/debian/changelog
===================================================================
--- trunk/packages/emboss/trunk/debian/changelog 2009-08-25 11:57:18 UTC (rev 3822)
+++ trunk/packages/emboss/trunk/debian/changelog 2009-08-25 14:45:51 UTC (rev 3823)
@@ -1,9 +1,17 @@
-emboss (6.1.0-3) UNRELEASED; urgency=low
+emboss (6.1.0-4) unstable; urgency=low
+ * New upstream patch (patch-1-2):
+ - Fix string extension so that pointers in lists remain valid.
+ - This fixes a bug in processing SwissProt complex descriptions.
+ - Fix definition of AJRESIZE0 macro.
+ - Fix processing of first match in a profile alignment (prophet).
* Delete /usr/share/EMBOSS/doc/programs/text/frestdist.txt, that
should belong to embassy-phylip (PHYLIPNEW). (debian/rules)
+ * Incremented Standards-Version in debian/control to reflect conformance
+ with Policy 3.8.3 (no changes needed).
+ * Removed the libtool libraries from the development packages (debian/rules).
- -- Charles Plessy <plessy at debian.org> Tue, 04 Aug 2009 21:56:45 +0900
+ -- Charles Plessy <plessy at debian.org> Tue, 25 Aug 2009 23:19:10 +0900
emboss (6.1.0-2) unstable; urgency=low
Modified: trunk/packages/emboss/trunk/debian/control
===================================================================
--- trunk/packages/emboss/trunk/debian/control 2009-08-25 11:57:18 UTC (rev 3822)
+++ trunk/packages/emboss/trunk/debian/control 2009-08-25 14:45:51 UTC (rev 3823)
@@ -8,7 +8,7 @@
Build-Depends-Indep: openjdk-6-jdk
Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/emboss/trunk/?rev=0&sc=0trunk
Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/emboss/trunk/
-Standards-Version: 3.8.2
+Standards-Version: 3.8.3
Homepage: http://emboss.sourceforge.net
Package: emboss
Modified: trunk/packages/emboss/trunk/debian/patches/official-upstream-patch.patch
===================================================================
--- trunk/packages/emboss/trunk/debian/patches/official-upstream-patch.patch 2009-08-25 11:57:18 UTC (rev 3822)
+++ trunk/packages/emboss/trunk/debian/patches/official-upstream-patch.patch 2009-08-25 14:45:51 UTC (rev 3823)
@@ -5,7 +5,11 @@
Correct FASTQ input searching for '@' to start next sequence
Standardize FASTQ sequence formats with other OpenBio projects
Correct issues in igstrict, genpept and refseqp formats
-Origin: ftp://emboss.open-bio.org/pub/EMBOSS/fixes/patches/patch-1-1.gz
+ 24-Aug-2009: Fix string extension so that pointers in lists remain valid.
+ This fixes a bug in processing SwissProt complex descriptions.
+ Fix definition of AJRESIZE0 macro.
+ Fix processing of first match in a profile alignment (prophet).
+Origin: ftp://emboss.open-bio.org/pub/EMBOSS/fixes/patches/patch-1-2.gz
Forwarded: not-needed
diff -c -N --recursive EMBOSS-6.1.0orig/ajax/ajfeat.c EMBOSS-6.1.0/ajax/ajfeat.c
*** EMBOSS-6.1.0orig/ajax/ajfeat.c 2009-07-06 16:48:46.000000000 +0100
@@ -37,6 +41,26 @@
/*ajDebug("ajFeatUfoRead UFO '%S'\n", ufo);*/
+diff -c -N --recursive EMBOSS-6.1.0orig/ajax/ajmem.h EMBOSS-6.1.0/ajax/ajmem.h
+*** EMBOSS-6.1.0orig/ajax/ajmem.h 2007-12-12 12:46:19.000000000 +0000
+--- EMBOSS-6.1.0/ajax/ajmem.h 2009-08-25 09:31:44.000000000 +0100
+***************
+*** 71,77 ****
+ #define AJFREE(ptr) ((void)(ajMemFree(ptr), (ptr) = 0))
+ #define AJRESIZE(ptr, nbytes) ((ptr) = ajMemResize((ptr), \
+ (nbytes), __FILE__, __LINE__, AJFALSE))
+! #define AJRESIZE0(ptr, oldbytes, nbytes) (ptr) = ajMemResizeZero((ptr), \
+ (oldbytes), (nbytes), __FILE__, __LINE__, AJFALSE))
+ #define AJCRESIZE(ptr, nbytes) ((ptr) = ajMemResize((ptr), \
+ (nbytes)*sizeof *(ptr), __FILE__, __LINE__, AJFALSE))
+--- 71,77 ----
+ #define AJFREE(ptr) ((void)(ajMemFree(ptr), (ptr) = 0))
+ #define AJRESIZE(ptr, nbytes) ((ptr) = ajMemResize((ptr), \
+ (nbytes), __FILE__, __LINE__, AJFALSE))
+! #define AJRESIZE0(ptr, oldbytes, nbytes) ((ptr) = ajMemResizeZero((ptr), \
+ (oldbytes), (nbytes), __FILE__, __LINE__, AJFALSE))
+ #define AJCRESIZE(ptr, nbytes) ((ptr) = ajMemResize((ptr), \
+ (nbytes)*sizeof *(ptr), __FILE__, __LINE__, AJFALSE))
diff -c -N --recursive EMBOSS-6.1.0orig/ajax/ajseqread.c EMBOSS-6.1.0/ajax/ajseqread.c
*** EMBOSS-6.1.0orig/ajax/ajseqread.c 2009-07-07 00:08:26.000000000 +0100
--- EMBOSS-6.1.0/ajax/ajseqread.c 2009-07-30 15:27:39.000000000 +0100
@@ -893,6 +917,220 @@
/* @funcstatic seqSeqFormat ***************************************************
**
** Initialises sequence output formatting parameters.
+diff -c -N --recursive EMBOSS-6.1.0orig/ajax/ajstr.c EMBOSS-6.1.0/ajax/ajstr.c
+*** EMBOSS-6.1.0orig/ajax/ajstr.c 2009-06-22 16:51:03.000000000 +0100
+--- EMBOSS-6.1.0/ajax/ajstr.c 2009-08-25 09:30:30.000000000 +0100
+***************
+*** 3,13 ****
+ **
+ ** AjPStr objects are reference counted strings
+ ** Any change will need a new string object if the use count
+! ** is greater than 1, so the original ajStr provided so that it can
+! ** be reallocated in any routine where string modification is possible.
+ **
+! ** In many cases
+! ** the text is always a copy, even of a constant original, so
+ ** that it can be simply freed.
+ **
+ ** @author Copyright (C) 1998 Peter Rice
+--- 3,13 ----
+ **
+ ** AjPStr objects are reference counted strings
+ ** Any change will need a new string object if the use count
+! ** is greater than 1, so the original AjPStr is provided as a pointer
+! ** so that it can be reallocated in any routine where string modification
+! ** may be needed.
+ **
+! ** In many cases the text is always a copy, even of a constant original, so
+ ** that it can be simply freed.
+ **
+ ** @author Copyright (C) 1998 Peter Rice
+***************
+*** 2042,2047 ****
+--- 2042,2048 ----
+ ** @nam4rule NewRes Construct with reserved size.
+ **
+ ** @argrule C txt [const char*] Text string
++ ** @argrule K ch [char] Single character
+ ** @argrule S str [const AjPStr] Text string
+ ** @argrule NewRes size [ajuint] Reserved size
+ ** @argrule NewRef refstr [AjPStr] Text string to be duplicated
+***************
+*** 2099,2104 ****
+--- 2100,2132 ----
+
+
+
++ /* @func ajStrNewK ************************************************************
++ **
++ ** String constructor which allocates memory for a string and initialises it
++ ** with the single character provided.
++ **
++ ** The string size is set just large enough to hold the supplied text.
++ **
++ ** @param [r] ch [char] Null-terminated character string to initialise
++ ** the new string.
++ ** @return [AjPStr] Pointer to a string containing the supplied text
++ ** @@
++ ******************************************************************************/
++
++ AjPStr ajStrNewK(char ch)
++ {
++ char txt[2] = " ";
++ AjPStr thys;
++
++ txt[0] = ch;
++ thys = ajStrNewResLenC(txt, 2, 1);
++
++ return thys;
++ }
++
++
++
++
+ /* @func ajStrNewS ************************************************************
+ **
+ ** String constructor which allocates memory for a string and initialises it
+***************
+*** 6106,6111 ****
+--- 6134,6157 ----
+
+
+
++ /* @func ajStrTrimWhiteStart **************************************************
++ **
++ ** Removes regions composed of white space characters only from the start of a
++ ** string.
++ **
++ ** @param [u] Pstr [AjPStr*] String
++ ** @return [AjBool] ajTrue if string was reallocated
++ ** @@
++ ******************************************************************************/
++
++ AjBool ajStrTrimWhiteStart(AjPStr* Pstr)
++ {
++ return ajStrTrimStartC(Pstr, "\t \n\r");
++ }
++
++
++
++
+ /* @func ajStrTruncateLen *****************************************************
+ **
+ ** Removes the end from a string reducing it to a defined length.
+***************
+*** 8512,8524 ****
+
+ thys = *Pstr;
+
+! if((thys->Use > 1) || (thys->Res < savesize))
+ {
+ strCloneL(Pstr, savesize);
+
+ return ajTrue;
+ }
+
+ return ajFalse;
+ }
+
+--- 8558,8578 ----
+
+ thys = *Pstr;
+
+! if(thys->Use > 1)
+ {
+ strCloneL(Pstr, savesize);
+
+ return ajTrue;
+ }
+
++ if(thys->Res < savesize)
++ {
++ AJRESIZE(thys->Ptr, savesize);
++ thys->Res = savesize;
++
++ return ajTrue;
++ }
++
+ return ajFalse;
+ }
+
+***************
+*** 8565,8570 ****
+--- 8619,8631 ----
+
+ thys = *Pstr;
+
++ if(thys->Use > 1)
++ {
++ strCloneL(Pstr, size);
++
++ return ajTrue;
++ }
++
+ if(thys->Res < size)
+ {
+ if(size >= LONGSTR)
+***************
+*** 8579,8592 ****
+ else
+ roundsize = ajRound(size, STRSIZE);
+
+! strCloneL(Pstr, roundsize);
+!
+! return ajTrue;
+! }
+!
+! if(thys->Use > 1)
+! {
+! strCloneL(Pstr, size);
+
+ return ajTrue;
+ }
+--- 8640,8647 ----
+ else
+ roundsize = ajRound(size, STRSIZE);
+
+! AJRESIZE(thys->Ptr, roundsize);
+! thys->Res = roundsize;
+
+ return ajTrue;
+ }
+diff -c -N --recursive EMBOSS-6.1.0orig/ajax/ajstr.h EMBOSS-6.1.0/ajax/ajstr.h
+*** EMBOSS-6.1.0orig/ajax/ajstr.h 2009-06-22 16:51:04.000000000 +0100
+--- EMBOSS-6.1.0/ajax/ajstr.h 2009-08-25 09:30:34.000000000 +0100
+***************
+*** 65,70 ****
+--- 65,73 ----
+ **
+ ** String iterator, used to test iterator functionality.
+ **
++ ** @alias AjSStrIter
++ ** @alias AjOStrIter
++ **
+ ** @new ajStrIter Creates and initializes an iterator for a string
+ **
+ ** @delete ajStrIterFree Destructor for a string iterator
+***************
+*** 192,197 ****
+--- 195,201 ----
+
+ AjPStr ajStrNew (void);
+ AjPStr ajStrNewC (const char *txt);
++ AjPStr ajStrNewK (char ch);
+ AjPStr ajStrNewS (const AjPStr str);
+ AjPStr ajStrNewRef(AjPStr str);
+ AjPStr ajStrNewRes(ajuint size);
+***************
+*** 296,301 ****
+--- 300,306 ----
+ AjBool ajStrTrimStartC (AjPStr* Pstr, const char* txt);
+ AjBool ajStrTrimWhite(AjPStr* Pstr);
+ AjBool ajStrTrimWhiteEnd(AjPStr* Pstr);
++ AjBool ajStrTrimWhiteStart(AjPStr* Pstr);
+ AjBool ajStrTruncateLen(AjPStr* Pstr, ajuint len);
+ AjBool ajStrTruncatePos(AjPStr* Pstr, ajint pos);
+
diff -c -N --recursive EMBOSS-6.1.0orig/jemboss/org/emboss/jemboss/gui/Browser.java EMBOSS-6.1.0/jemboss/org/emboss/jemboss/gui/Browser.java
*** EMBOSS-6.1.0orig/jemboss/org/emboss/jemboss/gui/Browser.java 2009-06-30 17:18:26.000000000 +0100
--- EMBOSS-6.1.0/jemboss/org/emboss/jemboss/gui/Browser.java 2009-07-30 15:29:18.000000000 +0100
@@ -1550,3 +1788,17 @@
#
--- 1261,1266 ----
+diff -c -N --recursive EMBOSS-6.1.0orig/nucleus/embaln.c EMBOSS-6.1.0/nucleus/embaln.c
+*** EMBOSS-6.1.0orig/nucleus/embaln.c 2009-06-12 19:02:30.000000000 +0100
+--- EMBOSS-6.1.0/nucleus/embaln.c 2009-08-25 09:31:28.000000000 +0100
+***************
+*** 2091,2096 ****
+--- 2091,2098 ----
+ ajStrAppendK(m,p[row--]);
+ ajStrAppendK(n,q[column--]);
+
++ if(row < 0 || column < 0)
++ break;
+ if(path[(row)*seqlen+(column)]<=0.)
+ break;
+
Modified: trunk/packages/emboss/trunk/debian/rules
===================================================================
--- trunk/packages/emboss/trunk/debian/rules 2009-08-25 11:57:18 UTC (rev 3822)
+++ trunk/packages/emboss/trunk/debian/rules 2009-08-25 14:45:51 UTC (rev 3823)
@@ -28,7 +28,6 @@
./configure $(CONFFLAGS)
include /usr/share/quilt/quilt.make
-QUILT_PATCH_DIR = debian/patch
build: config.status patch debian/copyright build-stamp
build-stamp:
@@ -91,11 +90,15 @@
# rm $(AJAX)/usr/include/pcre* # Not very elegant way to solve the conflict with libpcre-dev
mv $(AJAX)/usr/include $(AJAX)-dev/usr/include/ajax
mv $(AJAX)/usr/lib/*a $(AJAX)/usr/lib/*so $(AJAX)-dev/usr/lib
+ # Libtool .la libraries are not wanted anymore in Debian, see http://lists.debian.org/debian-devel/2009/08/msg00783.html
+ find $(AJAX)-dev/usr/lib -name '*.la' -exec rm {} \;
### Nuleus library: lib and libdevel packages. ###
$(MAKE) -C nucleus install DESTDIR=$(NUCLEUS)
mv $(NUCLEUS)/usr/include $(NUCLEUS)-dev/usr/include/nucleus
mv $(NUCLEUS)/usr/lib/*a $(NUCLEUS)/usr/lib/*so $(NUCLEUS)-dev/usr/lib
+ # Libtool .la libraries are not wanted anymore in Debian, see http://lists.debian.org/debian-devel/2009/08/msg00783.html
+ find $(NUCLEUS)-dev/usr/lib -name '*.la' -exec rm {} \;
### eplplot goes in emboss-lib, but lets'hope building on plplot some day. ###
$(MAKE) -C plplot install DESTDIR=$(CURDIR)/debian/emboss-lib
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