[med-svn] r3305 - in trunk/packages/emboss/trunk/debian: . patches
Charles Plessy
plessy at alioth.debian.org
Tue Apr 21 06:15:00 UTC 2009
Author: plessy
Date: 2009-04-21 06:14:59 +0000 (Tue, 21 Apr 2009)
New Revision: 3305
Modified:
trunk/packages/emboss/trunk/debian/changelog
trunk/packages/emboss/trunk/debian/patches/upstream.patch
Log:
New upstream patch (patch-1-8).
Modified: trunk/packages/emboss/trunk/debian/changelog
===================================================================
--- trunk/packages/emboss/trunk/debian/changelog 2009-04-21 01:49:04 UTC (rev 3304)
+++ trunk/packages/emboss/trunk/debian/changelog 2009-04-21 06:14:59 UTC (rev 3305)
@@ -1,3 +1,13 @@
+emboss (6.0.1-10) unstable; urgency=low
+
+ * New upstream patch (patch-1-8):
+ Incorrect information was often given in the subsidiary table
+ listing REs that would cut a greater number of times than an
+ optional user-supplied maximum number. The main role of
+ the program was unaffected.
+
+ -- Charles Plessy <plessy at debian.org> Tue, 21 Apr 2009 13:01:38 +0900
+
emboss (6.0.1-9) unstable; urgency=low
* New upstream patch (patch-1-7):
Modified: trunk/packages/emboss/trunk/debian/patches/upstream.patch
===================================================================
--- trunk/packages/emboss/trunk/debian/patches/upstream.patch 2009-04-21 01:49:04 UTC (rev 3304)
+++ trunk/packages/emboss/trunk/debian/patches/upstream.patch 2009-04-21 06:14:59 UTC (rev 3305)
@@ -3,10 +3,10 @@
This is an upstream patch, it does not need to be forwarded.
Description: Official upstream patch.
This patch was downloaded from:
- ftp://emboss.open-bio.org/pub/EMBOSS/fixes/patches/patch-1-7.gz
+ ftp://emboss.open-bio.org/pub/EMBOSS/fixes/patches/patch-1-8.gz
diff -c -N --recursive EMBOSS-6.0.1old/ajax/ajacd.c EMBOSS-6.0.1/ajax/ajacd.c
*** EMBOSS-6.0.1old/ajax/ajacd.c 2008-07-14 15:47:38.000000000 +0100
---- EMBOSS-6.0.1/ajax/ajacd.c 2009-04-07 11:40:02.000000000 +0100
+--- EMBOSS-6.0.1/ajax/ajacd.c 2009-04-20 14:45:27.000000000 +0100
***************
*** 8256,8263 ****
--- 8256,8271 ----
@@ -240,7 +240,7 @@
itestparam++)
diff -c -N --recursive EMBOSS-6.0.1old/ajax/ajseq.c EMBOSS-6.0.1/ajax/ajseq.c
*** EMBOSS-6.0.1old/ajax/ajseq.c 2008-07-14 15:54:44.000000000 +0100
---- EMBOSS-6.0.1/ajax/ajseq.c 2009-04-07 11:40:06.000000000 +0100
+--- EMBOSS-6.0.1/ajax/ajseq.c 2009-04-20 14:45:27.000000000 +0100
***************
*** 287,292 ****
--- 287,293 ----
@@ -378,7 +378,7 @@
ajSeqsetGetLen(seq), seq->Begin, seq->End);
diff -c -N --recursive EMBOSS-6.0.1old/ajax/ajseqread.c EMBOSS-6.0.1/ajax/ajseqread.c
*** EMBOSS-6.0.1old/ajax/ajseqread.c 2008-07-14 15:52:48.000000000 +0100
---- EMBOSS-6.0.1/ajax/ajseqread.c 2009-04-07 11:40:15.000000000 +0100
+--- EMBOSS-6.0.1/ajax/ajseqread.c 2009-04-20 14:45:27.000000000 +0100
***************
*** 1617,1623 ****
ajDebug("ready to start reading format '%S' '%S' %d..%d\n",
@@ -398,7 +398,7 @@
ajSeqinClearPos(seqin);
diff -c -N --recursive EMBOSS-6.0.1old/ajax/ajseqwrite.c EMBOSS-6.0.1/ajax/ajseqwrite.c
*** EMBOSS-6.0.1old/ajax/ajseqwrite.c 2008-07-14 15:58:07.000000000 +0100
---- EMBOSS-6.0.1/ajax/ajseqwrite.c 2009-04-07 11:39:40.000000000 +0100
+--- EMBOSS-6.0.1/ajax/ajseqwrite.c 2009-04-20 14:45:27.000000000 +0100
***************
*** 451,456 ****
--- 451,457 ----
@@ -456,7 +456,7 @@
diff -c -N --recursive EMBOSS-6.0.1old/emboss/acd/edialign.acd EMBOSS-6.0.1/emboss/acd/edialign.acd
*** EMBOSS-6.0.1old/emboss/acd/edialign.acd 2008-04-04 16:54:03.000000000 +0100
---- EMBOSS-6.0.1/emboss/acd/edialign.acd 2009-04-07 11:39:40.000000000 +0100
+--- EMBOSS-6.0.1/emboss/acd/edialign.acd 2009-04-20 14:45:27.000000000 +0100
***************
*** 26,32 ****
information: "Nucleic acid sequence alignment mode"
@@ -503,7 +503,7 @@
endsection: output
diff -c -N --recursive EMBOSS-6.0.1old/emboss/acd/Makefile.am EMBOSS-6.0.1/emboss/acd/Makefile.am
*** EMBOSS-6.0.1old/emboss/acd/Makefile.am 2008-07-14 16:46:31.000000000 +0100
---- EMBOSS-6.0.1/emboss/acd/Makefile.am 2009-04-07 11:39:40.000000000 +0100
+--- EMBOSS-6.0.1/emboss/acd/Makefile.am 2009-04-20 14:45:27.000000000 +0100
***************
*** 21,27 ****
fuzznuc.acd fuzzpro.acd fuzztran.acd \
@@ -543,7 +543,7 @@
diff -c -N --recursive EMBOSS-6.0.1old/emboss/acd/Makefile.in EMBOSS-6.0.1/emboss/acd/Makefile.in
*** EMBOSS-6.0.1old/emboss/acd/Makefile.in 2008-07-16 19:33:19.000000000 +0100
---- EMBOSS-6.0.1/emboss/acd/Makefile.in 2009-04-07 11:39:40.000000000 +0100
+--- EMBOSS-6.0.1/emboss/acd/Makefile.in 2009-04-20 14:45:27.000000000 +0100
***************
*** 209,215 ****
fuzznuc.acd fuzzpro.acd fuzztran.acd \
@@ -583,7 +583,7 @@
diff -c -N --recursive EMBOSS-6.0.1old/emboss/data/Makefile.am EMBOSS-6.0.1/emboss/data/Makefile.am
*** EMBOSS-6.0.1old/emboss/data/Makefile.am 2008-07-14 16:09:23.000000000 +0100
---- EMBOSS-6.0.1/emboss/data/Makefile.am 2009-04-07 11:39:40.000000000 +0100
+--- EMBOSS-6.0.1/emboss/data/Makefile.am 2009-04-20 14:45:27.000000000 +0100
***************
*** 30,36 ****
Epprofile Eprior1.plib Eprior30.plib Erna.melt Eresidues.iub \
@@ -603,7 +603,7 @@
embossre.equ Emwfilter.dat Emass.dat Emassmod.dat \
diff -c -N --recursive EMBOSS-6.0.1old/emboss/data/Makefile.in EMBOSS-6.0.1/emboss/data/Makefile.in
*** EMBOSS-6.0.1old/emboss/data/Makefile.in 2008-07-16 19:33:20.000000000 +0100
---- EMBOSS-6.0.1/emboss/data/Makefile.in 2009-04-07 11:39:40.000000000 +0100
+--- EMBOSS-6.0.1/emboss/data/Makefile.in 2009-04-20 14:45:27.000000000 +0100
***************
*** 228,234 ****
Epprofile Eprior1.plib Eprior30.plib Erna.melt Eresidues.iub \
@@ -623,7 +623,7 @@
embossre.equ Emwfilter.dat Emass.dat Emassmod.dat \
diff -c -N --recursive EMBOSS-6.0.1old/emboss/jaspscan.c EMBOSS-6.0.1/emboss/jaspscan.c
*** EMBOSS-6.0.1old/emboss/jaspscan.c 2008-06-26 09:39:09.000000000 +0100
---- EMBOSS-6.0.1/emboss/jaspscan.c 2009-04-07 11:39:40.000000000 +0100
+--- EMBOSS-6.0.1/emboss/jaspscan.c 2009-04-20 14:45:27.000000000 +0100
***************
*** 293,299 ****
@@ -656,7 +656,7 @@
ajStrDel(&excl);
diff -c -N --recursive EMBOSS-6.0.1old/emboss/needle.c EMBOSS-6.0.1/emboss/needle.c
*** EMBOSS-6.0.1old/emboss/needle.c 2008-06-10 13:48:04.000000000 +0100
---- EMBOSS-6.0.1/emboss/needle.c 2009-04-07 11:40:28.000000000 +0100
+--- EMBOSS-6.0.1/emboss/needle.c 2009-04-20 14:45:27.000000000 +0100
***************
*** 151,157 ****
{
@@ -674,9 +674,29 @@
id);
ajFmtPrintAppS(&tmpstr,"Longest_Similarity = %5.2f%%\n",
sim);
+diff -c -N --recursive EMBOSS-6.0.1old/emboss/remap.c EMBOSS-6.0.1/emboss/remap.c
+*** EMBOSS-6.0.1old/emboss/remap.c 2008-06-26 09:39:09.000000000 +0100
+--- EMBOSS-6.0.1/emboss/remap.c 2009-04-20 14:45:40.000000000 +0100
+***************
+*** 618,624 ****
+
+ for(i = 0; keyarray[i]; i++)
+ {
+! value = (PValue) valarray[i];
+ if(value->count > maxcuts)
+ ajFmtPrintF(outfile, "%10S\t %d\t%S\n",
+ (AjPStr) keyarray[i], value->count,
+--- 618,624 ----
+
+ for(i = 0; keyarray[i]; i++)
+ {
+! value = ajTableFetch(hittable,keyarray[i]);
+ if(value->count > maxcuts)
+ ajFmtPrintF(outfile, "%10S\t %d\t%S\n",
+ (AjPStr) keyarray[i], value->count,
diff -c -N --recursive EMBOSS-6.0.1old/emboss/vectorstrip.c EMBOSS-6.0.1/emboss/vectorstrip.c
*** EMBOSS-6.0.1old/emboss/vectorstrip.c 2008-06-26 09:39:09.000000000 +0100
---- EMBOSS-6.0.1/emboss/vectorstrip.c 2009-04-07 11:39:40.000000000 +0100
+--- EMBOSS-6.0.1/emboss/vectorstrip.c 2009-04-20 14:45:27.000000000 +0100
***************
*** 174,180 ****
vectorlist = ajListNew();
@@ -696,7 +716,7 @@
{
diff -c -N --recursive EMBOSS-6.0.1old/emboss/water.c EMBOSS-6.0.1/emboss/water.c
*** EMBOSS-6.0.1old/emboss/water.c 2008-06-26 09:39:09.000000000 +0100
---- EMBOSS-6.0.1/emboss/water.c 2009-04-07 11:40:31.000000000 +0100
+--- EMBOSS-6.0.1/emboss/water.c 2009-04-20 14:45:27.000000000 +0100
***************
*** 159,165 ****
{
@@ -716,7 +736,7 @@
sim);
diff -c -N --recursive EMBOSS-6.0.1old/nucleus/embaln.c EMBOSS-6.0.1/nucleus/embaln.c
*** EMBOSS-6.0.1old/nucleus/embaln.c 2008-07-15 15:41:05.000000000 +0100
---- EMBOSS-6.0.1/nucleus/embaln.c 2009-04-07 11:39:40.000000000 +0100
+--- EMBOSS-6.0.1/nucleus/embaln.c 2009-04-20 14:45:27.000000000 +0100
***************
*** 69,79 ****
ajint i;
@@ -1247,7 +1267,7 @@
if(path[row*seqlen+column] > pathmax)
diff -c -N --recursive EMBOSS-6.0.1old/nucleus/embprop.c EMBOSS-6.0.1/nucleus/embprop.c
*** EMBOSS-6.0.1old/nucleus/embprop.c 2008-07-14 23:13:33.000000000 +0100
---- EMBOSS-6.0.1/nucleus/embprop.c 2009-04-07 11:39:40.000000000 +0100
+--- EMBOSS-6.0.1/nucleus/embprop.c 2009-04-20 14:45:27.000000000 +0100
***************
*** 880,885 ****
--- 880,886 ----
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