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 <[email protected]> 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 ---- _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/mailman/listinfo/debian-med-commit
