Author: plessy Date: 2009-02-05 00:15:04 +0000 (Thu, 05 Feb 2009) New Revision: 3081
Modified: trunk/packages/emboss/trunk/debian/changelog trunk/packages/emboss/trunk/debian/patches/upstream.patch Log: Minor fix available. Modified: trunk/packages/emboss/trunk/debian/changelog =================================================================== --- trunk/packages/emboss/trunk/debian/changelog 2009-02-04 14:32:59 UTC (rev 3080) +++ trunk/packages/emboss/trunk/debian/changelog 2009-02-05 00:15:04 UTC (rev 3081) @@ -1,3 +1,14 @@ +emboss (6.0.1-4) UNRELEASED; urgency=low + + TODO: Let's wait the end of the freeze to upload to unstable. After this, it + would be much safer to rebuild the embassy packages and update their + orig.tar.gz, that did not change name upstream but was modified. + + * New upstream patch (patch-1-4), removing unnecessary whitespaces in + edialign.acd. + + -- Charles Plessy <[email protected]> Sun, 11 Jan 2009 15:09:08 +0900 + emboss (6.0.1-3) experimental; urgency=low * New upstream patch (patch-1-3). Modified: trunk/packages/emboss/trunk/debian/patches/upstream.patch =================================================================== --- trunk/packages/emboss/trunk/debian/patches/upstream.patch 2009-02-04 14:32:59 UTC (rev 3080) +++ trunk/packages/emboss/trunk/debian/patches/upstream.patch 2009-02-05 00:15:04 UTC (rev 3081) @@ -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-1-3.gz + ftp://emboss.open-bio.org/pub/EMBOSS/fixes/patches/patch-1-4.gz 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 2009-01-10 10:22:26.000000000 +0000 +--- EMBOSS-6.0.1/ajax/ajseqwrite.c 2009-02-04 12:58:15.000000000 +0000 *************** *** 3743,3749 **** ajFmtPrintF(outseq->File, "DE %S\n", outseq->Desc); @@ -24,9 +24,56 @@ if(ajListGetLength(outseq->Taxlist) > 1) { +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 2009-02-04 13:03:14.000000000 +0000 +*************** +*** 26,32 **** + information: "Nucleic acid sequence alignment mode" + help: "Nucleic acid sequence alignment mode (simple, translated or + mixed)" +! values: "n : simple ; nt : translation ; ma : mixed alignments" + default: "n" + ] + +--- 26,32 ---- + information: "Nucleic acid sequence alignment mode" + help: "Nucleic acid sequence alignment mode (simple, translated or + mixed)" +! values: "n: simple; nt: translation; ma: mixed alignments" + default: "n" + ] + +*************** +*** 50,56 **** + information: "Clustering method to construct sequence tree" + help: "Clustering method to construct sequence tree (UPGMA, + minimum linkage or maximum linkage)" +! values: "UPGMA : UPGMA ; max : maximum linkage ; min : minimum + linkage" + default: "UPGMA" + ] +--- 50,56 ---- + information: "Clustering method to construct sequence tree" + help: "Clustering method to construct sequence tree (UPGMA, + minimum linkage or maximum linkage)" +! values: "UPGMA: UPGMA; max: maximum linkage; min: minimum + linkage" + default: "UPGMA" + ] +*************** +*** 124,129 **** +--- 124,130 ---- + seqoutall: outseq [ + parameter: "Y" + type: "gapany" ++ aligned: "Y" + ] + + 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 2009-01-10 10:21:31.000000000 +0000 +--- EMBOSS-6.0.1/emboss/acd/Makefile.am 2009-02-04 12:58:15.000000000 +0000 *************** *** 21,27 **** fuzznuc.acd fuzzpro.acd fuzztran.acd \ @@ -66,7 +113,7 @@ 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 2009-01-10 10:21:31.000000000 +0000 +--- EMBOSS-6.0.1/emboss/acd/Makefile.in 2009-02-04 12:58:15.000000000 +0000 *************** *** 209,215 **** fuzznuc.acd fuzzpro.acd fuzztran.acd \ @@ -106,7 +153,7 @@ 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 2009-01-10 10:21:31.000000000 +0000 +--- EMBOSS-6.0.1/emboss/data/Makefile.am 2009-02-04 12:58:15.000000000 +0000 *************** *** 30,36 **** Epprofile Eprior1.plib Eprior30.plib Erna.melt Eresidues.iub \ @@ -126,7 +173,7 @@ 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 2009-01-10 10:21:31.000000000 +0000 +--- EMBOSS-6.0.1/emboss/data/Makefile.in 2009-02-04 12:58:15.000000000 +0000 *************** *** 228,234 **** Epprofile Eprior1.plib Eprior30.plib Erna.melt Eresidues.iub \ @@ -146,7 +193,7 @@ 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 2009-01-10 10:21:31.000000000 +0000 +--- EMBOSS-6.0.1/emboss/jaspscan.c 2009-02-04 12:58:15.000000000 +0000 *************** *** 293,299 **** @@ -179,7 +226,7 @@ ajStrDel(&excl); 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 2009-01-10 10:22:31.000000000 +0000 +--- EMBOSS-6.0.1/emboss/vectorstrip.c 2009-02-04 12:58:15.000000000 +0000 *************** *** 174,180 **** vectorlist = ajListNew(); @@ -199,7 +246,7 @@ { 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 2009-01-10 10:21:31.000000000 +0000 +--- EMBOSS-6.0.1/nucleus/embprop.c 2009-02-04 12:58:15.000000000 +0000 *************** *** 880,885 **** --- 880,886 ---- _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/mailman/listinfo/debian-med-commit
