[med-svn] r3081 - in trunk/packages/emboss/trunk/debian: . patches
plessy at alioth.debian.org
plessy at alioth.debian.org
Thu Feb 5 00:15:05 UTC 2009
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 <plessy at debian.org> 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 ----
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