[med-svn] r2945 - in trunk/packages/emboss/trunk/debian: . patches
plessy at alioth.debian.org
plessy at alioth.debian.org
Sat Jan 10 13:32:56 UTC 2009
Author: plessy
Date: 2009-01-10 13:32:56 +0000 (Sat, 10 Jan 2009)
New Revision: 2945
Modified:
trunk/packages/emboss/trunk/debian/TODO
trunk/packages/emboss/trunk/debian/changelog
trunk/packages/emboss/trunk/debian/patches/upstream.patch
Log:
New upstream patch. Cleaned TODO file.
Modified: trunk/packages/emboss/trunk/debian/TODO
===================================================================
--- trunk/packages/emboss/trunk/debian/TODO 2009-01-10 10:25:06 UTC (rev 2944)
+++ trunk/packages/emboss/trunk/debian/TODO 2009-01-10 13:32:56 UTC (rev 2945)
@@ -1,6 +1 @@
-- Use libpcre from Debian (needs #387557)
-- Check if external applications use the nucleus or ajax libraries (as a
- consequence, emboss-lib would need to be separated into libnucleus4 and
- libajax4).
-- Design an easy build system for embassy (makefile includes shipped in emboss-data?)
-- Implement tests.
+- Use libpcre from Debian (needs #387557).
Modified: trunk/packages/emboss/trunk/debian/changelog
===================================================================
--- trunk/packages/emboss/trunk/debian/changelog 2009-01-10 10:25:06 UTC (rev 2944)
+++ trunk/packages/emboss/trunk/debian/changelog 2009-01-10 13:32:56 UTC (rev 2945)
@@ -1,6 +1,10 @@
emboss (6.0.1-3) UNRELEASED; urgency=low
* jEMBOSS
+ * New upstream patch (patch-1-3).
+ - fixes segmentation fault in vectorscript when -auto is used with empty
+ vectorsfile.
+ - adds '.' trailer to the OS line in SwissProt output.
-- Charles Plessy <plessy at debian.org> Wed, 26 Nov 2008 08:57:20 +0900
Modified: trunk/packages/emboss/trunk/debian/patches/upstream.patch
===================================================================
--- trunk/packages/emboss/trunk/debian/patches/upstream.patch 2009-01-10 10:25:06 UTC (rev 2944)
+++ trunk/packages/emboss/trunk/debian/patches/upstream.patch 2009-01-10 13:32:56 UTC (rev 2945)
@@ -3,10 +3,150 @@
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-1-1.gz
+ ftp://emboss.open-bio.org/pub/EMBOSS/fixes/patches/patch-1-3.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
+***************
+*** 3743,3749 ****
+ ajFmtPrintF(outseq->File, "DE %S\n", outseq->Desc);
+
+ if(ajStrGetLen(outseq->Tax))
+! ajFmtPrintF(outseq->File, "OS %S\n", outseq->Tax);
+
+ if(ajListGetLength(outseq->Taxlist) > 1)
+ {
+--- 3743,3749 ----
+ ajFmtPrintF(outseq->File, "DE %S\n", outseq->Desc);
+
+ if(ajStrGetLen(outseq->Tax))
+! ajFmtPrintF(outseq->File, "OS %S.\n", outseq->Tax);
+
+ if(ajListGetLength(outseq->Taxlist) > 1)
+ {
+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
+***************
+*** 21,27 ****
+ fuzznuc.acd fuzzpro.acd fuzztran.acd \
+ garnier.acd geecee.acd getorf.acd giep.acd \
+ helixturnhelix.acd histogramtest.acd \
+! hmoment.acd iep.acd infoalign.acd infoseq.acd intconv.acd \
+ isochore.acd jaspextract.acd jaspscan.acd lindna.acd listor.acd \
+ makenucseq.acd makeprotseq.acd marscan.acd \
+ maskambignuc.acd maskambigprot.acd maskfeat.acd maskseq.acd \
+--- 21,28 ----
+ fuzznuc.acd fuzzpro.acd fuzztran.acd \
+ garnier.acd geecee.acd getorf.acd giep.acd \
+ helixturnhelix.acd histogramtest.acd \
+! hmoment.acd iep.acd infoalign.acd infobase.acd inforesidue.acd \
+! infoseq.acd intconv.acd \
+ isochore.acd jaspextract.acd jaspscan.acd lindna.acd listor.acd \
+ makenucseq.acd makeprotseq.acd marscan.acd \
+ maskambignuc.acd maskambigprot.acd maskfeat.acd maskseq.acd \
+***************
+*** 48,55 ****
+ splitter.acd stretcher.acd stssearch.acd supermatcher.acd syco.acd \
+ tcode.acd testplot.acd textsearch.acd tfextract.acd tfm.acd \
+ tfscan.acd tmap.acd tranalign.acd transeq.acd treetypedisplay.acd \
+! trimest.acd trimseq.acd twofeat.acd union.acd vectorstrip.acd \
+! water.acd whichdb.acd wobble.acd \
+ wordcount.acd wordfinder.acd wordmatch.acd \
+ wossname.acd yank.acd
+
+--- 49,56 ----
+ splitter.acd stretcher.acd stssearch.acd supermatcher.acd syco.acd \
+ tcode.acd testplot.acd textsearch.acd tfextract.acd tfm.acd \
+ tfscan.acd tmap.acd tranalign.acd transeq.acd treetypedisplay.acd \
+! trimest.acd trimseq.acd trimspace.acd twofeat.acd union.acd \
+! vectorstrip.acd water.acd whichdb.acd wobble.acd \
+ wordcount.acd wordfinder.acd wordmatch.acd \
+ wossname.acd yank.acd
+
+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
+***************
+*** 209,215 ****
+ fuzznuc.acd fuzzpro.acd fuzztran.acd \
+ garnier.acd geecee.acd getorf.acd giep.acd \
+ helixturnhelix.acd histogramtest.acd \
+! hmoment.acd iep.acd infoalign.acd infoseq.acd intconv.acd \
+ isochore.acd jaspextract.acd jaspscan.acd lindna.acd listor.acd \
+ makenucseq.acd makeprotseq.acd marscan.acd \
+ maskambignuc.acd maskambigprot.acd maskfeat.acd maskseq.acd \
+--- 209,216 ----
+ fuzznuc.acd fuzzpro.acd fuzztran.acd \
+ garnier.acd geecee.acd getorf.acd giep.acd \
+ helixturnhelix.acd histogramtest.acd \
+! hmoment.acd iep.acd infoalign.acd infobase.acd inforesidue.acd \
+! infoseq.acd intconv.acd \
+ isochore.acd jaspextract.acd jaspscan.acd lindna.acd listor.acd \
+ makenucseq.acd makeprotseq.acd marscan.acd \
+ maskambignuc.acd maskambigprot.acd maskfeat.acd maskseq.acd \
+***************
+*** 236,243 ****
+ splitter.acd stretcher.acd stssearch.acd supermatcher.acd syco.acd \
+ tcode.acd testplot.acd textsearch.acd tfextract.acd tfm.acd \
+ tfscan.acd tmap.acd tranalign.acd transeq.acd treetypedisplay.acd \
+! trimest.acd trimseq.acd twofeat.acd union.acd vectorstrip.acd \
+! water.acd whichdb.acd wobble.acd \
+ wordcount.acd wordfinder.acd wordmatch.acd \
+ wossname.acd yank.acd
+
+--- 237,244 ----
+ splitter.acd stretcher.acd stssearch.acd supermatcher.acd syco.acd \
+ tcode.acd testplot.acd textsearch.acd tfextract.acd tfm.acd \
+ tfscan.acd tmap.acd tranalign.acd transeq.acd treetypedisplay.acd \
+! trimest.acd trimseq.acd trimspace.acd twofeat.acd union.acd \
+! vectorstrip.acd water.acd whichdb.acd wobble.acd \
+ wordcount.acd wordfinder.acd wordmatch.acd \
+ wossname.acd yank.acd
+
+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
+***************
+*** 30,36 ****
+ Epprofile Eprior1.plib Eprior30.plib Erna.melt Eresidues.iub \
+ Esig.euk Esig.pro \
+ Etags.embl Etags.emboss \
+! Etags.gff Etags.gff3 Etags.gffprotein \
+ Etags.pir Etags.protein Etags.swiss \
+ Etcode.dat Evdw.dat Ewhite-wimley.dat \
+ embossre.equ Emwfilter.dat Emass.dat Emassmod.dat \
+--- 30,36 ----
+ Epprofile Eprior1.plib Eprior30.plib Erna.melt Eresidues.iub \
+ Esig.euk Esig.pro \
+ Etags.embl Etags.emboss \
+! Etags.gff Etags.gff3 Etags.gffprotein Etags.gff3protein \
+ Etags.pir Etags.protein Etags.swiss \
+ Etcode.dat Evdw.dat Ewhite-wimley.dat \
+ 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
+***************
+*** 228,234 ****
+ Epprofile Eprior1.plib Eprior30.plib Erna.melt Eresidues.iub \
+ Esig.euk Esig.pro \
+ Etags.embl Etags.emboss \
+! Etags.gff Etags.gff3 Etags.gffprotein \
+ Etags.pir Etags.protein Etags.swiss \
+ Etcode.dat Evdw.dat Ewhite-wimley.dat \
+ embossre.equ Emwfilter.dat Emass.dat Emassmod.dat \
+--- 228,234 ----
+ Epprofile Eprior1.plib Eprior30.plib Erna.melt Eresidues.iub \
+ Esig.euk Esig.pro \
+ Etags.embl Etags.emboss \
+! Etags.gff Etags.gff3 Etags.gffprotein Etags.gff3protein \
+ Etags.pir Etags.protein Etags.swiss \
+ Etcode.dat Evdw.dat Ewhite-wimley.dat \
+ 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 2008-08-26 15:30:06.000000000 +0100
+--- EMBOSS-6.0.1/emboss/jaspscan.c 2009-01-10 10:21:31.000000000 +0000
***************
*** 293,299 ****
@@ -37,9 +177,29 @@
ajStrDel(&dir);
ajStrDel(&menu);
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
+***************
+*** 174,180 ****
+ vectorlist = ajListNew();
+
+ /* data from command line or file? */
+! if(vec == AJTRUE)
+ vectorstrip_read_vector_data(vectorfile, vectorlist);
+ else
+ {
+--- 174,180 ----
+ vectorlist = ajListNew();
+
+ /* data from command line or file? */
+! if(vec && vectorfile)
+ vectorstrip_read_vector_data(vectorfile, vectorlist);
+ else
+ {
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 2008-08-26 15:29:44.000000000 +0100
+--- EMBOSS-6.0.1/nucleus/embprop.c 2009-01-10 10:21:31.000000000 +0000
***************
*** 880,885 ****
--- 880,886 ----
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