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