Author: plessy Date: 2009-04-08 05:47:28 +0000 (Wed, 08 Apr 2009) New Revision: 3268
Modified: trunk/packages/emboss/trunk/debian/changelog trunk/packages/emboss/trunk/debian/patches/upstream.patch Log: Preparing an update with the new upstream patch. Modified: trunk/packages/emboss/trunk/debian/changelog =================================================================== --- trunk/packages/emboss/trunk/debian/changelog 2009-04-06 21:17:10 UTC (rev 3267) +++ trunk/packages/emboss/trunk/debian/changelog 2009-04-08 05:47:28 UTC (rev 3268) @@ -1,3 +1,12 @@ +emboss (6.0.1-9) UNRELEASED; urgency=low + + * New upstream patch (patch-1-7): + - Corrections on syntax using the master qualifier name as a suffix. + - Better support of the --without-x (not used in this package). + - Bug corrected for needle and water using the -nobrief option. + + -- Charles Plessy <[email protected]> Wed, 08 Apr 2009 14:42:58 +0900 + emboss (6.0.1-8) unstable; urgency=low * debian/rules: Modified: trunk/packages/emboss/trunk/debian/patches/upstream.patch =================================================================== --- trunk/packages/emboss/trunk/debian/patches/upstream.patch 2009-04-06 21:17:10 UTC (rev 3267) +++ trunk/packages/emboss/trunk/debian/patches/upstream.patch 2009-04-08 05:47:28 UTC (rev 3268) @@ -3,10 +3,244 @@ 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-1-6.gz + ftp://emboss.open-bio.org/pub/EMBOSS/fixes/patches/patch-1-7.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 +*************** +*** 8256,8263 **** +--- 8256,8271 ---- + acdReplyInit(thys, ajStrGetPtr(gdev), &acdReplyDef); + else + #ifndef WIN32 ++ #ifndef X_DISPLAY_MISSING /* X11 is available */ + acdReplyInit(thys, "x11", &acdReplyDef); + #else ++ #ifdef PLD_png /* if png/gd/zlib libraries available for png driver */ ++ acdReplyInit(thys, "png", &acdReplyDef); ++ #else ++ acdReplyInit(thys, "ps", &acdReplyDef); ++ #endif ++ #endif ++ #else + acdReplyInit(thys, "win3", &acdReplyDef); + #endif + } +*************** +*** 8426,8433 **** +--- 8434,8449 ---- + acdReplyInit(thys, ajStrGetPtr(gdev), &acdReplyDef); + else + #ifndef WIN32 ++ #ifndef X_DISPLAY_MISSING /* X11 is available */ + acdReplyInit(thys, "x11", &acdReplyDef); + #else ++ #ifdef PLD_png /* if png/gd/zlib libraries available for png driver */ ++ acdReplyInit(thys, "png", &acdReplyDef); ++ #else ++ acdReplyInit(thys, "ps", &acdReplyDef); ++ #endif ++ #endif ++ #else + acdReplyInit(thys, "win3", &acdReplyDef); + #endif + } +*************** +*** 11433,11443 **** + + if(ajSeqIsNuc(val)) + { +- if(seqin->Rev) +- { +- okrev = ajTrue; +- } +- + for(itry=acdPromptTry; itry && !okrev; itry--) + { + ajStrAssignC(&acdReplyPrompt, "N"); +--- 11449,11454 ---- +*************** +*** 11631,11637 **** + okend = acdQualToSeqend(thys, "send", 0, + &seqin->End, &acdTmpStr); + okrev = acdQualToBool(thys, "sreverse", ajFalse, +! &seqin->Rev, &acdTmpStr); + + if(snuc) + ajSeqinSetNuc(seqin); +--- 11642,11648 ---- + okend = acdQualToSeqend(thys, "send", 0, + &seqin->End, &acdTmpStr); + okrev = acdQualToBool(thys, "sreverse", ajFalse, +! &sreverse, &acdTmpStr); + + if(snuc) + ajSeqinSetNuc(seqin); +*************** +*** 11723,11734 **** + + if(ajSeqIsNuc(seq)) + { +- if(seqin->Rev) +- { +- okrev = ajTrue; +- val->Rev = seq->Rev = seqin->Rev; +- } +- + for(itry=acdPromptTry; itry && !okrev; itry--) + { + ajStrAssignC(&acdReplyPrompt, "N"); +--- 11734,11739 ---- +*************** +*** 11753,11759 **** + } + } + +! /* no need to reverse - it should happen in ajSeqallNext */ + + acdLog("sbegin: %d, send: %d, sreverse: %B\n", + sbegin, send, sreverse); +--- 11758,11764 ---- + } + } + +! + + acdLog("sbegin: %d, send: %d, sreverse: %B\n", + sbegin, send, sreverse); +*************** +*** 11906,11912 **** + okend = acdQualToSeqend(thys, "send", 0, + &seqin->End, &acdTmpStr); + okrev = acdQualToBool(thys, "sreverse", ajFalse, +! &seqin->Rev, &acdTmpStr); + + if(snuc) + ajSeqinSetNuc(seqin); +--- 11911,11917 ---- + okend = acdQualToSeqend(thys, "send", 0, + &seqin->End, &acdTmpStr); + okrev = acdQualToBool(thys, "sreverse", ajFalse, +! &sreverse, &acdTmpStr); + + if(snuc) + ajSeqinSetNuc(seqin); +*************** +*** 12003,12015 **** + + if(ajSeqsetIsNuc(val[0])) + { +- if(seqin->Rev) +- { +- okrev = ajTrue; +- for(iset=0;iset<nsets;iset++) +- val[iset]->Rev = seqin->Rev; +- } +- + for(itry=acdPromptTry; itry && !okrev; itry--) + { + ajStrAssignC(&acdReplyPrompt, "N"); +--- 12008,12013 ---- +*************** +*** 12788,12794 **** + okend = acdQualToSeqend(thys, "send", 0, + &seqin->End, &acdTmpStr); + okrev = acdQualToBool(thys, "sreverse", ajFalse, +! &seqin->Rev, &acdTmpStr); + + if(snuc) + ajSeqinSetNuc(seqin); +--- 12786,12792 ---- + okend = acdQualToSeqend(thys, "send", 0, + &seqin->End, &acdTmpStr); + okrev = acdQualToBool(thys, "sreverse", ajFalse, +! &sreverse, &acdTmpStr); + + if(snuc) + ajSeqinSetNuc(seqin); +*************** +*** 12876,12887 **** + + if(ajSeqsetGetSize(val) && ajSeqsetIsNuc(val)) + { +- if(seqin->Rev) +- { +- okrev = ajTrue; +- val->Rev = seqin->Rev; +- } +- + for(itry=acdPromptTry; itry && !okrev; itry--) + { + ajStrAssignC(&acdReplyPrompt, "N"); +--- 12874,12879 ---- +*************** +*** 15461,15479 **** + + static void acdHelpExpectGraph(const AcdPAcd thys, AjBool table, AjPStr* str) + { +- if(!thys) return; +- + #ifndef WIN32 +! if(table) +! ajStrAppendC(str, "<i>EMBOSS_GRAPHICS</i> value, or x11"); +! else +! ajStrAppendC(str, "$EMBOSS_GRAPHICS value, or x11"); + #else + if(table) +! ajStrAppendC(str, "<i>EMBOSS_GRAPHICS</i> value, or win3"); + else +! ajStrAppendC(str, "$EMBOSS_GRAPHICS value, or win3"); +! #endif + return; + } + +--- 15453,15478 ---- + + static void acdHelpExpectGraph(const AcdPAcd thys, AjBool table, AjPStr* str) + { + #ifndef WIN32 +! #ifndef X_DISPLAY_MISSING /* X11 is available */ +! const char* defdev = "x11"; +! #else +! #ifdef PLD_png /* if png/gd/zlib libraries available for png driver */ +! const char* defdev = "png"; +! #else +! const char* defdev = "ps"; +! #endif +! #endif + #else ++ const char* defdev = "win3"; ++ #endif ++ ++ if(!thys) return; ++ + if(table) +! ajFmtPrintAppS(str, "<i>EMBOSS_GRAPHICS</i> value, or %s"), defdev; + else +! ajFmtPrintAppS(str, "$EMBOSS_GRAPHICS value, or %s", defdev); + return; + } + +*************** +*** 19171,19177 **** + acdLog("number: %d jparam: %d acd->PNum: %d acdNParam: %d\n", + number, jparam, acd->PNum, acdNParam); + +! if(!number && !jparam && acd->PNum) + { + for(itestparam = acd->PNum+1; itestparam <= acdNParam; + itestparam++) +--- 19170,19176 ---- + acdLog("number: %d jparam: %d acd->PNum: %d acdNParam: %d\n", + number, jparam, acd->PNum, acdNParam); + +! if(!ajStrGetLen(master) && !number && !jparam && acd->PNum) + { + for(itestparam = acd->PNum+1; itestparam <= acdNParam; + 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 2009-03-24 16:05:14.000000000 +0000 +--- EMBOSS-6.0.1/ajax/ajseq.c 2009-04-07 11:40:06.000000000 +0100 *************** *** 287,292 **** --- 287,293 ---- @@ -129,9 +363,42 @@ ajStrSetClear(&seq->Type); ajStrSetClear(&seq->Molecule); ajStrSetClear(&seq->Class); +*************** +*** 5364,5370 **** +--- 5387,5396 ---- + seq->Begin = -(iend); + + for(i=0; i < seq->Size; i++) ++ { ++ seq->Seq[i]->Rev = ajTrue; + ajSeqReverseDo(seq->Seq[i]); ++ } + + ajDebug(" set result len: %d Begin: %d End: %d\n", + 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 +*************** +*** 1617,1623 **** + ajDebug("ready to start reading format '%S' '%S' %d..%d\n", + seqin->Formatstr, seq->Formatstr, seqin->Begin, seqin->End); + +! while(ajSeqRead(seq, seqin)) + { + if (seqin->List) + ajSeqinClearPos(seqin); +--- 1617,1623 ---- + ajDebug("ready to start reading format '%S' '%S' %d..%d\n", + seqin->Formatstr, seq->Formatstr, seqin->Begin, seqin->End); + +! while(!seqin->multidone && ajSeqRead(seq, seqin)) + { + if (seqin->List) + 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 2009-03-24 16:05:14.000000000 +0000 +--- EMBOSS-6.0.1/ajax/ajseqwrite.c 2009-04-07 11:39:40.000000000 +0100 *************** *** 451,456 **** --- 451,457 ---- @@ -189,7 +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 2009-03-24 16:05:14.000000000 +0000 +--- EMBOSS-6.0.1/emboss/acd/edialign.acd 2009-04-07 11:39:40.000000000 +0100 *************** *** 26,32 **** information: "Nucleic acid sequence alignment mode" @@ -236,7 +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 2009-03-24 16:05:14.000000000 +0000 +--- EMBOSS-6.0.1/emboss/acd/Makefile.am 2009-04-07 11:39:40.000000000 +0100 *************** *** 21,27 **** fuzznuc.acd fuzzpro.acd fuzztran.acd \ @@ -276,7 +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 2009-03-24 16:05:14.000000000 +0000 +--- EMBOSS-6.0.1/emboss/acd/Makefile.in 2009-04-07 11:39:40.000000000 +0100 *************** *** 209,215 **** fuzznuc.acd fuzzpro.acd fuzztran.acd \ @@ -316,7 +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 2009-03-24 16:05:14.000000000 +0000 +--- EMBOSS-6.0.1/emboss/data/Makefile.am 2009-04-07 11:39:40.000000000 +0100 *************** *** 30,36 **** Epprofile Eprior1.plib Eprior30.plib Erna.melt Eresidues.iub \ @@ -336,7 +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 2009-03-24 16:05:14.000000000 +0000 +--- EMBOSS-6.0.1/emboss/data/Makefile.in 2009-04-07 11:39:40.000000000 +0100 *************** *** 228,234 **** Epprofile Eprior1.plib Eprior30.plib Erna.melt Eresidues.iub \ @@ -356,7 +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 2009-03-24 16:05:14.000000000 +0000 +--- EMBOSS-6.0.1/emboss/jaspscan.c 2009-04-07 11:39:40.000000000 +0100 *************** *** 293,299 **** @@ -387,9 +654,29 @@ ajStrDel(&dir); ajStrDel(&menu); 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 +*************** +*** 151,157 **** + { + embAlignCalcSimilarity(m,n,sub,cvt,lena,lenb,&id,&sim,&idx, + &simx); +! ajFmtPrintAppS(&tmpstr,"Longest_Identity = %5.2f%%\n", + id); + ajFmtPrintAppS(&tmpstr,"Longest_Similarity = %5.2f%%\n", + sim); +--- 151,157 ---- + { + embAlignCalcSimilarity(m,n,sub,cvt,lena,lenb,&id,&sim,&idx, + &simx); +! ajFmtPrintS(&tmpstr,"Longest_Identity = %5.2f%%\n", + id); + ajFmtPrintAppS(&tmpstr,"Longest_Similarity = %5.2f%%\n", + sim); 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 2009-03-24 16:05:14.000000000 +0000 +--- EMBOSS-6.0.1/emboss/vectorstrip.c 2009-04-07 11:39:40.000000000 +0100 *************** *** 174,180 **** vectorlist = ajListNew(); @@ -407,9 +694,29 @@ vectorstrip_read_vector_data(vectorfile, vectorlist); else { +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 +*************** +*** 159,165 **** + { + embAlignCalcSimilarity(m,n,sub,cvt,lena,lenb,&id,&sim,&idx, + &simx); +! ajFmtPrintAppS(&tmpstr,"Longest_Identity = %5.2f%%\n", + id); + ajFmtPrintAppS(&tmpstr,"Longest_Similarity = %5.2f%%\n", + sim); +--- 159,165 ---- + { + embAlignCalcSimilarity(m,n,sub,cvt,lena,lenb,&id,&sim,&idx, + &simx); +! ajFmtPrintS(&tmpstr,"Longest_Identity = %5.2f%%\n", + id); + ajFmtPrintAppS(&tmpstr,"Longest_Similarity = %5.2f%%\n", + 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 2009-03-24 16:06:15.000000000 +0000 +--- EMBOSS-6.0.1/nucleus/embaln.c 2009-04-07 11:39:40.000000000 +0100 *************** *** 69,79 **** ajint i; @@ -940,7 +1247,7 @@ 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 2009-03-24 16:05:14.000000000 +0000 +--- EMBOSS-6.0.1/nucleus/embprop.c 2009-04-07 11:39:40.000000000 +0100 *************** *** 880,885 **** --- 880,886 ---- _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/mailman/listinfo/debian-med-commit
