[med-svn] r3268 - in trunk/packages/emboss/trunk/debian: . patches
Charles Plessy
plessy at alioth.debian.org
Wed Apr 8 05:47:29 UTC 2009
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 <plessy at debian.org> 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 ----
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