Author: plessy Date: 2009-05-17 10:48:36 +0000 (Sun, 17 May 2009) New Revision: 3385
Modified: trunk/packages/emboss/trunk/debian/changelog trunk/packages/emboss/trunk/debian/patches/upstream.patch Log: New upstream patch. Package updated and uploaded. Modified: trunk/packages/emboss/trunk/debian/changelog =================================================================== --- trunk/packages/emboss/trunk/debian/changelog 2009-05-17 05:36:26 UTC (rev 3384) +++ trunk/packages/emboss/trunk/debian/changelog 2009-05-17 10:48:36 UTC (rev 3385) @@ -1,3 +1,17 @@ +emboss (6.0.1-11) unstable; urgency=low + + * New upstream patch (patch-1-12): + - Remove the 'aligned' attribute that was added in Fix 4. + - Fix crash if maxfragl > 40 selected. + - Update Entrez retrieval to cope with an extra line added + in the NCBI results. + - For phylogenetic applications (PHYLIPNEW) reading distance matrix files + failed for some formats written by other applications. Distance matrix + input now works for multiple matrices in square, upper-triangular and + lower-triangular formats. + + -- Charles Plessy <[email protected]> Sun, 17 May 2009 14:51:05 +0900 + emboss (6.0.1-10) unstable; urgency=low * New upstream patch (patch-1-8): Modified: trunk/packages/emboss/trunk/debian/patches/upstream.patch =================================================================== --- trunk/packages/emboss/trunk/debian/patches/upstream.patch 2009-05-17 05:36:26 UTC (rev 3384) +++ trunk/packages/emboss/trunk/debian/patches/upstream.patch 2009-05-17 10:48:36 UTC (rev 3385) @@ -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-1-8.gz + ftp://emboss.open-bio.org/pub/EMBOSS/fixes/patches/patch-1-12.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 2009-04-20 14:45:27.000000000 +0100 +--- EMBOSS-6.0.1/ajax/ajacd.c 2009-05-14 15:34:27.000000000 +0100 *************** *** 8256,8263 **** --- 8256,8271 ---- @@ -238,9 +238,353 @@ { for(itestparam = acd->PNum+1; itestparam <= acdNParam; itestparam++) +diff -c -N --recursive EMBOSS-6.0.1old/ajax/ajphylo.c EMBOSS-6.0.1/ajax/ajphylo.c +*** EMBOSS-6.0.1old/ajax/ajphylo.c 2008-06-26 09:38:43.000000000 +0100 +--- EMBOSS-6.0.1/ajax/ajphylo.c 2009-05-14 15:34:41.000000000 +0100 +*************** +*** 402,408 **** + AjPStr tmpval = NULL; + AjBool lowertri = ajFalse; + AjBool uppertri = ajFalse; +! + if(!phyloRegDistFloat) + phyloRegDistFloat = + ajRegCompC("^\\s*([0-9]+[.]?[0-9]*)\\s+(([0-9]+)[^0-9.])?"); +--- 402,412 ---- + AjPStr tmpval = NULL; + AjBool lowertri = ajFalse; + AjBool uppertri = ajFalse; +! AjPStr name = NULL; +! AjPStr rest = NULL; +! ajuint imaxlen; +! ajuint linenum = 0; +! + if(!phyloRegDistFloat) + phyloRegDistFloat = + ajRegCompC("^\\s*([0-9]+[.]?[0-9]*)\\s+(([0-9]+)[^0-9.])?"); +*************** +*** 413,439 **** + if(!distfile) + return NULL; + +- ajReadlineTrim(distfile, &rdline); +- if(!ajStrToInt(rdline, &count)) +- { +- ajErr("Distance file '%S' bad header record '%S'", +- filename, rdline); +- return NULL; +- } +- ajDebug("DistRead: row count: %d\n", count); +- +- if(size && (count != size)) +- { +- ajErr("Distance file '%S' found %d expected %d rows '%S'", +- filename, count, size); +- return NULL; +- } +- +- + done = ajTrue; + while(ajReadline(distfile, &rdline)) + { + if(done) { + irow = -1; + icol = 0; + +--- 417,445 ---- + if(!distfile) + return NULL; + + done = ajTrue; + while(ajReadline(distfile, &rdline)) + { ++ linenum++; ++ if(ajStrIsWhite(rdline)) continue; + if(done) { ++ ajStrTrimWhite(&rdline); ++ if(!ajStrToInt(rdline, &count)) ++ { ++ ajErr("Distance file '%S' line %u bad header record '%S'", ++ filename, linenum, rdline); ++ return NULL; ++ } ++ ajDebug("DistRead: row count: %d\n", count); ++ ++ if(size && (count != size)) ++ { ++ ajErr("Distance file '%S' line %u " ++ "found %d expected %d rows '%S'", ++ filename, linenum, count, size); ++ return NULL; ++ } ++ + irow = -1; + icol = 0; + +*************** +*** 446,458 **** + ncells = count*count; + AJCNEW0(dist->Data,ncells); + AJCNEW0(dist->Replicates,ncells); + } + + /*ajDebug("DistRead line: %S", rdline); */ + if(!i || !ajRegExec(phyloRegDistFloat, rdline)) + { +- if(ajStrGetLen(rdline) < 11) /* skip this line? */ +- continue; + if(!irow) /* how long was that first row */ + { + if(!icol) /* empty - lower triangular */ +--- 452,463 ---- + ncells = count*count; + AJCNEW0(dist->Data,ncells); + AJCNEW0(dist->Replicates,ncells); ++ continue; + } + + /*ajDebug("DistRead line: %S", rdline); */ + if(!i || !ajRegExec(phyloRegDistFloat, rdline)) + { + if(!irow) /* how long was that first row */ + { + if(!icol) /* empty - lower triangular */ +*************** +*** 475,482 **** + } + else if(icol != count) /* something wrong */ + { +! ajErr("Distance file %S: Row '%S' has %d values", +! filename, dist->Names[irow], icol); + } + } + else if(irow > 0) /* later rows - we know what to expect */ +--- 480,487 ---- + } + else if(icol != count) /* something wrong */ + { +! ajErr("Distance file %S: line %u Row '%S' has %d values", +! filename, linenum, dist->Names[irow], icol); + } + } + else if(irow > 0) /* later rows - we know what to expect */ +*************** +*** 486,523 **** + /*ajDebug("DistRead Lower irow: %d i: %d\n", + irow, i);*/ + if(icol != irow) +! ajErr("Distance file %S: Row '%S' has %d values" + " in lower-triangular format", +! filename, dist->Names[irow], icol); + } + else if(uppertri) + { + /*ajDebug("DistRead Upper irow: %d i: %d\n", + irow, i);*/ + if(i) +! ajErr("Distance file %S: Row '%S' has %d values" + " in upper-triangular format", +! filename, dist->Names[irow], icol - irow - 1); + } + else + { + /*ajDebug("DistRead Square irow: %d i: %d\n", + irow, i);*/ + if(icol != count) +! ajErr("Distance file %S: Row '%S' has %d values" + " in square format", +! filename, dist->Names[irow], icol); + } + } + + irow++; + if(irow > count) + { +! ajErr("Distances file read beyond %d rows", count); + return NULL; + } +! ajStrAssignSubS(&dist->Names[irow], rdline, 0, 9); +! ajStrCutStart(&rdline, 10); + ajStrTrimWhiteEnd(&dist->Names[irow]); + ajDebug("DistRead name [%d] '%S' i: %d\n", + irow, dist->Names[irow], i); +--- 491,536 ---- + /*ajDebug("DistRead Lower irow: %d i: %d\n", + irow, i);*/ + if(icol != irow) +! ajErr("Distance file %S: line %u Row '%S' has %d values" + " in lower-triangular format", +! filename, linenum, dist->Names[irow], icol); + } + else if(uppertri) + { + /*ajDebug("DistRead Upper irow: %d i: %d\n", + irow, i);*/ + if(i) +! ajErr("Distance file %S: line %u Row '%S' has %d values" + " in upper-triangular format", +! filename, linenum, +! dist->Names[irow], icol - irow - 1); + } + else + { + /*ajDebug("DistRead Square irow: %d i: %d\n", + irow, i);*/ + if(icol != count) +! ajErr("Distance file %S: line %u Row '%S' has %d values" + " in square format", +! filename, linenum, dist->Names[irow], icol); + } + } + + irow++; + if(irow > count) + { +! ajErr("Distances file line %u read beyond %d rows", +! linenum, count); + return NULL; + } +! ajStrExtractWord(rdline, &rest, &name); +! if(ajStrGetLen(name) >= 10) +! imaxlen = 10; +! else +! imaxlen = ajStrGetLen(name); +! ajStrAssignSubS(&dist->Names[irow], rdline, 0, imaxlen-1); +! +! ajStrCutStart(&rdline, imaxlen); + ajStrTrimWhiteEnd(&dist->Names[irow]); + ajDebug("DistRead name [%d] '%S' i: %d\n", + irow, dist->Names[irow], i); +*************** +*** 548,555 **** + { + if(!missing) + { +! ajErr("Distances file %S: Zero (%S) replicates for %S", +! filename, tmpval, dist->Names[irow]); + return NULL; + } + dist->HasMissing = ajTrue; +--- 561,569 ---- + { + if(!missing) + { +! ajErr("Distances file %S: line %u " +! "Zero (%S) replicates for %S", +! filename, linenum, tmpval, dist->Names[irow]); + return NULL; + } + dist->HasMissing = ajTrue; +*************** +*** 576,584 **** + } + if(irow == (count-1)) + { +! done = ajTrue; +! +! if(lowertri) /* fill in the rest */ + { + for(k=0; k < count; k++) + { +--- 590,596 ---- + } + if(irow == (count-1)) + { +! if(lowertri) /* fill in the rest */ + { + for(k=0; k < count; k++) + { +*************** +*** 596,607 **** + jpos += count; + } + } + } +! if(uppertri) /* fill in the rest */ + { + for(k=0; k < count; k++) + { +! idiag = k*count + i; /* diagonal */ + dist->Data[idiag] = 0.0; + dist->Replicates[idiag] = 1; + ipos = k*count; /* start of row*/ +--- 608,620 ---- + jpos += count; + } + } ++ done = ajTrue; + } +! else if(uppertri) /* fill in the rest */ + { + for(k=0; k < count; k++) + { +! idiag = k*count + k; /* diagonal */ + dist->Data[idiag] = 0.0; + dist->Replicates[idiag] = 1; + ipos = k*count; /* start of row*/ +*************** +*** 614,623 **** + jpos += count; + } + } + } +! +! ajListPushAppend(distlist, dist); +! dist = NULL; + } + } + +--- 627,643 ---- + jpos += count; + } + } ++ done = ajTrue; + } +! else if(icol == count) +! { +! done = ajTrue; +! } +! +! if(done){ +! ajListPushAppend(distlist, dist); +! dist = NULL; +! } + } + } + +*************** +*** 627,634 **** + return NULL; + } + +! ajDebug("Distances file '%S' has %d (%d) distance matrices\n", +! filename, i, ajListGetLength(distlist)); + ajFileClose(&distfile); + ajListToarray(distlist, (void***) &ret); + /*ret = (AjPPhyloTree*) trees;*/ +--- 647,654 ---- + return NULL; + } + +! ajDebug("Distances file '%S' has %u distance matrices\n", +! filename, ajListGetLength(distlist)); + ajFileClose(&distfile); + ajListToarray(distlist, (void***) &ret); + /*ret = (AjPPhyloTree*) trees;*/ +*************** +*** 636,641 **** +--- 656,663 ---- + for(i=0; ret[i]; i++) + ajPhyloDistTrace(ret[i]); + ++ ajStrDel(&name); ++ ajStrDel(&rest); + return ret; + } + 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 2009-04-20 14:45:27.000000000 +0100 +--- EMBOSS-6.0.1/ajax/ajseq.c 2009-05-14 15:34:27.000000000 +0100 *************** *** 287,292 **** --- 287,293 ---- @@ -376,9 +720,25 @@ 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/ajseqdb.c EMBOSS-6.0.1/ajax/ajseqdb.c +*** EMBOSS-6.0.1old/ajax/ajseqdb.c 2008-07-14 15:52:03.000000000 +0100 +--- EMBOSS-6.0.1/ajax/ajseqdb.c 2009-05-14 15:34:27.000000000 +0100 +*************** +*** 2005,2011 **** +--- 2005,2014 ---- + { + ajStrTrimWhite(&seqline); + if(!ajStrGetLen(seqline)) ++ { ++ ajBuffreadLine(seqfile, &seqline); + ihead=0; ++ } + } + else + { 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 2009-04-20 14:45:27.000000000 +0100 +--- EMBOSS-6.0.1/ajax/ajseqread.c 2009-05-14 15:34:27.000000000 +0100 *************** *** 1617,1623 **** ajDebug("ready to start reading format '%S' '%S' %d..%d\n", @@ -398,7 +758,7 @@ 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 2009-04-20 14:45:27.000000000 +0100 +--- EMBOSS-6.0.1/ajax/ajseqwrite.c 2009-05-14 15:34:27.000000000 +0100 *************** *** 451,456 **** --- 451,457 ---- @@ -456,7 +816,7 @@ 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 2009-04-20 14:45:27.000000000 +0100 +--- EMBOSS-6.0.1/emboss/acd/edialign.acd 2009-05-14 15:34:27.000000000 +0100 *************** *** 26,32 **** information: "Nucleic acid sequence alignment mode" @@ -491,19 +851,9 @@ 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 2009-04-20 14:45:27.000000000 +0100 +--- EMBOSS-6.0.1/emboss/acd/Makefile.am 2009-05-14 15:34:27.000000000 +0100 *************** *** 21,27 **** fuzznuc.acd fuzzpro.acd fuzztran.acd \ @@ -543,7 +893,7 @@ 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 2009-04-20 14:45:27.000000000 +0100 +--- EMBOSS-6.0.1/emboss/acd/Makefile.in 2009-05-14 15:34:27.000000000 +0100 *************** *** 209,215 **** fuzznuc.acd fuzzpro.acd fuzztran.acd \ @@ -583,7 +933,7 @@ 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 2009-04-20 14:45:27.000000000 +0100 +--- EMBOSS-6.0.1/emboss/data/Makefile.am 2009-05-14 15:34:27.000000000 +0100 *************** *** 30,36 **** Epprofile Eprior1.plib Eprior30.plib Erna.melt Eresidues.iub \ @@ -603,7 +953,7 @@ 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 2009-04-20 14:45:27.000000000 +0100 +--- EMBOSS-6.0.1/emboss/data/Makefile.in 2009-05-14 15:34:27.000000000 +0100 *************** *** 228,234 **** Epprofile Eprior1.plib Eprior30.plib Erna.melt Eresidues.iub \ @@ -621,9 +971,23 @@ 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/edialign.c EMBOSS-6.0.1/emboss/edialign.c +*** EMBOSS-6.0.1old/emboss/edialign.c 2008-06-26 09:39:09.000000000 +0100 +--- EMBOSS-6.0.1/emboss/edialign.c 2009-05-14 15:34:27.000000000 +0100 +*************** +*** 627,632 **** +--- 627,634 ---- + ajSeqsetFmtUpper(seqset); + n = ajSeqsetGetSize(seqset); + ++ max_dia = lmax; ++ + AJCNEW0(seq,n); + AJCNEW0(seq_name,n); + AJCNEW0(full_name,n); 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 2009-04-20 14:45:27.000000000 +0100 +--- EMBOSS-6.0.1/emboss/jaspscan.c 2009-05-14 15:34:27.000000000 +0100 *************** *** 293,299 **** @@ -656,7 +1020,7 @@ 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 2009-04-20 14:45:27.000000000 +0100 +--- EMBOSS-6.0.1/emboss/needle.c 2009-05-14 15:34:27.000000000 +0100 *************** *** 151,157 **** { @@ -676,7 +1040,7 @@ sim); diff -c -N --recursive EMBOSS-6.0.1old/emboss/remap.c EMBOSS-6.0.1/emboss/remap.c *** EMBOSS-6.0.1old/emboss/remap.c 2008-06-26 09:39:09.000000000 +0100 ---- EMBOSS-6.0.1/emboss/remap.c 2009-04-20 14:45:40.000000000 +0100 +--- EMBOSS-6.0.1/emboss/remap.c 2009-05-14 15:34:27.000000000 +0100 *************** *** 618,624 **** @@ -696,7 +1060,7 @@ (AjPStr) keyarray[i], value->count, 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 2009-04-20 14:45:27.000000000 +0100 +--- EMBOSS-6.0.1/emboss/vectorstrip.c 2009-05-14 15:34:27.000000000 +0100 *************** *** 174,180 **** vectorlist = ajListNew(); @@ -716,7 +1080,7 @@ { 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 2009-04-20 14:45:27.000000000 +0100 +--- EMBOSS-6.0.1/emboss/water.c 2009-05-14 15:34:27.000000000 +0100 *************** *** 159,165 **** { @@ -736,7 +1100,7 @@ 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 2009-04-20 14:45:27.000000000 +0100 +--- EMBOSS-6.0.1/nucleus/embaln.c 2009-05-14 15:34:27.000000000 +0100 *************** *** 69,79 **** ajint i; @@ -1267,7 +1631,7 @@ 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 2009-04-20 14:45:27.000000000 +0100 +--- EMBOSS-6.0.1/nucleus/embprop.c 2009-05-14 15:34:27.000000000 +0100 *************** *** 880,885 **** --- 880,886 ---- _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/mailman/listinfo/debian-med-commit
