[med-svn] r3385 - in trunk/packages/emboss/trunk/debian: . patches
Charles Plessy
plessy at alioth.debian.org
Sun May 17 10:48:37 UTC 2009
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 <plessy at debian.org> 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 ----
More information about the debian-med-commit
mailing list