[med-svn] r1487 - in trunk/packages/emboss/trunk/debian: . patches
charles-guest at alioth.debian.org
charles-guest at alioth.debian.org
Sat Mar 1 02:55:33 UTC 2008
Author: charles-guest
Date: 2008-03-01 02:55:33 +0000 (Sat, 01 Mar 2008)
New Revision: 1487
Added:
trunk/packages/emboss/trunk/debian/patches/patch-1-3
Removed:
trunk/packages/emboss/trunk/debian/patches/ajindex-fix-2008-01-09.patch
trunk/packages/emboss/trunk/debian/patches/embindex-fix-2008-01-19.patch
trunk/packages/emboss/trunk/debian/patches/psiphi-fix-2007-07-27.patch
Modified:
trunk/packages/emboss/trunk/debian/changelog
trunk/packages/emboss/trunk/debian/patches/series
Log:
New usptream patches released
Modified: trunk/packages/emboss/trunk/debian/changelog
===================================================================
--- trunk/packages/emboss/trunk/debian/changelog 2008-02-29 23:47:57 UTC (rev 1486)
+++ trunk/packages/emboss/trunk/debian/changelog 2008-03-01 02:55:33 UTC (rev 1487)
@@ -1,3 +1,19 @@
+emboss (5.0.0-5) unstable; urgency=low
+
+ * New bugfixes released upstream.
+ - Fixes changed ID format in GCG databases.
+ - Fixes reading from PIR databases.
+ - Fixes a problem with O in protein sequences for pyrrolysine.
+ - Fixes a problem in GENBANK output format.
+ - Fixes a problem in reading protein sequences from Staden
+ "spin" interface.
+ - Fixes tokens that are longer than the maximum length.
+ - debian/patches now uses the monolithic upstream patch instead of
+ file-per-file fixes. You can find longer explanations in the header
+ of debian/patches/patch-1-3.
+
+ -- Charles Plessy <charles-debian-nospam at plessy.org> Sat, 01 Mar 2008 11:46:26 +0900
+
emboss (5.0.0-4) unstable; urgency=low
* debian/patches:
Deleted: trunk/packages/emboss/trunk/debian/patches/ajindex-fix-2008-01-09.patch
===================================================================
--- trunk/packages/emboss/trunk/debian/patches/ajindex-fix-2008-01-09.patch 2008-02-29 23:47:57 UTC (rev 1486)
+++ trunk/packages/emboss/trunk/debian/patches/ajindex-fix-2008-01-09.patch 2008-03-01 02:55:33 UTC (rev 1487)
@@ -1,36 +0,0 @@
-Fixes rare secondary index problem with input files over 2Gb.
---- a/ajax/ajindex.c
-+++ b/ajax/ajindex.c
-@@ -2516,7 +2516,14 @@
-
- static ajint btreeNumIdCompare(const void *a, const void *b)
- {
-- return (*(AjPBtNumId const *)a)->offset - (*(AjPBtNumId const *)b)->offset;
-+ ajlong val;
-+
-+ val = (*(AjPBtNumId const *)a)->offset - (*(AjPBtNumId const *)b)->offset;
-+
-+ if(!val)
-+ return 0;
-+
-+ return (val < 0L) ? -1 : 1;
- }
-
-
-@@ -11956,8 +11963,14 @@
-
- static ajint btreeOffsetCompare(const void *a, const void *b)
- {
-- return (*(AjPBtId const *)a)->offset -
-- (*(AjPBtId const *)b)->offset;
-+ ajlong val;
-+
-+ val = (*(AjPBtId const *)a)->offset - (*(AjPBtId const *)b)->offset;
-+
-+ if(!val)
-+ return 0;
-+
-+ return (val < 0L) ? -1 : 1;
- }
-
-
Deleted: trunk/packages/emboss/trunk/debian/patches/embindex-fix-2008-01-19.patch
===================================================================
--- trunk/packages/emboss/trunk/debian/patches/embindex-fix-2008-01-19.patch 2008-02-29 23:47:57 UTC (rev 1486)
+++ trunk/packages/emboss/trunk/debian/patches/embindex-fix-2008-01-19.patch 2008-03-01 02:55:33 UTC (rev 1487)
@@ -1,56 +0,0 @@
-Fix 3. EMBOSS-5.0.0/nucleus/embindex.c
-
-18 Jan 2008: Order and fill fixes to sort out potential problems
- with kw/de/tx indexes.
-Index: EMBOSS-5.0.0/nucleus/embindex.c
-===================================================================
---- EMBOSS-5.0.0.orig/nucleus/embindex.c
-+++ EMBOSS-5.0.0/nucleus/embindex.c
-@@ -1196,13 +1196,13 @@
- entry->txorder = (entry->pagesize - 60) / ((entry->txlen + 1) + 12);
- entry->txfill = (entry->pagesize - 16) / (entry->txlen + 28);
-
-- entry->kwsecorder = (entry->pagesize - 60) / ((entry->idlen + 1) + 12);
-- entry->desecorder = (entry->pagesize - 60) / ((entry->idlen + 1) + 12);
-- entry->txsecorder = (entry->pagesize - 60) / ((entry->idlen + 1) + 12);
--
-- entry->kwsecfill = (entry->pagesize - 16) / (entry->idlen + 4);
-- entry->desecfill = (entry->pagesize - 16) / (entry->idlen + 4);
-- entry->txsecfill = (entry->pagesize - 16) / (entry->idlen + 4);
-+ entry->kwsecorder = (entry->pagesize - 60) / ((entry->kwlen + 1) + 12);
-+ entry->desecorder = (entry->pagesize - 60) / ((entry->delen + 1) + 12);
-+ entry->txsecorder = (entry->pagesize - 60) / ((entry->txlen + 1) + 12);
-+
-+ entry->kwsecfill = (entry->pagesize - 16) / (entry->kwlen + 4);
-+ entry->desecfill = (entry->pagesize - 16) / (entry->delen + 4);
-+ entry->txsecfill = (entry->pagesize - 16) / (entry->txlen + 4);
-
- entry->idsecorder = (entry->pagesize - 60) / 24;
- entry->idsecfill = (entry->pagesize - 60) / 20;
-@@ -1251,7 +1251,7 @@
- entry->cachesize,
- entry->idsecorder, slevel,
- entry->idsecfill, count,
-- entry->kwlen);
-+ entry->idlen);
- if(!entry->idcache)
- ajFatal("Cannot open ID index");
-
-@@ -1267,7 +1267,7 @@
- entry->cachesize,
- entry->acsecorder, slevel,
- entry->acsecfill, count,
-- entry->kwlen);
-+ entry->aclen);
- if(!entry->accache)
- ajFatal("Cannot open ACC index");
-
-@@ -1282,7 +1282,7 @@
- entry->cachesize,
- entry->svsecorder, slevel,
- entry->svsecfill, count,
-- entry->kwlen);
-+ entry->svlen);
- if(!entry->svcache)
- ajFatal("Cannot open SV index");
-
Added: trunk/packages/emboss/trunk/debian/patches/patch-1-3
===================================================================
--- trunk/packages/emboss/trunk/debian/patches/patch-1-3 (rev 0)
+++ trunk/packages/emboss/trunk/debian/patches/patch-1-3 2008-03-01 02:55:33 UTC (rev 1487)
@@ -0,0 +1,220 @@
+This patch was downloaded from:
+ftp://emboss.open-bio.org/pub/EMBOSS/fixes/patches/patch-1-3.gz
+
+Explanations for the changes are pasted from:
+ftp://emboss.open-bio.org/pub/EMBOSS/fixes/README.fixes
+
+Fix 1. EMBOSS-5.0.0/emboss/psiphi.c
+
+27 Jul 2007: Fixes a problem with reading more recent CCF files.
+ Error traps cases where chains have no atom information.
+
+Fix 2. EMBOSS-5.0.0/ajax/ajindex.c
+
+9 Jan 2008: Fixes rare secondary index problem with input files over 2Gb.
+
+Fix 3. EMBOSS-5.0.0/nucleus/embindex.c
+
+18 Jan 2008: Order and fill fixes to sort out potential problems
+ with kw/de/tx indexes.
+
+Fix 4. EMBOSS-5.0.0/ajax/ajseqdb.c
+
+19 Feb 2008: Fixes changed ID format in GCG databases.
+ Fixes reading from PIR databases
+
+Fix 5. EMBOSS-5.0.0/ajax/ajseqtype.c
+
+19 Feb 2008: Fixes a problem with O in protein sequences for pyrrolysine.
+ Lower case o worked, but upper case O was excluded as a
+ gap character in early versions of PHYLIP. 'O' is no
+ longer a gap character in EMBOSS.
+
+Fix 6. EMBOSS-5.0.0/ajax/ajseqwrite.c
+
+19 Feb 2008: Fixes a problem in GENBANK output format for mulitple
+ lines of ACCESSION or KEYWORD records in an entry.
+
+Fix 7. EMBOSS-5.0.0/ajax/ajseqread.c
+
+19 Feb 2008: Fixes a problem in reading protein sequences from the
+ Staden "spin" interface. The partial EMBL/SwissProt
+ format was set to "nucleotide". All incomplete
+ EMBL/SwissProt entries are now tested for amino acid
+ characters and set to protein if any non-nucleotide
+ characters are found.
+
+
+Fix 8. EMBOSS-5.0.0/emboss/dbxfasta.c
+
+19 Feb 2008: Fixes tokens that are longer than the maximum length in
+ the resource definition.
+ For IDs issues a warning when any ID is truncated.
+
+diff -c -N --recursive EMBOSS-5.0.0old/ajax/ajindex.c EMBOSS-5.0.0/ajax/ajindex.c
+*** EMBOSS-5.0.0old/ajax/ajindex.c 2007-07-06 13:18:48.000000000 +0100
+--- EMBOSS-5.0.0/ajax/ajindex.c 2008-01-19 13:05:35.000000000 +0000
+***************
+*** 2516,2522 ****
+
+ static ajint btreeNumIdCompare(const void *a, const void *b)
+ {
+! return (*(AjPBtNumId const *)a)->offset - (*(AjPBtNumId const *)b)->offset;
+ }
+
+
+--- 2516,2529 ----
+
+ static ajint btreeNumIdCompare(const void *a, const void *b)
+ {
+! ajlong val;
+!
+! val = (*(AjPBtNumId const *)a)->offset - (*(AjPBtNumId const *)b)->offset;
+!
+! if(!val)
+! return 0;
+!
+! return (val < 0L) ? -1 : 1;
+ }
+
+
+***************
+*** 11956,11963 ****
+
+ static ajint btreeOffsetCompare(const void *a, const void *b)
+ {
+! return (*(AjPBtId const *)a)->offset -
+! (*(AjPBtId const *)b)->offset;
+ }
+
+
+--- 11963,11976 ----
+
+ static ajint btreeOffsetCompare(const void *a, const void *b)
+ {
+! ajlong val;
+!
+! val = (*(AjPBtId const *)a)->offset - (*(AjPBtId const *)b)->offset;
+!
+! if(!val)
+! return 0;
+!
+! return (val < 0L) ? -1 : 1;
+ }
+
+
+diff -c -N --recursive EMBOSS-5.0.0old/emboss/psiphi.c EMBOSS-5.0.0/emboss/psiphi.c
+*** EMBOSS-5.0.0old/emboss/psiphi.c 2007-07-06 13:15:29.000000000 +0100
+--- EMBOSS-5.0.0/emboss/psiphi.c 2008-01-19 13:05:35.000000000 +0000
+***************
+*** 160,166 ****
+ finishres = ajAcdGetInt("finishresiduenumber");
+
+ /* reserve memory for and read in structure */
+! /* JISON */ pdb = ajPdbReadoldNew(pdbfile);
+
+ /* check and set number of chain to be analysed */
+ highest = pdb->Nchn;
+--- 160,166 ----
+ finishres = ajAcdGetInt("finishresiduenumber");
+
+ /* reserve memory for and read in structure */
+! /* JISON */ pdb = ajPdbReadNew(pdbfile,0);
+
+ /* check and set number of chain to be analysed */
+ highest = pdb->Nchn;
+***************
+*** 440,445 ****
+--- 440,448 ----
+ ajint lowestres = 0;
+
+ AjPAtom inlist = NULL;
++
++ if(!ajListGetLength(pdb->Chains[myindex]->Atoms))
++ ajFatal("Chain %d has no atoms",myindex+1);
+
+ /* read first atom in list into memory, but keep it on list */
+ ajListPeek(pdb->Chains[myindex]->Atoms,
+diff -c -N --recursive EMBOSS-5.0.0old/nucleus/embindex.c EMBOSS-5.0.0/nucleus/embindex.c
+*** EMBOSS-5.0.0old/nucleus/embindex.c 2007-07-06 13:15:00.000000000 +0100
+--- EMBOSS-5.0.0/nucleus/embindex.c 2008-01-19 13:05:44.000000000 +0000
+***************
+*** 1196,1208 ****
+ entry->txorder = (entry->pagesize - 60) / ((entry->txlen + 1) + 12);
+ entry->txfill = (entry->pagesize - 16) / (entry->txlen + 28);
+
+! entry->kwsecorder = (entry->pagesize - 60) / ((entry->idlen + 1) + 12);
+! entry->desecorder = (entry->pagesize - 60) / ((entry->idlen + 1) + 12);
+! entry->txsecorder = (entry->pagesize - 60) / ((entry->idlen + 1) + 12);
+!
+! entry->kwsecfill = (entry->pagesize - 16) / (entry->idlen + 4);
+! entry->desecfill = (entry->pagesize - 16) / (entry->idlen + 4);
+! entry->txsecfill = (entry->pagesize - 16) / (entry->idlen + 4);
+
+ entry->idsecorder = (entry->pagesize - 60) / 24;
+ entry->idsecfill = (entry->pagesize - 60) / 20;
+--- 1196,1208 ----
+ entry->txorder = (entry->pagesize - 60) / ((entry->txlen + 1) + 12);
+ entry->txfill = (entry->pagesize - 16) / (entry->txlen + 28);
+
+! entry->kwsecorder = (entry->pagesize - 60) / ((entry->kwlen + 1) + 12);
+! entry->desecorder = (entry->pagesize - 60) / ((entry->delen + 1) + 12);
+! entry->txsecorder = (entry->pagesize - 60) / ((entry->txlen + 1) + 12);
+!
+! entry->kwsecfill = (entry->pagesize - 16) / (entry->kwlen + 4);
+! entry->desecfill = (entry->pagesize - 16) / (entry->delen + 4);
+! entry->txsecfill = (entry->pagesize - 16) / (entry->txlen + 4);
+
+ entry->idsecorder = (entry->pagesize - 60) / 24;
+ entry->idsecfill = (entry->pagesize - 60) / 20;
+***************
+*** 1251,1257 ****
+ entry->cachesize,
+ entry->idsecorder, slevel,
+ entry->idsecfill, count,
+! entry->kwlen);
+ if(!entry->idcache)
+ ajFatal("Cannot open ID index");
+
+--- 1251,1257 ----
+ entry->cachesize,
+ entry->idsecorder, slevel,
+ entry->idsecfill, count,
+! entry->idlen);
+ if(!entry->idcache)
+ ajFatal("Cannot open ID index");
+
+***************
+*** 1267,1273 ****
+ entry->cachesize,
+ entry->acsecorder, slevel,
+ entry->acsecfill, count,
+! entry->kwlen);
+ if(!entry->accache)
+ ajFatal("Cannot open ACC index");
+
+--- 1267,1273 ----
+ entry->cachesize,
+ entry->acsecorder, slevel,
+ entry->acsecfill, count,
+! entry->aclen);
+ if(!entry->accache)
+ ajFatal("Cannot open ACC index");
+
+***************
+*** 1282,1288 ****
+ entry->cachesize,
+ entry->svsecorder, slevel,
+ entry->svsecfill, count,
+! entry->kwlen);
+ if(!entry->svcache)
+ ajFatal("Cannot open SV index");
+
+--- 1282,1288 ----
+ entry->cachesize,
+ entry->svsecorder, slevel,
+ entry->svsecfill, count,
+! entry->svlen);
+ if(!entry->svcache)
+ ajFatal("Cannot open SV index");
+
Deleted: trunk/packages/emboss/trunk/debian/patches/psiphi-fix-2007-07-27.patch
===================================================================
--- trunk/packages/emboss/trunk/debian/patches/psiphi-fix-2007-07-27.patch 2008-02-29 23:47:57 UTC (rev 1486)
+++ trunk/packages/emboss/trunk/debian/patches/psiphi-fix-2007-07-27.patch 2008-03-01 02:55:33 UTC (rev 1487)
@@ -1,25 +0,0 @@
-Fixes a problem with reading more recent CCF files.
-Error traps cases where chains have no atom information.
-Index: EMBOSS-5.0.0/emboss/psiphi.c
-===================================================================
---- EMBOSS-5.0.0.orig/emboss/psiphi.c
-+++ EMBOSS-5.0.0/emboss/psiphi.c
-@@ -160,7 +160,7 @@
- finishres = ajAcdGetInt("finishresiduenumber");
-
- /* reserve memory for and read in structure */
-- /* JISON */ pdb = ajPdbReadoldNew(pdbfile);
-+ /* JISON */ pdb = ajPdbReadNew(pdbfile,0);
-
- /* check and set number of chain to be analysed */
- highest = pdb->Nchn;
-@@ -440,6 +440,9 @@
- ajint lowestres = 0;
-
- AjPAtom inlist = NULL;
-+
-+ if(!ajListGetLength(pdb->Chains[myindex]->Atoms))
-+ ajFatal("Chain %d has no atoms",myindex+1);
-
- /* read first atom in list into memory, but keep it on list */
- ajListPeek(pdb->Chains[myindex]->Atoms,
Modified: trunk/packages/emboss/trunk/debian/patches/series
===================================================================
--- trunk/packages/emboss/trunk/debian/patches/series 2008-02-29 23:47:57 UTC (rev 1486)
+++ trunk/packages/emboss/trunk/debian/patches/series 2008-03-01 02:55:33 UTC (rev 1487)
@@ -1,4 +1,2 @@
-embindex-fix-2008-01-19.patch
using-pager-in-tfm.patch
-psiphi-fix-2007-07-27.patch
-ajindex-fix-2008-01-09.patch
+patch-1-3
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