[med-svn] r15103 - trunk/packages/tigr-glimmer/trunk/debian/patches
Andreas Tille
tille at alioth.debian.org
Tue Nov 5 08:59:18 UTC 2013
Author: tille
Date: 2013-11-05 08:59:17 +0000 (Tue, 05 Nov 2013)
New Revision: 15103
Modified:
trunk/packages/tigr-glimmer/trunk/debian/patches/01_Makefile.patch
trunk/packages/tigr-glimmer/trunk/debian/patches/10_gcc4.3.patch
trunk/packages/tigr-glimmer/trunk/debian/patches/10_gcc4.4.patch
Log:
Refreshed patches
Modified: trunk/packages/tigr-glimmer/trunk/debian/patches/01_Makefile.patch
===================================================================
--- trunk/packages/tigr-glimmer/trunk/debian/patches/01_Makefile.patch 2013-11-05 08:48:48 UTC (rev 15102)
+++ trunk/packages/tigr-glimmer/trunk/debian/patches/01_Makefile.patch 2013-11-05 08:59:17 UTC (rev 15103)
@@ -1,5 +1,9 @@
+Author: Steffen Moeller <moeller at pzr.uni-rostock.de>
+LastChanged: Thu, 16 Oct 2003 17:33:46 +0200
+Description: Provide main Makefile
+
--- /dev/null
-+++ glimmer3.02/Makefile
++++ b/Makefile
@@ -0,0 +1,7 @@
+all:
+ cd src; make
Modified: trunk/packages/tigr-glimmer/trunk/debian/patches/10_gcc4.3.patch
===================================================================
--- trunk/packages/tigr-glimmer/trunk/debian/patches/10_gcc4.3.patch 2013-11-05 08:48:48 UTC (rev 15102)
+++ trunk/packages/tigr-glimmer/trunk/debian/patches/10_gcc4.3.patch 2013-11-05 08:59:17 UTC (rev 15103)
@@ -1,8 +1,8 @@
Author: Kumar Appaiah
Description: Fix #461691
---- glimmer3.02.orig/src/Common/delcher.cc
-+++ glimmer3.02/src/Common/delcher.cc
+--- a/src/Common/delcher.cc
++++ b/src/Common/delcher.cc
@@ -9,6 +9,7 @@
#include "delcher.hh"
@@ -11,8 +11,8 @@
const int COMMATIZE_BUFF_LEN = 50;
// Length of buffer for creating string with commas
---- glimmer3.02.orig/src/Common/fasta.cc
-+++ glimmer3.02/src/Common/fasta.cc
+--- a/src/Common/fasta.cc
++++ b/src/Common/fasta.cc
@@ -9,7 +9,7 @@
#include "fasta.hh"
@@ -22,8 +22,8 @@
void Fasta_Print
(FILE * fp, const char * s, const char * hdr, int fasta_width)
---- glimmer3.02.orig/src/Common/gene.cc
-+++ glimmer3.02/src/Common/gene.cc
+--- a/src/Common/gene.cc
++++ b/src/Common/gene.cc
@@ -10,6 +10,7 @@
#include "delcher.hh"
#include "gene.hh"
@@ -32,8 +32,8 @@
static const char COMPLEMENT_TABLE []
= "nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn"
---- glimmer3.02.orig/src/Glimmer/anomaly.cc
-+++ glimmer3.02/src/Glimmer/anomaly.cc
+--- a/src/Glimmer/anomaly.cc
++++ b/src/Glimmer/anomaly.cc
@@ -12,6 +12,7 @@
#include "anomaly.hh"
@@ -42,8 +42,8 @@
// Global variables
---- glimmer3.02.orig/src/ICM/icm.cc
-+++ glimmer3.02/src/ICM/icm.cc
+--- a/src/ICM/icm.cc
++++ b/src/ICM/icm.cc
@@ -15,6 +15,8 @@
#include "icm.hh"
@@ -53,8 +53,8 @@
using namespace std;
extern int Verbose;
---- glimmer3.02.orig/src/Util/entropy-score.cc
-+++ glimmer3.02/src/Util/entropy-score.cc
+--- a/src/Util/entropy-score.cc
++++ b/src/Util/entropy-score.cc
@@ -9,7 +9,7 @@
// regions in it by entropy distance. Results are output
// to stdout .
@@ -64,8 +64,8 @@
#include "entropy-score.hh"
---- glimmer3.02.orig/src/Glimmer/glimmer3.cc
-+++ glimmer3.02/src/Glimmer/glimmer3.cc
+--- a/src/Glimmer/glimmer3.cc
++++ b/src/Glimmer/glimmer3.cc
@@ -12,11 +12,10 @@
// Copyright (c) 2006 University of Maryland Center for Bioinformatics
// & Computational Biology
@@ -79,8 +79,8 @@
static int For_Edwin = 0;
---- glimmer3.02.orig/src/ICM/build-icm.cc
-+++ glimmer3.02/src/ICM/build-icm.cc
+--- a/src/ICM/build-icm.cc
++++ b/src/ICM/build-icm.cc
@@ -13,6 +13,7 @@
#include "build-icm.hh"
@@ -89,8 +89,8 @@
static int Genbank_Xlate_Code = 0;
// Holds the Genbank translation table number that determines
---- glimmer3.02.orig/src/Util/extract.cc
-+++ glimmer3.02/src/Util/extract.cc
+--- a/src/Util/extract.cc
++++ b/src/Util/extract.cc
@@ -9,7 +9,7 @@
// sequences specified by coordinates. The resulting sequences
// are output (in multifasta or two-string format) to stdout.
@@ -100,8 +100,8 @@
#include "extract.hh"
---- glimmer3.02.orig/src/Glimmer/glimmer2.cc
-+++ glimmer3.02/src/Glimmer/glimmer2.cc
+--- a/src/Glimmer/glimmer2.cc
++++ b/src/Glimmer/glimmer2.cc
@@ -37,6 +37,7 @@
#include "delcher.h"
#include "gene.h"
@@ -110,8 +110,8 @@
const int DEFAULT_MIN_GENE_LEN = 90;
const double DEFAULT_MIN_OLAP_PERCENT = 0.10;
---- glimmer3.02.orig/src/Glimmer/long-orfs.cc
-+++ glimmer3.02/src/Glimmer/long-orfs.cc
+--- a/src/Glimmer/long-orfs.cc
++++ b/src/Glimmer/long-orfs.cc
@@ -15,7 +15,7 @@
#include "long-orfs.hh"
@@ -121,8 +121,8 @@
// External variables
---- glimmer3.02.orig/src/ICM/build-fixed.cc
-+++ glimmer3.02/src/ICM/build-fixed.cc
+--- a/src/ICM/build-fixed.cc
++++ b/src/ICM/build-fixed.cc
@@ -12,6 +12,7 @@
#include "build-fixed.hh"
@@ -131,8 +131,8 @@
static FILE * Index_File_fp = NULL;
// File containing a list of subscripts of strings to train model
---- glimmer3.02.orig/src/ICM/score-fixed.cc
-+++ glimmer3.02/src/ICM/score-fixed.cc
+--- a/src/ICM/score-fixed.cc
++++ b/src/ICM/score-fixed.cc
@@ -8,6 +8,7 @@
#include "score-fixed.hh"
@@ -141,8 +141,8 @@
static char * Pos_Model_Path;
// Name of file containing the positive model
---- glimmer3.02.orig/src/Util/multi-extract.cc
-+++ glimmer3.02/src/Util/multi-extract.cc
+--- a/src/Util/multi-extract.cc
++++ b/src/Util/multi-extract.cc
@@ -10,7 +10,7 @@
// resulting sequences are output (in multifasta or two-string format)
// to stdout.
@@ -152,8 +152,8 @@
#include "multi-extract.hh"
---- glimmer3.02.orig/src/Util/start-codon-distrib.cc
-+++ glimmer3.02/src/Util/start-codon-distrib.cc
+--- a/src/Util/start-codon-distrib.cc
++++ b/src/Util/start-codon-distrib.cc
@@ -17,6 +17,7 @@
#include "start-codon-distrib.hh"
@@ -162,8 +162,8 @@
// External variables
---- glimmer3.02.orig/src/Util/uncovered.cc
-+++ glimmer3.02/src/Util/uncovered.cc
+--- a/src/Util/uncovered.cc
++++ b/src/Util/uncovered.cc
@@ -10,7 +10,7 @@
// specified in the file named as the second command-line argument.
// Output is a multifasta file sent to stdout.
Modified: trunk/packages/tigr-glimmer/trunk/debian/patches/10_gcc4.4.patch
===================================================================
--- trunk/packages/tigr-glimmer/trunk/debian/patches/10_gcc4.4.patch 2013-11-05 08:48:48 UTC (rev 15102)
+++ trunk/packages/tigr-glimmer/trunk/debian/patches/10_gcc4.4.patch 2013-11-05 08:59:17 UTC (rev 15103)
@@ -1,9 +1,9 @@
Author: Andreas Tille <tille at debian.org>
Description: Fix FTBFS #560442
---- tigr-glimmer-3.02.orig/src/Common/gene.cc
-+++ tigr-glimmer-3.02/src/Common/gene.cc
-@@ -444,7 +444,7 @@
+--- a/src/Common/gene.cc
++++ b/src/Common/gene.cc
+@@ -444,7 +444,7 @@ int Char_Sub
// Return a subscript corresponding to character ch .
{
@@ -12,9 +12,9 @@
p = strchr (CONVERSION_STRING, tolower (ch));
if (p == NULL)
---- tigr-glimmer-3.02.orig/src/ICM/icm.cc
-+++ tigr-glimmer-3.02/src/ICM/icm.cc
-@@ -1983,7 +1983,7 @@
+--- a/src/ICM/icm.cc
++++ b/src/ICM/icm.cc
+@@ -1983,7 +1983,7 @@ int Subscript
// model) for character ch .
{
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