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 <[email protected]> +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 <[email protected]> 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 . { _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
