gcc-4.3 patches
Andreas Tille
16 years ago
| 0 | --- glimmer3.02.orig/src/Common/delcher.cc | |
| 1 | +++ glimmer3.02/src/Common/delcher.cc | |
| 2 | @@ -9,6 +9,7 @@ | |
| 3 | ||
| 4 | #include "delcher.hh" | |
| 5 | ||
| 6 | +#include <cstring> | |
| 7 | ||
| 8 | const int COMMATIZE_BUFF_LEN = 50; | |
| 9 | // Length of buffer for creating string with commas | |
| 10 | --- glimmer3.02.orig/src/Common/fasta.cc | |
| 11 | +++ glimmer3.02/src/Common/fasta.cc | |
| 12 | @@ -9,7 +9,7 @@ | |
| 13 | ||
| 14 | #include "fasta.hh" | |
| 15 | ||
| 16 | - | |
| 17 | +#include <cstring> | |
| 18 | ||
| 19 | void Fasta_Print | |
| 20 | (FILE * fp, const char * s, const char * hdr, int fasta_width) | |
| 21 | --- glimmer3.02.orig/src/Common/gene.cc | |
| 22 | +++ glimmer3.02/src/Common/gene.cc | |
| 23 | @@ -10,6 +10,7 @@ | |
| 24 | #include "delcher.hh" | |
| 25 | #include "gene.hh" | |
| 26 | ||
| 27 | +#include <cstring> | |
| 28 | ||
| 29 | static const char COMPLEMENT_TABLE [] | |
| 30 | = "nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn" | |
| 31 | --- glimmer3.02.orig/src/Glimmer/anomaly.cc | |
| 32 | +++ glimmer3.02/src/Glimmer/anomaly.cc | |
| 33 | @@ -12,6 +12,7 @@ | |
| 34 | ||
| 35 | #include "anomaly.hh" | |
| 36 | ||
| 37 | +#include <cstring> | |
| 38 | ||
| 39 | // Global variables | |
| 40 | ||
| 41 | --- glimmer3.02.orig/src/ICM/icm.cc | |
| 42 | +++ glimmer3.02/src/ICM/icm.cc | |
| 43 | @@ -15,6 +15,8 @@ | |
| 44 | ||
| 45 | #include "icm.hh" | |
| 46 | ||
| 47 | +#include <cstring> | |
| 48 | + | |
| 49 | using namespace std; | |
| 50 | ||
| 51 | extern int Verbose; | |
| 52 | --- glimmer3.02.orig/src/Util/entropy-score.cc | |
| 53 | +++ glimmer3.02/src/Util/entropy-score.cc | |
| 54 | @@ -9,7 +9,7 @@ | |
| 55 | // regions in it by entropy distance. Results are output | |
| 56 | // to stdout . | |
| 57 | ||
| 58 | - | |
| 59 | +#include <cstring> | |
| 60 | ||
| 61 | #include "entropy-score.hh" | |
| 62 | ||
| 63 | --- glimmer3.02.orig/src/Glimmer/glimmer3.cc | |
| 64 | +++ glimmer3.02/src/Glimmer/glimmer3.cc | |
| 65 | @@ -12,11 +12,10 @@ | |
| 66 | // Copyright (c) 2006 University of Maryland Center for Bioinformatics | |
| 67 | // & Computational Biology | |
| 68 | ||
| 69 | - | |
| 70 | +#include <cstring> | |
| 71 | ||
| 72 | #include "glimmer3.hh" | |
| 73 | ||
| 74 | - | |
| 75 | static int For_Edwin = 0; | |
| 76 | ||
| 77 | ||
| 78 | --- glimmer3.02.orig/src/ICM/build-icm.cc | |
| 79 | +++ glimmer3.02/src/ICM/build-icm.cc | |
| 80 | @@ -13,6 +13,7 @@ | |
| 81 | ||
| 82 | #include "build-icm.hh" | |
| 83 | ||
| 84 | +#include <cstring> | |
| 85 | ||
| 86 | static int Genbank_Xlate_Code = 0; | |
| 87 | // Holds the Genbank translation table number that determines | |
| 88 | --- glimmer3.02.orig/src/Util/extract.cc | |
| 89 | +++ glimmer3.02/src/Util/extract.cc | |
| 90 | @@ -9,7 +9,7 @@ | |
| 91 | // sequences specified by coordinates. The resulting sequences | |
| 92 | // are output (in multifasta or two-string format) to stdout. | |
| 93 | ||
| 94 | - | |
| 95 | +#include <cstring> | |
| 96 | ||
| 97 | #include "extract.hh" | |
| 98 | ||
| 99 | --- glimmer3.02.orig/src/Glimmer/glimmer2.cc | |
| 100 | +++ glimmer3.02/src/Glimmer/glimmer2.cc | |
| 101 | @@ -37,6 +37,7 @@ | |
| 102 | #include "delcher.h" | |
| 103 | #include "gene.h" | |
| 104 | ||
| 105 | +#include <cstring> | |
| 106 | ||
| 107 | const int DEFAULT_MIN_GENE_LEN = 90; | |
| 108 | const double DEFAULT_MIN_OLAP_PERCENT = 0.10; | |
| 109 | --- glimmer3.02.orig/src/Glimmer/long-orfs.cc | |
| 110 | +++ glimmer3.02/src/Glimmer/long-orfs.cc | |
| 111 | @@ -15,7 +15,7 @@ | |
| 112 | ||
| 113 | #include "long-orfs.hh" | |
| 114 | ||
| 115 | - | |
| 116 | +#include <cstring> | |
| 117 | ||
| 118 | // External variables | |
| 119 | ||
| 120 | --- glimmer3.02.orig/src/ICM/build-fixed.cc | |
| 121 | +++ glimmer3.02/src/ICM/build-fixed.cc | |
| 122 | @@ -12,6 +12,7 @@ | |
| 123 | ||
| 124 | #include "build-fixed.hh" | |
| 125 | ||
| 126 | +#include <cstring> | |
| 127 | ||
| 128 | static FILE * Index_File_fp = NULL; | |
| 129 | // File containing a list of subscripts of strings to train model | |
| 130 | --- glimmer3.02.orig/src/ICM/score-fixed.cc | |
| 131 | +++ glimmer3.02/src/ICM/score-fixed.cc | |
| 132 | @@ -8,6 +8,7 @@ | |
| 133 | ||
| 134 | #include "score-fixed.hh" | |
| 135 | ||
| 136 | +#include <cstring> | |
| 137 | ||
| 138 | static char * Pos_Model_Path; | |
| 139 | // Name of file containing the positive model | |
| 140 | --- glimmer3.02.orig/src/Util/multi-extract.cc | |
| 141 | +++ glimmer3.02/src/Util/multi-extract.cc | |
| 142 | @@ -10,7 +10,7 @@ | |
| 143 | // resulting sequences are output (in multifasta or two-string format) | |
| 144 | // to stdout. | |
| 145 | ||
| 146 | - | |
| 147 | +#include <cstring> | |
| 148 | ||
| 149 | #include "multi-extract.hh" | |
| 150 | ||
| 151 | --- glimmer3.02.orig/src/Util/start-codon-distrib.cc | |
| 152 | +++ glimmer3.02/src/Util/start-codon-distrib.cc | |
| 153 | @@ -17,6 +17,7 @@ | |
| 154 | ||
| 155 | #include "start-codon-distrib.hh" | |
| 156 | ||
| 157 | +#include <cstring> | |
| 158 | ||
| 159 | // External variables | |
| 160 | ||
| 161 | --- glimmer3.02.orig/src/Util/uncovered.cc | |
| 162 | +++ glimmer3.02/src/Util/uncovered.cc | |
| 163 | @@ -10,7 +10,7 @@ | |
| 164 | // specified in the file named as the second command-line argument. | |
| 165 | // Output is a multifasta file sent to stdout. | |
| 166 | ||
| 167 | - | |
| 168 | +#include <cstring> | |
| 169 | ||
| 170 | #include "uncovered.hh" | |
| 171 |