1 |
ssuominen 09/08/05 19:42:01 |
2 |
|
3 |
Added: wise-2.2.0-glibc-2.10.patch |
4 |
Log: |
5 |
Fix building with GLIBC 2.10+ wrt #278307. |
6 |
(Portage version: 2.2_rc36/cvs/Linux x86_64) |
7 |
|
8 |
Revision Changes Path |
9 |
1.1 sci-biology/wise/files/wise-2.2.0-glibc-2.10.patch |
10 |
|
11 |
file : http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-biology/wise/files/wise-2.2.0-glibc-2.10.patch?rev=1.1&view=markup |
12 |
plain: http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-biology/wise/files/wise-2.2.0-glibc-2.10.patch?rev=1.1&content-type=text/plain |
13 |
|
14 |
Index: wise-2.2.0-glibc-2.10.patch |
15 |
=================================================================== |
16 |
diff -ur wise2.2.0.orig/src/HMMer2/sqio.c wise2.2.0/src/HMMer2/sqio.c |
17 |
--- wise2.2.0.orig/src/HMMer2/sqio.c 2001-06-18 16:59:51.000000000 +0300 |
18 |
+++ wise2.2.0/src/HMMer2/sqio.c 2009-08-05 22:39:04.000000000 +0300 |
19 |
@@ -213,7 +213,7 @@ |
20 |
} |
21 |
} |
22 |
|
23 |
-/* Function: getline() |
24 |
+/* Function: get_line() |
25 |
* Date: SRE, Tue Mar 3 08:30:01 1998 [St. Louis] |
26 |
* |
27 |
* Purpose: read a line from a sequence file into V->sbuffer. |
28 |
@@ -229,7 +229,7 @@ |
29 |
* Returns: (void) |
30 |
*/ |
31 |
static void |
32 |
-getline(struct ReadSeqVars *V) |
33 |
+get_line(struct ReadSeqVars *V) |
34 |
{ |
35 |
char *cp; |
36 |
|
37 |
@@ -299,7 +299,7 @@ |
38 |
V->seqlen = 0; |
39 |
if (addfirst) addseq(V->sbuffer, V); |
40 |
do { |
41 |
- getline(V); |
42 |
+ get_line(V); |
43 |
/* feof() alone is a bug; files not necessarily \n terminated */ |
44 |
if (*(V->sbuffer) == '\0' && feof(V->f)) |
45 |
done = TRUE; |
46 |
@@ -327,7 +327,7 @@ |
47 |
char *sptr; |
48 |
/* load first line of entry */ |
49 |
while (!feof(V->f) && strncmp(V->sbuffer, "ENTRY", 5) != 0) |
50 |
- getline(V); |
51 |
+ get_line(V); |
52 |
if (feof(V->f)) return; |
53 |
|
54 |
if ((sptr = strtok(V->sbuffer + 15, "\n\t ")) != NULL) |
55 |
@@ -336,7 +336,7 @@ |
56 |
SetSeqinfoString(V->sqinfo, sptr, SQINFO_ID); |
57 |
} |
58 |
do { |
59 |
- getline(V); |
60 |
+ get_line(V); |
61 |
if (!feof(V->f) && strncmp(V->sbuffer, "TITLE", 5) == 0) |
62 |
SetSeqinfoString(V->sqinfo, V->sbuffer+15, SQINFO_DESC); |
63 |
else if (!feof(V->f) && strncmp(V->sbuffer, "ACCESSION", 9) == 0) |
64 |
@@ -345,7 +345,7 @@ |
65 |
SetSeqinfoString(V->sqinfo, sptr, SQINFO_ACC); |
66 |
} |
67 |
} while (! feof(V->f) && (strncmp(V->sbuffer,"SEQUENCE", 8) != 0)); |
68 |
- getline(V); /* skip next line, coords */ |
69 |
+ get_line(V); /* skip next line, coords */ |
70 |
|
71 |
readLoop(0, endPIR, V); |
72 |
|
73 |
@@ -359,7 +359,7 @@ |
74 |
/* get next line |
75 |
*/ |
76 |
while (!feof(V->f) && strncmp(V->sbuffer, "ENTRY", 5) != 0) |
77 |
- getline(V); |
78 |
+ get_line(V); |
79 |
} |
80 |
|
81 |
|
82 |
@@ -377,7 +377,7 @@ |
83 |
char *nm; |
84 |
/* position past ';' comments */ |
85 |
do { |
86 |
- getline(V); |
87 |
+ get_line(V); |
88 |
} while (! (feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer != ';')) )); |
89 |
|
90 |
if (!feof(V->f)) |
91 |
@@ -389,7 +389,7 @@ |
92 |
} |
93 |
|
94 |
while (!(feof(V->f) || ((*V->sbuffer != '\0') && (*V->sbuffer == ';')))) |
95 |
- getline(V); |
96 |
+ get_line(V); |
97 |
} |
98 |
|
99 |
static int |
100 |
@@ -411,7 +411,7 @@ |
101 |
if ((nm = strtok(V->sbuffer+16, ",\n\t ")) != NULL) |
102 |
SetSeqinfoString(V->sqinfo, nm, SQINFO_NAME); |
103 |
} |
104 |
- getline(V); |
105 |
+ get_line(V); |
106 |
} |
107 |
|
108 |
if (! feof(V->f)) |
109 |
@@ -420,7 +420,7 @@ |
110 |
/* load next line |
111 |
*/ |
112 |
while ((!feof(V->f)) && (*V->sbuffer != ';')) |
113 |
- getline(V); |
114 |
+ get_line(V); |
115 |
} |
116 |
|
117 |
|
118 |
@@ -438,7 +438,7 @@ |
119 |
int in_definition; |
120 |
|
121 |
while (strncmp(V->sbuffer, "LOCUS", 5) != 0) |
122 |
- getline(V); |
123 |
+ get_line(V); |
124 |
|
125 |
if ((sptr = strtok(V->sbuffer+12, "\n\t ")) != NULL) |
126 |
{ |
127 |
@@ -449,7 +449,7 @@ |
128 |
in_definition = FALSE; |
129 |
while (! feof(V->f)) |
130 |
{ |
131 |
- getline(V); |
132 |
+ get_line(V); |
133 |
if (! feof(V->f) && strstr(V->sbuffer, "DEFINITION") == V->sbuffer) |
134 |
{ |
135 |
if ((sptr = strtok(V->sbuffer+12, "\n")) != NULL) |
136 |
@@ -482,11 +482,11 @@ |
137 |
|
138 |
|
139 |
while (!(feof(V->f) || ((*V->sbuffer!=0) && (strstr(V->sbuffer,"LOCUS") == V->sbuffer)))) |
140 |
- getline(V); |
141 |
+ get_line(V); |
142 |
/* SRE: V->s now holds "//", so sequential |
143 |
reads are wedged: fixed Tue Jul 13 1993 */ |
144 |
while (!feof(V->f) && strstr(V->sbuffer, "LOCUS ") != V->sbuffer) |
145 |
- getline(V); |
146 |
+ get_line(V); |
147 |
} |
148 |
|
149 |
static int |
150 |
@@ -515,7 +515,7 @@ |
151 |
Die("bogus GCGdata format? %s", V->sbuffer); |
152 |
|
153 |
/* second line contains free text description */ |
154 |
- getline(V); |
155 |
+ get_line(V); |
156 |
SetSeqinfoString(V->sqinfo, V->sbuffer, SQINFO_DESC); |
157 |
|
158 |
if (binary) { |
159 |
@@ -535,7 +535,7 @@ |
160 |
else readLoop(0, endGCGdata, V); |
161 |
|
162 |
while (!(feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer == '>')))) |
163 |
- getline(V); |
164 |
+ get_line(V); |
165 |
} |
166 |
|
167 |
static int |
168 |
@@ -555,12 +555,12 @@ |
169 |
if ((sptr = strtok(NULL, "\n")) != NULL) |
170 |
SetSeqinfoString(V->sqinfo, sptr, SQINFO_DESC); |
171 |
/* workaround for long NCBI NR lines */ |
172 |
- while (V->longline && ! feof(V->f)) getline(V); |
173 |
+ while (V->longline && ! feof(V->f)) get_line(V); |
174 |
|
175 |
readLoop(0, endPearson, V); |
176 |
|
177 |
while (!(feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer == '>')))) |
178 |
- getline(V); |
179 |
+ get_line(V); |
180 |
} |
181 |
|
182 |
|
183 |
@@ -587,7 +587,7 @@ |
184 |
|
185 |
/* make sure we have first line */ |
186 |
while (!feof(V->f) && strncmp(V->sbuffer, "ID ", 4) != 0) |
187 |
- getline(V); |
188 |
+ get_line(V); |
189 |
|
190 |
if ((sptr = strtok(V->sbuffer+5, "\n\t ")) != NULL) |
191 |
{ |
192 |
@@ -596,7 +596,7 @@ |
193 |
} |
194 |
|
195 |
do { |
196 |
- getline(V); |
197 |
+ get_line(V); |
198 |
if (!feof(V->f) && strstr(V->sbuffer, "AC ") == V->sbuffer) |
199 |
{ |
200 |
if ((sptr = strtok(V->sbuffer+5, "; \t\n")) != NULL) |
201 |
@@ -620,7 +620,7 @@ |
202 |
|
203 |
/* load next record's ID line */ |
204 |
while (!feof(V->f) && strncmp(V->sbuffer, "ID ", 4) != 0) |
205 |
- getline(V); |
206 |
+ get_line(V); |
207 |
} |
208 |
|
209 |
|
210 |
@@ -636,7 +636,7 @@ |
211 |
{ |
212 |
char *sptr; |
213 |
|
214 |
- getline(V); /*s == "seqLen seqid string..."*/ |
215 |
+ get_line(V); /*s == "seqLen seqid string..."*/ |
216 |
|
217 |
if ((sptr = strtok(V->sbuffer+6, " \t\n")) != NULL) |
218 |
SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME); |
219 |
@@ -647,7 +647,7 @@ |
220 |
readLoop(0, endZuker, V); |
221 |
|
222 |
while (!(feof(V->f) | ((*V->sbuffer != '\0') & (*V->sbuffer == '(')))) |
223 |
- getline(V); |
224 |
+ get_line(V); |
225 |
} |
226 |
|
227 |
static void |
228 |
@@ -669,7 +669,7 @@ |
229 |
|
230 |
do { |
231 |
done = feof(V->f); |
232 |
- getline(V); |
233 |
+ get_line(V); |
234 |
if (! done) addseq(V->sbuffer, V); |
235 |
} while (!done); |
236 |
} |
237 |
@@ -681,7 +681,7 @@ |
238 |
char *sptr; |
239 |
int dostruc = FALSE; |
240 |
|
241 |
- while (strncmp(V->sbuffer, "NAM ", 4) != 0) getline(V); |
242 |
+ while (strncmp(V->sbuffer, "NAM ", 4) != 0) get_line(V); |
243 |
|
244 |
if ((sptr = strtok(V->sbuffer+4, "\n\t ")) != NULL) |
245 |
SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME); |
246 |
@@ -689,7 +689,7 @@ |
247 |
/*CONSTCOND*/ |
248 |
while (1) |
249 |
{ |
250 |
- getline(V); |
251 |
+ get_line(V); |
252 |
if (feof(V->f)) {squid_errno = SQERR_FORMAT; return; } |
253 |
|
254 |
if (strncmp(V->sbuffer, "SRC ", 4) == 0) |
255 |
@@ -721,14 +721,14 @@ |
256 |
while (1) |
257 |
{ |
258 |
/* sequence line */ |
259 |
- getline(V); |
260 |
+ get_line(V); |
261 |
if (feof(V->f) || strncmp(V->sbuffer, "++", 2) == 0) |
262 |
break; |
263 |
addseq(V->sbuffer, V); |
264 |
/* structure line */ |
265 |
if (dostruc) |
266 |
{ |
267 |
- getline(V); |
268 |
+ get_line(V); |
269 |
if (feof(V->f)) { squid_errno = SQERR_FORMAT; return; } |
270 |
addstruc(V->sbuffer, V); |
271 |
} |
272 |
@@ -736,7 +736,7 @@ |
273 |
|
274 |
|
275 |
while (!feof(V->f) && strncmp(V->sbuffer, "NAM ", 4) != 0) |
276 |
- getline(V); |
277 |
+ get_line(V); |
278 |
} |
279 |
|
280 |
|
281 |
@@ -816,7 +816,7 @@ |
282 |
|
283 |
/* Load the first line. |
284 |
*/ |
285 |
- getline(dbfp); |
286 |
+ get_line(dbfp); |
287 |
|
288 |
return dbfp; |
289 |
} |
290 |
@@ -833,7 +833,7 @@ |
291 |
Die("SeqfilePosition() failed: in a nonrewindable data file or stream"); |
292 |
|
293 |
fseek(sqfp->f, offset, SEEK_SET); |
294 |
- getline(sqfp); |
295 |
+ get_line(sqfp); |
296 |
} |
297 |
|
298 |
|
299 |
@@ -853,7 +853,7 @@ |
300 |
if (sqfp->ali_aseqs != NULL) sqfp->ali_curridx = 0; |
301 |
else { |
302 |
rewind(sqfp->f); |
303 |
- getline(sqfp); |
304 |
+ get_line(sqfp); |
305 |
} |
306 |
} |
307 |
|
308 |
@@ -949,7 +949,7 @@ |
309 |
do { /* skip leading comments on GCG file */ |
310 |
gotuw = (strstr(V->sbuffer,"..") != NULL); |
311 |
if (gotuw) readUWGCG(V); |
312 |
- getline(V); |
313 |
+ get_line(V); |
314 |
} while (! feof(V->f)); |
315 |
break; |