Codebase list vmatch / 8ac29e1
add patch to set PATH_MAX if not available Sascha Steinbiss 4 years ago
2 changed file(s) with 358 addition(s) and 0 deletion(s). Raw diff Collapse all Expand all
+357
-0
debian/patches/pathmax.patch less more
0 --- /dev/null
1 +++ b/src/include/pathmax.h
2 @@ -0,0 +1,3 @@
3 +#ifndef PATH_MAX
4 +# define PATH_MAX 8192
5 +#endif
6 --- a/src/include/virtualdef.h
7 +++ b/src/include/virtualdef.h
8 @@ -9,6 +9,8 @@
9 #include "alphadef.h"
10 #include "multidef.h"
11
12 +#include "pathmax.h"
13 +
14 /*
15 This file defines the datatype \texttt{virtualtree} which stores
16 a virtual suffix tree.
17 --- a/src/kurtz-basic/filehandle.c
18 +++ b/src/kurtz-basic/filehandle.c
19 @@ -18,6 +18,8 @@
20 #include "debugdef.h"
21 #include "failures.h"
22
23 +#include "pathmax.h"
24 +
25 //}
26
27 /*EE
28 --- a/src/kurtz-basic/multiseq-adv.c
29 +++ b/src/kurtz-basic/multiseq-adv.c
30 @@ -26,6 +26,8 @@
31 #include "genfile.h"
32 #include "cmp-tabdef.h"
33
34 +#include "pathmax.h"
35 +
36 #include "compfilenm.pr"
37 #include "dstrdup.pr"
38 #include "filehandle.pr"
39 --- a/src/kurtz-basic/readmulti.c
40 +++ b/src/kurtz-basic/readmulti.c
41 @@ -15,6 +15,8 @@
42 #include "alphadef.h"
43 #include "fhandledef.h"
44
45 +#include "pathmax.h"
46 +
47 #include "filehandle.pr"
48 #include "alphabet.pr"
49 #include "checkgzip.pr"
50 --- a/src/kurtz-basic/readvirt.c
51 +++ b/src/kurtz-basic/readvirt.c
52 @@ -32,6 +32,8 @@
53 #include "codondef.h"
54 #include "megabytes.h"
55
56 +#include "pathmax.h"
57 +
58 #include "dstrdup.pr"
59 #include "compfilenm.pr"
60 #include "multiseq.pr"
61 --- a/src/kurtz-basic/scanpaths.c
62 +++ b/src/kurtz-basic/scanpaths.c
63 @@ -10,6 +10,8 @@
64 #include "fhandledef.h"
65 #include "file.h"
66
67 +#include "pathmax.h"
68 +
69 #include "filehandle.pr"
70 #include "dstrdup.pr"
71
72 --- a/src/kurtz/outindextab.c
73 +++ b/src/kurtz/outindextab.c
74 @@ -8,6 +8,8 @@
75 #include "errordef.h"
76 #include "fhandledef.h"
77
78 +#include "pathmax.h"
79 +
80 #include "filehandle.pr"
81
82 Sint outindextab(const char *indexname,
83 --- a/src/Mkvtree/inputdef.h
84 +++ b/src/Mkvtree/inputdef.h
85 @@ -4,6 +4,7 @@
86 #include <stdio.h>
87 #include "types.h"
88 #include "virtualdef.h"
89 +#include "pathmax.h"
90
91 #define ALLDEMANDTABS (LCPTAB | SUFTAB | SKPTAB | BWTTAB | BCKTAB |\
92 TISTAB | OISTAB | STITAB | STI1TAB | ISOTAB | CLDTAB)
93 --- a/src/Mkvtree/mapcfrcrf.c
94 +++ b/src/Mkvtree/mapcfrcrf.c
95 @@ -15,6 +15,8 @@
96 #include "safescpy.pr"
97 #include "filehandle.pr"
98
99 +#include "pathmax.h"
100 +
101 /*
102 This file contains the function makereversetable for the construction of
103 the reverse tables in the affix affix array data structure
104 --- a/src/Mkvtree/mkcfr.c
105 +++ b/src/Mkvtree/mkcfr.c
106 @@ -18,6 +18,8 @@
107 #include "safescpy.pr"
108 #include "filehandle.pr"
109
110 +#include "pathmax.h"
111 +
112 /*
113 This file contains the function makereversetable for the construction of
114 the reverse tables in the affix affix array data structure
115 --- a/src/Mkvtree/mkdna6idx.c
116 +++ b/src/Mkvtree/mkdna6idx.c
117 @@ -30,6 +30,8 @@
118 #include "mkvprocess.pr"
119 #include "mkvtree.pr"
120
121 +#include "pathmax.h"
122 +
123 #ifndef NOLICENSEMANAGER
124 #include "licensemanager.h"
125 #endif
126 --- a/src/Mkvtree/mkrcidx.c
127 +++ b/src/Mkvtree/mkrcidx.c
128 @@ -30,6 +30,8 @@
129 #include "mkvprocess.pr"
130 #include "mkvtree.pr"
131
132 +#include "pathmax.h"
133 +
134 static void showonstdout(char *s)
135 {
136 printf("%s\n",s);
137 --- a/src/Mkvtree/mkvinput.c
138 +++ b/src/Mkvtree/mkvinput.c
139 @@ -20,6 +20,8 @@
140 #include "parsemultiform.pr"
141 #include "reverse.pr"
142
143 +#include "pathmax.h"
144 +
145 #define MAXINPUTSIZE32BITVERSION (UintConst(1) << 30)
146
147 static void transformstringlocalinplace(Uchar *sequence,
148 --- a/src/Mkvtree/mkvprocess.c
149 +++ b/src/Mkvtree/mkvprocess.c
150 @@ -32,6 +32,8 @@
151
152 #include "cprsuf.pr"
153
154 +#include "pathmax.h"
155 +
156 #define EXTRASUFFIXLENGTH 5 // dot and suffix of length at most 4
157 #define NUMOFBASES UintConst(4) // number of bases in DNA alphabet
158
159 --- a/src/Mkvtree/mkvtree.c
160 +++ b/src/Mkvtree/mkvtree.c
161 @@ -25,6 +25,8 @@
162 #include "mkvprocess.pr"
163 #include "getbasename.pr"
164
165 +#include "pathmax.h"
166 +
167 #ifndef NOLICENSEMANAGER
168 #include "licensemanager.h"
169 #endif
170 --- a/src/Mkvtree/vseqselect.c
171 +++ b/src/Mkvtree/vseqselect.c
172 @@ -25,6 +25,8 @@
173 #include "safescpy.pr"
174 #include "filehandle.pr"
175
176 +#include "pathmax.h"
177 +
178 #ifndef NOLICENSEMANAGER
179 #include "licensemanager.h"
180 #endif
181 --- a/src/Mkvtree/vstree2tex.c
182 +++ b/src/Mkvtree/vstree2tex.c
183 @@ -17,6 +17,8 @@
184 #include "filehandle.pr"
185 #include "safescpy.pr"
186
187 +#include "pathmax.h"
188 +
189 #ifndef NOLICENSEMANAGER
190 #include "licensemanager.h"
191 #endif
192 --- a/src/Mkvtree/vsubseqselect.c
193 +++ b/src/Mkvtree/vsubseqselect.c
194 @@ -12,6 +12,8 @@
195 #include "programversion.h"
196 #include "drand48.h"
197
198 +#include "pathmax.h"
199 +
200 #include "accvirt.pr"
201 #include "procopt.pr"
202 #include "multiseq-adv.pr"
203 --- a/src/Vmatch/chain2dim.mn.c
204 +++ b/src/Vmatch/chain2dim.mn.c
205 @@ -14,6 +14,8 @@
206 #include "chaincall.h"
207 #include "programversion.h"
208
209 +#include "pathmax.h"
210 +
211 #include "dstrdup.pr"
212 #include "procopt.pr"
213 #include "filehandle.pr"
214 --- a/src/Vmatch/chaincall.h
215 +++ b/src/Vmatch/chaincall.h
216 @@ -6,6 +6,8 @@
217
218 #include "chaindef.h"
219
220 +#include "pathmax.h"
221 +
222 //}
223
224 #define CHAINPREFIX "chain"
225 --- a/src/Vmatch/chainof.c
226 +++ b/src/Vmatch/chainof.c
227 @@ -11,6 +11,8 @@
228 #include "genfile.h"
229 #include "chaincall.h"
230
231 +#include "pathmax.h"
232 +
233 #include "filehandle.pr"
234 #include "redblack.pr"
235 #include "chain2dim.pr"
236 --- a/src/Vmatch/chainvm.c
237 +++ b/src/Vmatch/chainvm.c
238 @@ -8,6 +8,8 @@
239 #include "chaincall.h"
240 #include "threaddef.h"
241
242 +#include "pathmax.h"
243 +
244 #include "matsort.pr"
245 #include "chain2dim.pr"
246 #include "filehandle.pr"
247 --- a/src/Vmatch/chncallparse.c
248 +++ b/src/Vmatch/chncallparse.c
249 @@ -13,6 +13,8 @@
250 #include "qualint.h"
251 #include "chaincall.h"
252
253 +#include "pathmax.h"
254 +
255 #include "dstrdup.pr"
256 #include "prsqualint.pr"
257 #include "procopt.pr"
258 --- a/src/Vmatch/clpos.c
259 +++ b/src/Vmatch/clpos.c
260 @@ -2,6 +2,8 @@
261 #include "debugdef.h"
262 #include "mcldef.h"
263
264 +#include "pathmax.h"
265 +
266 #include "matchclust.pr"
267 #include "safescpy.pr"
268
269 --- a/src/Vmatch/cluedist.c
270 +++ b/src/Vmatch/cluedist.c
271 @@ -10,6 +10,8 @@
272 #include "galigndef.h"
273 #include "mcldef.h"
274
275 +#include "pathmax.h"
276 +
277 #include "frontSEP.pr"
278 #include "matchclust.pr"
279 #include "safescpy.pr"
280 --- a/src/Vmatch/matchtask.h
281 +++ b/src/Vmatch/matchtask.h
282 @@ -17,6 +17,8 @@
283 #include "fqfinfo.h"
284 #include "outinfo.h"
285
286 +#include "pathmax.h"
287 +
288 #ifdef VMATCHDB
289 #include "vmdbparms.h"
290 #endif
291 --- a/src/Vmatch/mcldef.h
292 +++ b/src/Vmatch/mcldef.h
293 @@ -8,6 +8,8 @@
294 #include "alphadef.h"
295 #include "match.h"
296
297 +#include "pathmax.h"
298 +
299 #define MATCHCLUSTERNAME "matchcluster"
300
301 typedef struct
302 --- a/src/Vmatch/parsemcl.c
303 +++ b/src/Vmatch/parsemcl.c
304 @@ -6,6 +6,8 @@
305 #include "mcldef.h"
306 #include "galigndef.h"
307
308 +#include "pathmax.h"
309 +
310 #include "dstrdup.pr"
311 #include "procopt.pr"
312 #include "frontSEP.pr"
313 --- a/src/Vmatch/parsevm.c
314 +++ b/src/Vmatch/parsevm.c
315 @@ -20,6 +20,8 @@
316 #include "visible.h"
317 #include "multidef.h"
318
319 +#include "pathmax.h"
320 +
321 #include "dstrdup.pr"
322 #include "checkonoff.pr"
323 #include "matsort.pr"
324 --- a/src/Vmatch/procargs.c
325 +++ b/src/Vmatch/procargs.c
326 @@ -9,6 +9,8 @@
327 #include "optdesc.h"
328 #include "file.h"
329
330 +#include "pathmax.h"
331 +
332 #include "checkonoff.pr"
333 #include "splitargs.pr"
334
335 --- a/src/Vmatch/procmatch.c
336 +++ b/src/Vmatch/procmatch.c
337 @@ -8,6 +8,8 @@
338 #include "scoredef.h"
339 #include "procmultiseq.h"
340
341 +#include "pathmax.h"
342 +
343 #include "dstrdup.pr"
344 #include "detpfxlen.pr"
345 #include "readvirt.pr"
346 --- a/src/Vmatch/vmcluster.c
347 +++ b/src/Vmatch/vmcluster.c
348 @@ -9,6 +9,8 @@
349 #include "genfile.h"
350 #include "fhandledef.h"
351
352 +#include "pathmax.h"
353 +
354 #include "multiseq-adv.pr"
355
356 #include "procargs.pr"
+1
-0
debian/patches/series less more
33 skip-doc-installation.patch
44 hardening.patch
55 reproducible-build.patch
6 pathmax.patch