Last updated on 2019-01-22 06:47:04 CET.
Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
---|---|---|---|---|---|---|
r-devel-linux-x86_64-debian-clang | 0.1-16 | 8.58 | 74.91 | 83.49 | OK | --no-examples --no-vignettes |
r-devel-linux-x86_64-debian-gcc | 0.1-16 | 7.27 | 57.14 | 64.41 | OK | --no-examples --no-vignettes |
r-devel-linux-x86_64-fedora-clang | 0.1-16 | 120.95 | ERROR | |||
r-devel-linux-x86_64-fedora-gcc | 0.1-16 | 113.76 | ERROR | |||
r-devel-windows-ix86+x86_64 | 0.1-16 | 21.00 | 148.00 | 169.00 | ERROR | |
r-patched-linux-x86_64 | 0.1-16 | 5.97 | 69.89 | 75.86 | OK | --no-examples --no-vignettes |
r-patched-solaris-x86 | 0.1-16 | 167.50 | ERROR | |||
r-release-linux-x86_64 | 0.1-16 | 7.01 | 68.83 | 75.84 | OK | --no-examples --no-vignettes |
r-release-windows-ix86+x86_64 | 0.1-16 | 25.00 | 161.00 | 186.00 | ERROR | |
r-release-osx-x86_64 | 0.1-16 | OK | ||||
r-oldrel-windows-ix86+x86_64 | 0.1-16 | 17.00 | 164.00 | 181.00 | ERROR | |
r-oldrel-osx-x86_64 | 0.1-16 | OK |
Version: 0.1-16
Check: examples
Result: ERROR
Running examples in ‘OutbreakTools-Ex.R’ failed
The error most likely occurred in:
> ### Name: ToyOutbreakRaw
> ### Title: Raw simulated outbreak dataset
> ### Aliases: ToyOutbreakRaw
> ### Keywords: dataset
>
> ### ** Examples
>
> ## Load data ##
> data(ToyOutbreakRaw)
> attach(ToyOutbreakRaw)
The following object is masked from package:datasets:
trees
>
> ## Constructing an obkData object ##
> x <- new ("obkData", individuals=individuals, records=records,
+ contacts=contacts, contacts.start=contacts.start,
+ contacts.end=contacts.end, dna=dna,
+ dna.individualID=dna.info$individualID,
+ dna.date=dna.info$date, sample=dna.info$sample, trees=trees)
>
> detach(ToyOutbreakRaw)
>
>
> ## Examining the object ##
> summary(x)
Dataset of 418 individuals with...
== @individuals ==
individuals information
418 entries
recorded fields are:
<infector> class: numeric, mean: 84.26139, sd:67.48384, range: [1;245], 1 NAs
<DateInfected> class: character, 10 unique values, frequency range: [1;173], 0 NAs
<Sex> class: character, 2 unique values, frequency range: [192;226], 0 NAs
<Age> class: numeric, mean: 35.09809, sd:6.10833, range: [19;56], 0 NAs
<lat> class: numeric, mean: 51.51644, sd:0.00304656, range: [51.50711;51.52625], 0 NAs
<lon> class: numeric, mean: -0.1711455, sd:0.01051185, range: [-0.2013245;-0.140349], 0 NAs
== @records ==
records on: Fever
$Fever
418 entries, 418 individuals, from 2000-01-03 to 2000-01-17
recorded fields are:
<temperature> class: numeric, mean: 39.48541, sd:0.5310073, range: [38;40.9], 0 NAs
== @dna ==
836 sequences across 2 loci, 418 individuals, from 2000-01-01 to 2000-01-10
length of concatenated alignment: 1600 nucleotides
Attached meta data:
836 entries, 418 individuals, from 2000-01-01 to 2000-01-10
recorded fields are:
<locus> class: character, 2 unique values, frequency range: [418;418], 0 NAs
<sample> class: character, 418 unique values, frequency range: [2;2], 0 NAs
== @contacts ==
19 contacts between 20 individuals
== @trees ==
1 phylogenetic trees with 418 tips
>
> head(x@individuals)
infector DateInfected Sex Age lat lon
1 NA 2000-01-01 M 33 51.52152 -0.1805272
2 1 2000-01-02 F 42 51.51502 -0.1770907
3 2 2000-01-03 F 44 51.51885 -0.1614321
4 2 2000-01-03 M 49 51.51672 -0.1706063
5 2 2000-01-03 M 34 51.51797 -0.1685206
6 2 2000-01-03 M 31 51.51401 -0.1662320
> head(x@records)
$Fever
individualID date temperature
1 1 2000-01-03 39.1
2 2 2000-01-03 40.4
3 3 2000-01-07 40.0
4 4 2000-01-08 39.8
5 5 2000-01-04 39.4
6 6 2000-01-06 39.3
7 7 2000-01-13 39.3
8 8 2000-01-07 39.4
9 9 2000-01-06 38.0
10 10 2000-01-07 39.5
11 11 2000-01-09 39.5
12 12 2000-01-09 39.3
13 13 2000-01-10 39.8
14 14 2000-01-09 38.6
15 15 2000-01-09 39.5
16 16 2000-01-05 39.0
17 17 2000-01-06 39.0
18 18 2000-01-09 39.6
19 19 2000-01-07 38.9
20 20 2000-01-08 39.5
21 21 2000-01-11 39.7
22 22 2000-01-08 39.6
23 23 2000-01-08 39.9
24 24 2000-01-10 39.5
25 25 2000-01-08 39.6
26 26 2000-01-10 40.6
27 27 2000-01-10 39.9
28 28 2000-01-07 39.1
29 29 2000-01-09 38.8
30 30 2000-01-09 39.5
31 31 2000-01-10 39.6
32 32 2000-01-10 39.5
33 33 2000-01-11 39.2
34 34 2000-01-10 40.0
35 35 2000-01-06 39.3
36 36 2000-01-10 39.1
37 37 2000-01-10 38.8
38 38 2000-01-10 39.8
39 39 2000-01-10 39.3
40 40 2000-01-08 38.9
41 41 2000-01-08 39.4
42 42 2000-01-11 39.0
43 43 2000-01-10 39.7
44 44 2000-01-07 39.1
45 45 2000-01-10 39.5
46 46 2000-01-10 40.1
47 47 2000-01-10 39.6
48 48 2000-01-08 38.7
49 49 2000-01-09 39.7
50 50 2000-01-08 39.6
51 51 2000-01-08 39.2
52 52 2000-01-10 39.9
53 53 2000-01-09 39.9
54 54 2000-01-08 40.1
55 55 2000-01-09 39.2
56 56 2000-01-11 39.7
57 57 2000-01-11 40.2
58 58 2000-01-10 40.5
59 59 2000-01-10 38.9
60 60 2000-01-10 39.2
61 61 2000-01-11 39.1
62 62 2000-01-09 39.7
63 63 2000-01-07 39.4
64 64 2000-01-08 39.6
65 65 2000-01-13 39.0
66 66 2000-01-12 39.0
67 67 2000-01-07 39.5
68 68 2000-01-08 39.6
69 69 2000-01-07 39.8
70 70 2000-01-09 40.3
71 71 2000-01-11 39.7
72 72 2000-01-12 39.6
73 73 2000-01-09 40.1
74 74 2000-01-11 39.8
75 75 2000-01-09 39.9
76 76 2000-01-09 40.0
77 77 2000-01-07 40.0
78 78 2000-01-10 38.9
79 79 2000-01-11 39.4
80 80 2000-01-09 39.3
81 81 2000-01-11 38.8
82 82 2000-01-11 38.7
83 83 2000-01-09 40.3
84 84 2000-01-12 38.5
85 85 2000-01-09 39.4
86 86 2000-01-11 39.7
87 87 2000-01-09 39.6
88 88 2000-01-10 38.0
89 89 2000-01-10 39.1
90 90 2000-01-09 38.7
91 91 2000-01-09 39.5
92 92 2000-01-11 39.7
93 93 2000-01-10 39.3
94 94 2000-01-12 39.7
95 95 2000-01-13 39.0
96 96 2000-01-10 39.6
97 97 2000-01-11 39.9
98 98 2000-01-08 40.7
99 99 2000-01-10 40.8
100 100 2000-01-12 39.4
101 101 2000-01-13 39.8
102 102 2000-01-11 39.5
103 103 2000-01-12 39.2
104 104 2000-01-09 40.1
105 105 2000-01-12 39.2
106 106 2000-01-10 39.9
107 107 2000-01-10 39.3
108 108 2000-01-08 40.1
109 109 2000-01-12 39.4
110 110 2000-01-09 38.8
111 111 2000-01-09 39.3
112 112 2000-01-10 39.4
113 113 2000-01-09 39.5
114 114 2000-01-10 40.7
115 115 2000-01-11 39.5
116 116 2000-01-10 38.6
117 117 2000-01-11 38.9
118 118 2000-01-10 39.5
119 119 2000-01-12 38.5
120 120 2000-01-10 38.5
121 121 2000-01-09 39.0
122 122 2000-01-12 40.2
123 123 2000-01-11 39.8
124 124 2000-01-11 39.8
125 125 2000-01-10 39.0
126 126 2000-01-13 38.7
127 127 2000-01-10 40.2
128 128 2000-01-10 39.9
129 129 2000-01-09 39.7
130 130 2000-01-09 39.1
131 131 2000-01-13 39.6
132 132 2000-01-12 40.3
133 133 2000-01-08 38.6
134 134 2000-01-10 39.3
135 135 2000-01-08 39.7
136 136 2000-01-11 39.3
137 137 2000-01-10 39.0
138 138 2000-01-10 39.9
139 139 2000-01-14 39.0
140 140 2000-01-13 38.6
141 141 2000-01-15 38.8
142 142 2000-01-11 40.3
143 143 2000-01-10 39.4
144 144 2000-01-12 39.0
145 145 2000-01-11 40.1
146 146 2000-01-11 39.5
147 147 2000-01-11 39.9
148 148 2000-01-13 40.2
149 149 2000-01-10 39.7
150 150 2000-01-12 39.9
151 151 2000-01-10 40.0
152 152 2000-01-12 39.8
153 153 2000-01-11 38.8
154 154 2000-01-09 39.6
155 155 2000-01-11 39.1
156 156 2000-01-10 39.2
157 157 2000-01-09 38.1
158 158 2000-01-11 40.5
159 159 2000-01-13 39.5
160 160 2000-01-11 40.7
161 161 2000-01-12 39.3
162 162 2000-01-11 38.9
163 163 2000-01-11 39.5
164 164 2000-01-13 39.1
165 165 2000-01-13 39.8
166 166 2000-01-12 40.0
167 167 2000-01-14 38.8
168 168 2000-01-15 39.7
169 169 2000-01-13 40.2
170 170 2000-01-12 39.5
171 171 2000-01-13 38.7
172 172 2000-01-11 40.1
173 173 2000-01-10 38.8
174 174 2000-01-10 39.7
175 175 2000-01-13 40.4
176 176 2000-01-10 39.5
177 177 2000-01-11 40.0
178 178 2000-01-14 39.2
179 179 2000-01-10 39.0
180 180 2000-01-13 38.7
181 181 2000-01-10 39.5
182 182 2000-01-14 39.5
183 183 2000-01-10 39.5
184 184 2000-01-13 39.8
185 185 2000-01-10 39.9
186 186 2000-01-09 39.4
187 187 2000-01-12 39.6
188 188 2000-01-13 39.2
189 189 2000-01-11 38.9
190 190 2000-01-12 39.3
191 191 2000-01-14 39.5
192 192 2000-01-11 39.3
193 193 2000-01-12 39.6
194 194 2000-01-12 39.6
195 195 2000-01-11 39.9
196 196 2000-01-11 39.7
197 197 2000-01-11 39.7
198 198 2000-01-12 39.9
199 199 2000-01-11 39.2
200 200 2000-01-11 38.8
201 201 2000-01-11 39.6
202 202 2000-01-09 38.7
203 203 2000-01-11 39.4
204 204 2000-01-11 39.1
205 205 2000-01-11 40.7
206 206 2000-01-10 39.4
207 207 2000-01-11 39.0
208 208 2000-01-12 38.9
209 209 2000-01-11 39.7
210 210 2000-01-12 38.6
211 211 2000-01-10 39.7
212 212 2000-01-10 39.1
213 213 2000-01-11 38.6
214 214 2000-01-10 39.9
215 215 2000-01-13 39.4
216 216 2000-01-12 39.7
217 217 2000-01-11 39.2
218 218 2000-01-14 39.4
219 219 2000-01-14 40.3
220 220 2000-01-14 38.7
221 221 2000-01-11 38.9
222 222 2000-01-13 38.7
223 223 2000-01-12 40.2
224 224 2000-01-14 39.7
225 225 2000-01-15 39.2
226 226 2000-01-12 39.5
227 227 2000-01-12 40.0
228 228 2000-01-11 39.2
229 229 2000-01-15 39.4
230 230 2000-01-12 39.1
231 231 2000-01-11 38.5
232 232 2000-01-12 38.7
233 233 2000-01-11 39.1
234 234 2000-01-12 39.4
235 235 2000-01-11 39.5
236 236 2000-01-09 38.5
237 237 2000-01-11 39.4
238 238 2000-01-13 39.6
239 239 2000-01-12 39.6
240 240 2000-01-10 38.9
241 241 2000-01-12 39.9
242 242 2000-01-13 38.6
243 243 2000-01-11 40.1
244 244 2000-01-15 39.2
245 245 2000-01-10 39.5
246 246 2000-01-15 39.4
247 247 2000-01-11 38.5
248 248 2000-01-14 39.9
249 249 2000-01-12 39.3
250 250 2000-01-12 38.8
251 251 2000-01-12 39.0
252 252 2000-01-15 40.3
253 253 2000-01-11 40.0
254 254 2000-01-12 39.4
255 255 2000-01-11 39.7
256 256 2000-01-14 40.2
257 257 2000-01-13 39.8
258 258 2000-01-13 39.6
259 259 2000-01-13 38.7
260 260 2000-01-12 39.2
261 261 2000-01-15 39.5
262 262 2000-01-15 38.7
263 263 2000-01-12 39.3
264 264 2000-01-12 39.4
265 265 2000-01-13 39.0
266 266 2000-01-13 39.5
267 267 2000-01-16 38.8
268 268 2000-01-11 39.2
269 269 2000-01-12 39.3
270 270 2000-01-12 38.5
271 271 2000-01-12 39.9
272 272 2000-01-12 38.5
273 273 2000-01-13 39.4
274 274 2000-01-12 39.4
275 275 2000-01-11 39.9
276 276 2000-01-14 38.6
277 277 2000-01-16 39.6
278 278 2000-01-11 39.3
279 279 2000-01-13 39.3
280 280 2000-01-11 39.7
281 281 2000-01-13 38.6
282 282 2000-01-12 39.8
283 283 2000-01-13 38.5
284 284 2000-01-12 39.7
285 285 2000-01-14 39.5
286 286 2000-01-12 38.8
287 287 2000-01-13 39.7
288 288 2000-01-14 39.9
289 289 2000-01-13 39.7
290 290 2000-01-12 40.3
291 291 2000-01-13 40.1
292 292 2000-01-13 38.6
293 293 2000-01-13 40.2
294 294 2000-01-12 39.9
295 295 2000-01-11 40.4
296 296 2000-01-13 39.7
297 297 2000-01-13 39.9
298 298 2000-01-14 39.7
299 299 2000-01-11 40.2
300 300 2000-01-13 39.2
301 301 2000-01-14 39.0
302 302 2000-01-13 39.5
303 303 2000-01-12 40.5
304 304 2000-01-11 40.1
305 305 2000-01-13 38.7
306 306 2000-01-13 39.8
307 307 2000-01-11 38.6
308 308 2000-01-13 38.8
309 309 2000-01-14 38.9
310 310 2000-01-12 39.2
311 311 2000-01-11 39.6
312 312 2000-01-13 39.8
313 313 2000-01-14 40.4
314 314 2000-01-14 39.6
315 315 2000-01-13 39.9
316 316 2000-01-16 39.7
317 317 2000-01-12 40.0
318 318 2000-01-10 39.5
319 319 2000-01-13 39.5
320 320 2000-01-12 39.3
321 321 2000-01-11 40.2
322 322 2000-01-13 39.5
323 323 2000-01-11 40.2
324 324 2000-01-15 39.3
325 325 2000-01-14 39.5
326 326 2000-01-13 39.9
327 327 2000-01-12 40.2
328 328 2000-01-13 40.7
329 329 2000-01-10 39.5
330 330 2000-01-11 39.9
331 331 2000-01-12 39.0
332 332 2000-01-11 39.5
333 333 2000-01-13 39.9
334 334 2000-01-12 39.8
335 335 2000-01-13 39.9
336 336 2000-01-14 39.4
337 337 2000-01-10 40.1
338 338 2000-01-11 39.3
339 339 2000-01-16 38.5
340 340 2000-01-13 39.2
341 341 2000-01-12 40.8
342 342 2000-01-12 39.4
343 343 2000-01-10 39.7
344 344 2000-01-15 39.7
345 345 2000-01-10 39.7
346 346 2000-01-12 39.8
347 347 2000-01-15 39.5
348 348 2000-01-11 39.6
349 349 2000-01-12 40.8
350 350 2000-01-15 39.6
351 351 2000-01-17 39.9
352 352 2000-01-12 40.4
353 353 2000-01-16 39.0
354 354 2000-01-14 39.9
355 355 2000-01-12 39.9
356 356 2000-01-11 38.8
357 357 2000-01-13 39.9
358 358 2000-01-15 39.3
359 359 2000-01-15 39.8
360 360 2000-01-13 39.2
361 361 2000-01-11 39.0
362 362 2000-01-10 38.7
363 363 2000-01-14 39.9
364 364 2000-01-11 39.0
365 365 2000-01-11 39.2
366 366 2000-01-12 39.0
367 367 2000-01-16 39.4
368 368 2000-01-15 39.5
369 369 2000-01-12 38.7
370 370 2000-01-12 39.3
371 371 2000-01-13 39.9
372 372 2000-01-11 38.6
373 373 2000-01-12 38.6
374 374 2000-01-13 39.0
375 375 2000-01-17 39.2
376 376 2000-01-13 40.1
377 377 2000-01-15 39.2
378 378 2000-01-11 38.6
379 379 2000-01-12 39.1
380 380 2000-01-13 38.9
381 381 2000-01-13 39.6
382 382 2000-01-13 39.6
383 383 2000-01-14 39.2
384 384 2000-01-11 38.8
385 385 2000-01-15 40.3
386 386 2000-01-14 39.9
387 387 2000-01-15 39.5
388 388 2000-01-13 39.6
389 389 2000-01-12 39.9
390 390 2000-01-10 39.8
391 391 2000-01-13 39.4
392 392 2000-01-13 39.6
393 393 2000-01-12 39.8
394 394 2000-01-12 39.5
395 395 2000-01-13 39.9
396 396 2000-01-10 39.6
397 397 2000-01-13 38.7
398 398 2000-01-14 40.9
399 399 2000-01-12 40.1
400 400 2000-01-11 40.1
401 401 2000-01-10 40.1
402 402 2000-01-11 39.6
403 403 2000-01-13 40.3
404 404 2000-01-11 39.4
405 405 2000-01-15 39.9
406 406 2000-01-15 39.6
407 407 2000-01-12 40.5
408 408 2000-01-12 39.2
409 409 2000-01-12 40.8
410 410 2000-01-14 39.4
411 411 2000-01-16 40.4
412 412 2000-01-12 39.0
413 413 2000-01-10 39.5
414 414 2000-01-14 40.1
415 415 2000-01-13 40.5
416 416 2000-01-13 39.4
417 417 2000-01-13 39.0
418 418 2000-01-13 39.3
> names(x@records)
[1] "Fever"
> head(x@records$Fever)
individualID date temperature
1 1 2000-01-03 39.1
2 2 2000-01-03 40.4
3 3 2000-01-07 40.0
4 4 2000-01-08 39.8
5 5 2000-01-04 39.4
6 6 2000-01-06 39.3
> x@contacts
Number of individuals = 20
Number of contacts = 19
Contacts = dynamic
NetworkDynamic properties:
distinct change times: 5
maximal time range: 0 until 4
Network attributes:
vertices = 20
directed = FALSE
hyper = FALSE
loops = FALSE
multiple = TRUE
bipartite = FALSE
total edges= 19
missing edges= 0
non-missing edges= 19
Vertex attribute names:
vertex.names
Edge attribute names:
active
Date of origin: [1] "2000-01-01"
> x@dna
= @dna =
[ 836 DNA sequences in 2 loci ]
$gene1
418 DNA sequences in binary format stored in a matrix.
All sequences of same length: 600
Labels:
1
2
3
4
5
6
...
Base composition:
a c g t
0.237 0.248 0.252 0.263
(Total: 250.8 kb)
$gene2
418 DNA sequences in binary format stored in a matrix.
All sequences of same length: 1000
Labels:
419
420
421
422
423
424
...
Base composition:
a c g t
0.223 0.243 0.257 0.276
(Total: 418 kb)
= @meta =
[ meta information on the sequences ]
individualID date locus sample
1 1 2000-01-01 gene1 1
2 2 2000-01-02 gene1 2
3 3 2000-01-03 gene1 3
4 4 2000-01-03 gene1 4
...
individualID date locus sample
833 415 2000-01-10 gene2 415
834 416 2000-01-10 gene2 416
835 417 2000-01-10 gene2 417
836 418 2000-01-10 gene2 418
> x@trees
1 phylogenetic trees
>
> ## Plotting the dynamic contact network ##
> par(mfrow=c(2,2))
> plot(get.contacts(x),main="Contact network - days 0-3",displaylabels=TRUE)
> plot(get.contacts(x, from=0, to=1.1), main="Contact network - days 0-1",
+ displaylabels=TRUE)
> plot(get.contacts(x, from=2, to=2.1), main="Contact network - day 2",
+ displaylabels=TRUE)
> plot(get.contacts(x, from=3, to=3.1), main="Contact network - day 3",
+ displaylabels=TRUE)
>
> ## Mapping the outbreak (by sex) ##
> plot(x,'geo',location=c('lon','lat'),zoom=13,colorBy='Sex')
Warning in download.file(url, destfile = tmp, quiet = !messaging, mode = "wb") :
cannot open URL 'http://maps.googleapis.com/maps/api/staticmap?center=51.516439,-0.171146&zoom=13&size=640x640&scale=2&maptype=terrain&language=en-EN&sensor=false': HTTP status was '403 Forbidden'
Error in download.file(url, destfile = tmp, quiet = !messaging, mode = "wb") :
cannot open URL 'http://maps.googleapis.com/maps/api/staticmap?center=51.516439,-0.171146&zoom=13&size=640x640&scale=2&maptype=terrain&language=en-EN&sensor=false'
Calls: plot ... plotGeo -> get_map -> get_googlemap -> download.file
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-ix86+x86_64, r-patched-solaris-x86, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64
Version: 0.1-16
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
--- re-building ‘OutbreakTools.Rnw’ using knitr
Warning in .local(x, ...) :
The following sequence IDs are not in the dataset: 311, 222
Warning in .local(x, ...) :
The following sequence IDs are not in the dataset: 311, 222
Warning in (if (out_format(c("latex", "sweave", "listings"))) sanitize_fn else paste0)(path, :
replaced special characters in figure filename "figs/OutbreakTools-out.width==".8\\textwidth"" -> "figs/OutbreakTools-out.width___.8\\textwidth_"
Warning in (if (out_format(c("latex", "sweave", "listings"))) sanitize_fn else paste0)(path, :
dots in figure paths replaced with _ ("figs/OutbreakTools-out_width____8//textwidth_")
Warning: The shape palette can deal with a maximum of 6 discrete values because
more than 6 becomes difficult to discriminate; you have 11. Consider
specifying shapes manually if you must have them.
Warning: Removed 58 rows containing missing values (geom_point).
Warning: `show_guide` has been deprecated. Please use `show.legend` instead.
Warning: `show_guide` has been deprecated. Please use `show.legend` instead.
Warning in download.file(url, destfile = tmp, quiet = !messaging, mode = "wb") :
cannot open URL 'http://maps.googleapis.com/maps/api/staticmap?center=51.516439,-0.171146&zoom=14&size=640x640&scale=2&maptype=terrain&language=en-EN&sensor=false': HTTP status was '403 Forbidden'
Quitting from lines 1022-1023 (OutbreakTools.Rnw)
Error: processing vignette 'OutbreakTools.Rnw' failed with diagnostics:
cannot open URL 'http://maps.googleapis.com/maps/api/staticmap?center=51.516439,-0.171146&zoom=14&size=640x640&scale=2&maptype=terrain&language=en-EN&sensor=false'
--- failed re-building ‘OutbreakTools.Rnw’
SUMMARY: processing the following file failed:
‘OutbreakTools.Rnw’
Error: Vignette re-building failed.
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-ix86+x86_64
Version: 0.1-16
Check: re-building of vignette outputs
Result: WARN
Error in re-building vignettes:
...
Warning in .local(x, ...) :
The following sequence IDs are not in the dataset: 311, 222
Warning in .local(x, ...) :
The following sequence IDs are not in the dataset: 311, 222
Warning in (if (out_format(c("latex", "sweave", "listings"))) sanitize_fn else paste0)(path, :
replaced special characters in figure filename "figs/OutbreakTools-out.width==".8\\textwidth"" -> "figs/OutbreakTools-out.width___.8\\textwidth_"
Warning in (if (out_format(c("latex", "sweave", "listings"))) sanitize_fn else paste0)(path, :
dots in figure paths replaced with _ ("figs/OutbreakTools-out_width____8//textwidth_")
Warning: The shape palette can deal with a maximum of 6 discrete values because
more than 6 becomes difficult to discriminate; you have 11. Consider
specifying shapes manually if you must have them.
Warning: Removed 58 rows containing missing values (geom_point).
Warning: `show_guide` has been deprecated. Please use `show.legend` instead.
Warning: `show_guide` has been deprecated. Please use `show.legend` instead.
Warning in download.file(url, destfile = tmp, quiet = !messaging, mode = "wb") :
cannot open URL 'http://maps.googleapis.com/maps/api/staticmap?center=51.516439,-0.171146&zoom=14&size=640x640&scale=2&maptype=terrain&language=en-EN&sensor=false': HTTP status was '403 Forbidden'
Quitting from lines 1022-1023 (OutbreakTools.Rnw)
Error: processing vignette 'OutbreakTools.Rnw' failed with diagnostics:
cannot open URL 'http://maps.googleapis.com/maps/api/staticmap?center=51.516439,-0.171146&zoom=14&size=640x640&scale=2&maptype=terrain&language=en-EN&sensor=false'
Execution halted
Flavors: r-patched-solaris-x86, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64