CRAN Package Check Results for Package OutbreakTools

Last updated on 2019-01-22 06:47:04 CET.

Check Details

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