* using log directory 'd:/Rcompile/CRANpkg/local/2.13/pomp.Rcheck'
* using R version 2.13.2 (2011-09-30)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* checking for file 'pomp/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'pomp' version '0.40-2'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'pomp' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* checking for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable compilation flags in Makevars ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking sizes of PDF files under inst/doc ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
** running tests for arch 'i386' OK
  Running 'examples.R'
  Running 'fhn.R'
  Comparing 'fhn.Rout' to 'fhn.Rout.save' ...99,100c99,100
< V -1.3052928  1.273978759
< R -0.5591607 -0.006917772
---
> V -1.3052919  1.27398107
> R -0.5591608 -0.00692014
105,106c105,106
< V -1.4459065 1.19169607
< R -0.5707824 0.02732723
---
> V -1.4459045 1.19170161
> R -0.5707824 0.02732499
111,112c111,112
< V -1.4714053 1.32436782
< R -0.5861062 0.06164554
---
> V -1.4714039 1.32437192
> R -0.5861061 0.06164339
  Running 'filtfail.R'
  Comparing 'filtfail.Rout' to 'filtfail.Rout.save' ... OK
  Running 'gillespie.R'
  Comparing 'gillespie.Rout' to 'gillespie.Rout.save' ... OK
  Running 'gompertz.R'
  Comparing 'gompertz.Rout' to 'gompertz.Rout.save' ... OK
  Running 'logistic.R'
  Comparing 'logistic.Rout' to 'logistic.Rout.save' ... OK
  Running 'ou2-bsmc.R'
  Comparing 'ou2-bsmc.Rout' to 'ou2-bsmc.Rout.save' ...1a2,17
> R Under development (unstable) (2011-12-13 r57882)
> Copyright (C) 2011 The R Foundation for Statistical Computing
> ISBN 3-900051-07-0
> Platform: x86_64-unknown-linux-gnu (64-bit)
> 
> R is free software and comes with ABSOLUTELY NO WARRANTY.
> You are welcome to redistribute it under certain conditions.
> Type 'license()' or 'licence()' for distribution details.
> 
> R is a collaborative project with many contributors.
> Type 'contributors()' for more information and
> 'citation()' on how to cite R or R packages in publications.
> 
> Type 'demo()' for some demos, 'help()' for on-line help, or
> 'help.start()' for an HTML browser interface to help.
> Type 'q()' to quit R.
70c86
< [1] -4.705647
---
> [1] -30.90868
77c93
< [1] -4.250385
---
> [1] -30.27596
  Running 'ou2-forecast.R'
  Comparing 'ou2-forecast.Rout' to 'ou2-forecast.Rout.save' ... OK
  Running 'ou2-icfit.R'
  Comparing 'ou2-icfit.Rout' to 'ou2-icfit.Rout.save' ...1a2,17
> R Under development (unstable) (2011-09-03 r56917)
> Copyright (C) 2011 The R Foundation for Statistical Computing
> ISBN 3-900051-07-0
> Platform: x86_64-unknown-linux-gnu (64-bit)
> 
> R is free software and comes with ABSOLUTELY NO WARRANTY.
> You are welcome to redistribute it under certain conditions.
> Type 'license()' or 'licence()' for distribution details.
> 
> R is a collaborative project with many contributors.
> Type 'contributors()' for more information and
> 'citation()' on how to cite R or R packages in publications.
> 
> Type 'demo()' for some demos, 'help()' for on-line help, or
> 'help.start()' for an HTML browser interface to help.
> Type 'q()' to quit R.
  Running 'ou2-kalman.R'
  Comparing 'ou2-kalman.Rout' to 'ou2-kalman.Rout.save' ... OK
  Running 'ou2-mif.R'
  Comparing 'ou2-mif.Rout' to 'ou2-mif.Rout.save' ... OK
  Running 'ou2-nlf.R'
  Comparing 'ou2-nlf.Rout' to 'ou2-nlf.Rout.save' ... OK
  Running 'ou2-pmcmc.R'
  Comparing 'ou2-pmcmc.Rout' to 'ou2-pmcmc.Rout.save' ... OK
  Running 'ou2-probe.R'
  Comparing 'ou2-probe.Rout' to 'ou2-probe.Rout.save' ...208c208
< [1] 97.56677
---
> [1] 93.95585
  Running 'ou2-procmeas.R'
  Comparing 'ou2-procmeas.Rout' to 'ou2-procmeas.Rout.save' ... OK
  Running 'ou2-simulate.R'
  Comparing 'ou2-simulate.Rout' to 'ou2-simulate.Rout.save' ... OK
  Running 'ou2-trajmatch.R'
  Comparing 'ou2-trajmatch.Rout' to 'ou2-trajmatch.Rout.save' ... OK
  Running 'pfilter.R'
  Comparing 'pfilter.Rout' to 'pfilter.Rout.save' ... OK
  Running 'pomppomp.R'
  Comparing 'pomppomp.Rout' to 'pomppomp.Rout.save' ... OK
  Running 'ricker-probe.R'
  Comparing 'ricker-probe.Rout' to 'ricker-probe.Rout.save' ...36c36
< [1] -2.438191
---
> [1] -2.437844
56c56
<    0.166    0.250    0.803 
---
>    0.166    0.251    0.803 
60c60
< 0.3336663 0.5014985 0.3956044 
---
> 0.3336663 0.5034965 0.3956044 
63c63
< [1] 2.805535
---
> [1] 2.805501
83c83
<    0.166    0.250    0.803 
---
>    0.166    0.251    0.803 
87c87
< 0.3336663 0.5014985 0.3956044 
---
> 0.3336663 0.5034965 0.3956044 
90c90
< [1] 2.805535
---
> [1] 2.805501
110c110
<    0.405    0.804    0.322 
---
>    0.403    0.805    0.323 
114c114
< 0.8111888 0.3936064 0.6453546 
---
> 0.8071928 0.3916084 0.6473526 
117c117
< [1] 7.380701
---
> [1] 7.383561
134c134
<  1.000000e+00 -2.309820e-18 -9.901576e-19 
---
> 1.000000e+00 2.308125e-18 9.896164e-19 
145c145
<  0.855  0.284  0.273 
---
>  0.855  0.284  0.275 
149c149
< 0.2917083 0.5694306 0.5474525 
---
> 0.2917083 0.5694306 0.5514486 
152c152
< [1] 12.41934
---
> [1] 12.42156
177c177
<  1.000000e+00 -2.309820e-18 -9.901576e-19  3.679493e+03 -1.275470e+03 
---
>  1.000000e+00  2.308125e-18  9.896164e-19  3.679493e+03 -1.275470e+03 
190c190
<   0.855   0.284   0.273   0.646   0.035   0.920   0.686   0.838 
---
>   0.855   0.284   0.275   0.647   0.034   0.920   0.686   0.838 
194c194
< 0.29170829 0.56943057 0.54745255 0.70929071 0.07192807 0.16183816 0.62937063 
---
> 0.29170829 0.56943057 0.55144855 0.70729271 0.06993007 0.16183816 0.62937063 
199c199
< [1] -14.8925
---
> [1] -14.89908
215c215
<   0.846   0.265   0.266   0.644   0.037   0.905   0.712   0.821 
---
>   0.857   0.281   0.276   0.648   0.035   0.899   0.708   0.830 
219c219
< 0.30969031 0.53146853 0.53346653 0.71328671 0.07592408 0.19180819 0.57742258 
---
> 0.28771229 0.56343656 0.55344655 0.70529471 0.07192807 0.20379620 0.58541459 
221c221
< 0.35964036 
---
> 0.34165834 
224c224
< [1] -14.77554
---
> [1] -14.7743
233c233
< [1] 15.39317
---
> [1] 15.31774
261c261
<  1.000000e+00 -2.309820e-18 -9.901576e-19 
---
> 1.000000e+00 2.308125e-18 9.896164e-19 
296c296
<   26.24    0.22   26.71 
---
>   7.680   0.008   7.713 
355c355
<   18.95    0.12   19.44 
---
>   5.668   0.000   5.683 
382c382
<  39.47310  -9.04665 -18.05277 
---
> 24.879460 -5.950185 -2.211594 
393c393
<      1      0      0 
---
>   1.00   0.00   0.32 
397c397
< 0.001998002 0.001998002 0.001998002 
---
> 0.001998002 0.001998002 0.641358641 
400c400
< [1] -48.29627
---
> [1] -56.62876
428c428
<   0.591   0.067   0.315   0.907   0.144   0.658 
---
>   0.592   0.067   0.315   0.907   0.144   0.658 
432c432
< 0.8191808 0.1358641 0.6313686 0.1878122 0.2897103 0.6853147 
---
> 0.8171828 0.1358641 0.6313686 0.1878122 0.2897103 0.6853147 
435c435
< [1] -12.45567
---
> [1] -12.45474
463c463
<   0.151   0.317   0.896   0.143   0.653 
---
>   0.152   0.317   0.896   0.143   0.653 
467c467
< 0.3036963 0.6353646 0.2097902 0.2877123 0.6953047 
---
> 0.3056943 0.6353646 0.2097902 0.2877123 0.6953047 
470c470
< [1] 5.174442
---
> [1] 5.174849
507c507
<    0.591    0.591    0.067    0.315    0.106    0.133 
---
>    0.592    0.592    0.067    0.315    0.105    0.133 
511c511
< 0.8191808 0.8191808 0.1358641 0.6313686 0.2137862 0.2677323 
---
> 0.8171828 0.8171828 0.1358641 0.6313686 0.2117882 0.2677323 
514c514
< [1] 31.75692
---
> [1] 29.82456
  Running 'ricker-spect.R'
  Comparing 'ricker-spect.Rout' to 'ricker-spect.Rout.save' ...43c43
< 0.6303696 0.6303696 
---
> 0.6423576 0.6423576 
49c49
< [1] 3.245378
---
> [1] 3.242017
  Running 'ricker.R'
  Comparing 'ricker.Rout' to 'ricker.Rout.save' ...82,83c82,83
< EXTENSION          8 22.272926 -5.684056
< EXTENSION         10 21.237763 -12.104646
---
> EXTENSION          8 22.273083 -5.683156
> EXTENSION         10 21.238197 -12.104646
85c85
< LO-REDUCTION      14 -5.684056 -12.104646
---
> LO-REDUCTION      14 -5.683156 -12.104646
87,220c87,204
< EXTENSION         18 -10.237581 -16.111313
< LO-REDUCTION      20 -10.432496 -16.111313
< LO-REDUCTION      22 -12.104646 -16.111313
< EXTENSION         24 -13.678744 -17.524605
< EXTENSION         26 -14.637732 -18.127097
< LO-REDUCTION      28 -16.111313 -18.398334
< REFLECTION        30 -17.524605 -18.911731
< HI-REDUCTION      32 -18.127097 -19.026135
< HI-REDUCTION      34 -18.398334 -19.026135
< REFLECTION        36 -18.825988 -19.669926
< HI-REDUCTION      38 -18.911731 -19.669926
< HI-REDUCTION      40 -19.026135 -19.669926
< SHRINK            45 -18.984642 -19.913286
< LO-REDUCTION      47 -19.238865 -19.913286
< LO-REDUCTION      49 -19.669926 -19.913286
< LO-REDUCTION      51 -19.779466 -19.913286
< SHRINK            56 -19.112904 -19.913286
< LO-REDUCTION      58 -19.259618 -19.913286
< HI-REDUCTION      60 -19.334925 -19.913286
< HI-REDUCTION      62 -19.426101 -19.913286
< HI-REDUCTION      64 -19.498300 -19.913286
< HI-REDUCTION      66 -19.631040 -19.913286
< LO-REDUCTION      68 -19.818904 -19.913286
< SHRINK            73 -19.233802 -19.913286
< LO-REDUCTION      75 -19.564238 -19.913286
< SHRINK            80 -19.307755 -19.913286
< LO-REDUCTION      82 -19.378968 -19.913286
< HI-REDUCTION      84 -19.517284 -19.913286
< SHRINK            89 -19.373262 -19.913286
< LO-REDUCTION      91 -19.556558 -19.913286
< LO-REDUCTION      93 -19.591896 -19.913286
< SHRINK            98 -19.230599 -19.913286
< LO-REDUCTION     100 -19.546415 -19.913286
< REFLECTION       102 -19.623190 -19.951911
< SHRINK           107 -19.421078 -19.951911
< LO-REDUCTION     109 -19.655716 -19.951911
< SHRINK           114 -19.442526 -19.951911
< LO-REDUCTION     116 -19.459757 -19.951911
< LO-REDUCTION     118 -19.480120 -19.951911
< LO-REDUCTION     120 -19.602389 -19.951911
< SHRINK           125 -19.471524 -19.951911
< LO-REDUCTION     127 -19.728631 -19.951911
< HI-REDUCTION     129 -19.759755 -19.951911
< SHRINK           134 -19.357886 -19.951911
< LO-REDUCTION     136 -19.413637 -19.951911
< LO-REDUCTION     138 -19.666133 -19.951911
< HI-REDUCTION     140 -19.666654 -19.951911
< SHRINK           145 -19.349582 -20.037785
< LO-REDUCTION     147 -19.505323 -20.037785
< LO-REDUCTION     149 -19.742983 -20.037785
< HI-REDUCTION     151 -19.761865 -20.037785
< SHRINK           156 -19.680484 -20.037785
< LO-REDUCTION     158 -19.733452 -20.037785
< SHRINK           163 -19.681596 -20.037785
< LO-REDUCTION     165 -19.692664 -20.037785
< HI-REDUCTION     167 -19.836726 -20.037785
< SHRINK           172 -19.206245 -20.037785
< LO-REDUCTION     174 -19.617948 -20.037785
< LO-REDUCTION     176 -19.681934 -20.037785
< SHRINK           181 -19.346740 -20.037785
< LO-REDUCTION     183 -19.394254 -20.037785
< LO-REDUCTION     185 -19.625763 -20.037785
< SHRINK           190 -19.889415 -20.037785
< SHRINK           195 -19.579456 -20.037785
< REFLECTION       197 -19.652681 -20.049669
< LO-REDUCTION     199 -19.679811 -20.049669
< SHRINK           204 -19.348488 -20.049669
< LO-REDUCTION     206 -19.582927 -20.049669
< SHRINK           211 -19.380916 -20.049669
< LO-REDUCTION     213 -19.381948 -20.049669
< LO-REDUCTION     215 -19.797656 -20.068942
< SHRINK           220 -19.417378 -20.068942
< LO-REDUCTION     222 -19.727723 -20.068942
< LO-REDUCTION     224 -19.740942 -20.068942
< HI-REDUCTION     226 -19.784062 -20.068942
< SHRINK           231 -19.246301 -20.068942
< LO-REDUCTION     233 -19.576009 -20.068942
< LO-REDUCTION     235 -19.668819 -20.068942
< SHRINK           240 -19.608829 -20.068942
< LO-REDUCTION     242 -19.612804 -20.068942
< HI-REDUCTION     244 -19.705411 -20.068942
< HI-REDUCTION     246 -19.712504 -20.068942
< HI-REDUCTION     248 -19.818946 -20.068942
< LO-REDUCTION     250 -19.833230 -20.068942
< SHRINK           255 -19.371218 -20.068942
< LO-REDUCTION     257 -19.624027 -20.068942
< HI-REDUCTION     259 -19.671503 -20.068942
< SHRINK           264 -19.389065 -20.068942
< HI-REDUCTION     266 -19.397484 -20.068942
< LO-REDUCTION     268 -19.505390 -20.068942
< SHRINK           273 -19.486121 -20.068942
< HI-REDUCTION     275 -19.569359 -20.068942
< LO-REDUCTION     277 -19.616537 -20.068942
< LO-REDUCTION     279 -19.861810 -20.160036
< LO-REDUCTION     281 -20.018955 -20.160036
< HI-REDUCTION     283 -20.068942 -20.160036
< SHRINK           288 -19.789550 -20.189982
< LO-REDUCTION     290 -19.905692 -20.189982
< LO-REDUCTION     292 -20.041886 -20.189982
< HI-REDUCTION     294 -20.104284 -20.189982
< HI-REDUCTION     296 -20.127377 -20.246207
< HI-REDUCTION     298 -20.160036 -20.246207
< HI-REDUCTION     300 -20.175492 -20.263210
< SHRINK           305 -20.035679 -20.263210
< LO-REDUCTION     307 -20.082321 -20.263210
< LO-REDUCTION     309 -20.147163 -20.263210
< LO-REDUCTION     311 -20.157209 -20.263210
< HI-REDUCTION     313 -20.188336 -20.263210
< SHRINK           318 -20.249805 -20.276030
< SHRINK           323 -20.079067 -20.276030
< REFLECTION       325 -20.167727 -20.291197
< LO-REDUCTION     327 -20.180620 -20.291197
< SHRINK           332 -20.042132 -20.291197
< LO-REDUCTION     334 -20.185242 -20.291197
< SHRINK           339 -20.195093 -20.291197
< LO-REDUCTION     341 -20.202394 -20.294900
< LO-REDUCTION     343 -20.210239 -20.334585
< HI-REDUCTION     345 -20.291197 -20.341237
< HI-REDUCTION     347 -20.294900 -20.370635
< SHRINK           352 -20.198790 -20.390802
< LO-REDUCTION     354 -20.274755 -20.390802
< LO-REDUCTION     356 -20.299180 -20.390802
< HI-REDUCTION     358 -20.320130 -20.390802
< SHRINK           363 -20.313165 -20.390802
< SHRINK           368 -20.298792 -20.390802
< LO-REDUCTION     370 -20.323202 -20.390802
< SHRINK           375 -20.312042 -20.392027
< LO-REDUCTION     377 -20.384099 -20.392027
< LO-REDUCTION     379 -20.390508 -20.392027
< HI-REDUCTION     381 -20.390802 -20.392027
< REFLECTION       383 -20.390802 -20.393570
< LO-REDUCTION     385 -20.392027 -20.393570
< SHRINK           390 -20.392027 -20.393570
< SHRINK           395 -20.392027 -20.393570
---
> EXTENSION         18 -10.238701 -16.111147
> LO-REDUCTION      20 -10.432496 -16.111147
> LO-REDUCTION      22 -12.104646 -16.111147
> EXTENSION         24 -13.678744 -17.527973
> EXTENSION         26 -14.637732 -18.135507
> LO-REDUCTION      28 -16.111147 -18.406162
> REFLECTION        30 -17.527973 -18.901071
> HI-REDUCTION      32 -18.135507 -19.025728
> HI-REDUCTION      34 -18.406162 -19.025728
> REFLECTION        36 -18.822244 -19.711127
> HI-REDUCTION      38 -18.901071 -19.711127
> HI-REDUCTION      40 -19.025728 -19.711127
> SHRINK            45 -18.987087 -19.858319
> LO-REDUCTION      47 -19.288693 -19.858319
> LO-REDUCTION      49 -19.711127 -19.858319
> LO-REDUCTION      51 -19.779236 -19.858319
> SHRINK            56 -19.098736 -19.858319
> LO-REDUCTION      58 -19.213348 -19.858319
> LO-REDUCTION      60 -19.230757 -19.858319
> SHRINK            65 -19.572673 -19.858319
> HI-REDUCTION      67 -19.622339 -19.858319
> SHRINK            72 -19.417796 -19.883729
> LO-REDUCTION      74 -19.441471 -19.883729
> HI-REDUCTION      76 -19.458238 -19.883729
> LO-REDUCTION      78 -19.622452 -19.883729
> LO-REDUCTION      80 -19.692344 -19.883729
> SHRINK            85 -19.276517 -19.883729
> HI-REDUCTION      87 -19.332435 -19.883729
> LO-REDUCTION      89 -19.391462 -19.883729
> LO-REDUCTION      91 -19.766486 -19.883729
> SHRINK            96 -19.508802 -19.883729
> LO-REDUCTION      98 -19.685618 -19.883729
> SHRINK           103 -19.279074 -19.883729
> SHRINK           108 -19.498156 -20.036526
> SHRINK           113 -19.163003 -20.036526
> LO-REDUCTION     115 -19.685799 -20.036526
> SHRINK           120 -19.437896 -20.036526
> HI-REDUCTION     122 -19.594982 -20.036526
> LO-REDUCTION     124 -19.655126 -20.036526
> HI-REDUCTION     126 -19.693313 -20.036526
> HI-REDUCTION     128 -19.710519 -20.036526
> SHRINK           133 -19.212997 -20.036526
> LO-REDUCTION     135 -19.632972 -20.036526
> SHRINK           140 -19.318310 -20.036526
> LO-REDUCTION     142 -19.429013 -20.036526
> LO-REDUCTION     144 -19.541768 -20.036526
> SHRINK           149 -19.499454 -20.036526
> HI-REDUCTION     151 -19.643647 -20.036526
> HI-REDUCTION     153 -19.665508 -20.036526
> LO-REDUCTION     155 -19.842500 -20.036526
> SHRINK           160 -19.714203 -20.036526
> LO-REDUCTION     162 -19.900941 -20.036526
> SHRINK           167 -19.494052 -20.036526
> LO-REDUCTION     169 -19.557532 -20.036526
> LO-REDUCTION     171 -19.635954 -20.036526
> SHRINK           176 -19.571857 -20.036526
> HI-REDUCTION     178 -19.633935 -20.036526
> LO-REDUCTION     180 -19.773673 -20.036526
> SHRINK           185 -19.580741 -20.036526
> LO-REDUCTION     187 -19.713589 -20.036526
> SHRINK           192 -19.778851 -20.075344
> LO-REDUCTION     194 -19.920306 -20.075344
> SHRINK           199 -19.253544 -20.075344
> LO-REDUCTION     201 -19.563461 -20.075344
> LO-REDUCTION     203 -19.657461 -20.075344
> SHRINK           208 -19.386987 -20.075344
> LO-REDUCTION     210 -19.445799 -20.075344
> LO-REDUCTION     212 -19.595884 -20.075344
> SHRINK           217 -19.582926 -20.151824
> LO-REDUCTION     219 -19.753819 -20.151824
> LO-REDUCTION     221 -19.772159 -20.151824
> LO-REDUCTION     223 -19.782335 -20.151824
> SHRINK           228 -19.596088 -20.151824
> LO-REDUCTION     230 -19.681504 -20.151824
> SHRINK           235 -19.609725 -20.151824
> HI-REDUCTION     237 -19.615594 -20.151824
> HI-REDUCTION     239 -19.651915 -20.151824
> LO-REDUCTION     241 -19.694368 -20.151824
> LO-REDUCTION     243 -19.769449 -20.151824
> HI-REDUCTION     245 -19.782970 -20.151824
> SHRINK           250 -19.592628 -20.151824
> LO-REDUCTION     252 -19.877327 -20.151824
> HI-REDUCTION     254 -19.966120 -20.151824
> SHRINK           259 -19.757861 -20.151824
> LO-REDUCTION     261 -19.978390 -20.151824
> SHRINK           266 -19.866279 -20.151824
> HI-REDUCTION     268 -20.048979 -20.151824
> LO-REDUCTION     270 -20.073212 -20.164817
> HI-REDUCTION     272 -20.082314 -20.265947
> LO-REDUCTION     274 -20.151824 -20.265947
> SHRINK           279 -20.086588 -20.265947
> SHRINK           284 -20.054913 -20.265947
> REFLECTION       286 -20.079536 -20.312392
> LO-REDUCTION     288 -20.216102 -20.312392
> SHRINK           293 -20.153482 -20.312392
> SHRINK           298 -20.097052 -20.312392
> LO-REDUCTION     300 -20.118531 -20.312392
> LO-REDUCTION     302 -20.165018 -20.312392
> LO-REDUCTION     304 -20.176834 -20.312392
> SHRINK           309 -20.130573 -20.312392
> LO-REDUCTION     311 -20.175138 -20.312392
> HI-REDUCTION     313 -20.232404 -20.312392
> SHRINK           318 -20.158381 -20.340133
> LO-REDUCTION     320 -20.250809 -20.340133
> SHRINK           325 -20.236229 -20.340133
> LO-REDUCTION     327 -20.270202 -20.340133
> LO-REDUCTION     329 -20.313522 -20.340133
> SHRINK           334 -20.301190 -20.340133
> LO-REDUCTION     336 -20.320514 -20.340133
> SHRINK           341 -20.309539 -20.340133
> LO-REDUCTION     343 -20.328223 -20.340133
> SHRINK           348 -20.316445 -20.341834
> LO-REDUCTION     350 -20.337619 -20.341834
> HI-REDUCTION     352 -20.340133 -20.341834
> HI-REDUCTION     354 -20.341082 -20.341834
> SHRINK           359 -20.341834 -20.343672
> SHRINK           364 -20.341834 -20.343672
> SHRINK           369 -20.341834 -20.343672
223c207
<     397 function evaluations used
---
>     371 function evaluations used
250,251c234,235
< log.r           3.0    3.8    3.79    3.75
< log.sigma       0.0   -1.2   -1.69   -1.12
---
> log.r           3.0    3.8    3.79    3.74
> log.sigma       0.0   -1.2   -1.74   -1.12
255,256c239,240
< loglik       -230.9 -139.5 -137.15 -143.87
< synth.loglik  -12.3   17.4   17.64   20.39
---
> loglik       -230.9 -139.5 -137.35 -143.33
> synth.loglik  -12.3   17.5   16.47   20.34
  Running 'rw2.R'
  Comparing 'rw2.Rout' to 'rw2.Rout.save' ...377c377
< [1] 8.881784e-16
---
> [1] 1.110223e-16
  Running 'sir.R'
  Comparing 'sir.Rout' to 'sir.Rout.save' ...571c571
< [1] 5.329e-15
---
> [1] 7.105e-15
573c573
< [1] 3.638e-11
---
> [1] 9.459e-11
  Running 'skeleton.R'
  Comparing 'skeleton.Rout' to 'skeleton.Rout.save' ... OK
  Running 'steps.R'
  Comparing 'steps.Rout' to 'steps.Rout.save' ... OK
  Running 'synlik.R'
  Comparing 'synlik.Rout' to 'synlik.Rout.save' ... OK
  Running 'verhulst.R'
  Comparing 'verhulst.Rout' to 'verhulst.Rout.save' ... OK
** running tests for arch 'x64' OK
  Running 'examples.R'
  Running 'fhn.R'
  Comparing 'fhn.Rout' to 'fhn.Rout.save' ...99,100c99,100
< V -1.3052964  1.27395190
< R -0.5591594 -0.00688812
---
> V -1.3052919  1.27398107
> R -0.5591608 -0.00692014
105,106c105,106
< V -1.4459084 1.19166498
< R -0.5707813 0.02735605
---
> V -1.4459045 1.19170161
> R -0.5707824 0.02732499
111,112c111,112
< V -1.4714085 1.32432718
< R -0.5861052 0.06167327
---
> V -1.4714039 1.32437192
> R -0.5861061 0.06164339
  Running 'filtfail.R'
  Comparing 'filtfail.Rout' to 'filtfail.Rout.save' ... OK
  Running 'gillespie.R'
  Comparing 'gillespie.Rout' to 'gillespie.Rout.save' ... OK
  Running 'gompertz.R'
  Comparing 'gompertz.Rout' to 'gompertz.Rout.save' ... OK
  Running 'logistic.R'
  Comparing 'logistic.Rout' to 'logistic.Rout.save' ... OK
  Running 'ou2-bsmc.R'
  Comparing 'ou2-bsmc.Rout' to 'ou2-bsmc.Rout.save' ...1a2,17
> R Under development (unstable) (2011-12-13 r57882)
> Copyright (C) 2011 The R Foundation for Statistical Computing
> ISBN 3-900051-07-0
> Platform: x86_64-unknown-linux-gnu (64-bit)
> 
> R is free software and comes with ABSOLUTELY NO WARRANTY.
> You are welcome to redistribute it under certain conditions.
> Type 'license()' or 'licence()' for distribution details.
> 
> R is a collaborative project with many contributors.
> Type 'contributors()' for more information and
> 'citation()' on how to cite R or R packages in publications.
> 
> Type 'demo()' for some demos, 'help()' for on-line help, or
> 'help.start()' for an HTML browser interface to help.
> Type 'q()' to quit R.
70c86
< [1] -4.705647
---
> [1] -30.90868
77c93
< [1] -4.250385
---
> [1] -30.27596
  Running 'ou2-forecast.R'
  Comparing 'ou2-forecast.Rout' to 'ou2-forecast.Rout.save' ... OK
  Running 'ou2-icfit.R'
  Comparing 'ou2-icfit.Rout' to 'ou2-icfit.Rout.save' ...1a2,17
> R Under development (unstable) (2011-09-03 r56917)
> Copyright (C) 2011 The R Foundation for Statistical Computing
> ISBN 3-900051-07-0
> Platform: x86_64-unknown-linux-gnu (64-bit)
> 
> R is free software and comes with ABSOLUTELY NO WARRANTY.
> You are welcome to redistribute it under certain conditions.
> Type 'license()' or 'licence()' for distribution details.
> 
> R is a collaborative project with many contributors.
> Type 'contributors()' for more information and
> 'citation()' on how to cite R or R packages in publications.
> 
> Type 'demo()' for some demos, 'help()' for on-line help, or
> 'help.start()' for an HTML browser interface to help.
> Type 'q()' to quit R.
  Running 'ou2-kalman.R'
  Comparing 'ou2-kalman.Rout' to 'ou2-kalman.Rout.save' ... OK
  Running 'ou2-mif.R'
  Comparing 'ou2-mif.Rout' to 'ou2-mif.Rout.save' ... OK
  Running 'ou2-nlf.R'
  Comparing 'ou2-nlf.Rout' to 'ou2-nlf.Rout.save' ... OK
  Running 'ou2-pmcmc.R'
  Comparing 'ou2-pmcmc.Rout' to 'ou2-pmcmc.Rout.save' ... OK
  Running 'ou2-probe.R'
  Comparing 'ou2-probe.Rout' to 'ou2-probe.Rout.save' ...178c178
< [1] 1.221245e-15
---
> [1] 1.110223e-16
208c208
< [1] 90.5961
---
> [1] 93.95585
  Running 'ou2-procmeas.R'
  Comparing 'ou2-procmeas.Rout' to 'ou2-procmeas.Rout.save' ... OK
  Running 'ou2-simulate.R'
  Comparing 'ou2-simulate.Rout' to 'ou2-simulate.Rout.save' ... OK
  Running 'ou2-trajmatch.R'
  Comparing 'ou2-trajmatch.Rout' to 'ou2-trajmatch.Rout.save' ... OK
  Running 'pfilter.R'
  Comparing 'pfilter.Rout' to 'pfilter.Rout.save' ... OK
  Running 'pomppomp.R'
  Comparing 'pomppomp.Rout' to 'pomppomp.Rout.save' ... OK
  Running 'ricker-probe.R'
  Comparing 'ricker-probe.Rout' to 'ricker-probe.Rout.save' ...134c134
<  1.000000e+00 -3.470661e-18 -1.108330e-18 
---
> 1.000000e+00 2.308125e-18 9.896164e-19 
177c177
<  1.000000e+00 -3.470661e-18 -1.108330e-18  3.679493e+03 -1.275470e+03 
---
>  1.000000e+00  2.308125e-18  9.896164e-19  3.679493e+03 -1.275470e+03 
261c261
<  1.000000e+00 -3.470661e-18 -1.108330e-18 
---
> 1.000000e+00 2.308125e-18 9.896164e-19 
296c296
<   16.07    0.18   16.58 
---
>   7.680   0.008   7.713 
355c355
<   10.55    0.22   11.25 
---
>   5.668   0.000   5.683 
514c514
< [1] 30.22958
---
> [1] 29.82456
  Running 'ricker-spect.R'
  Comparing 'ricker-spect.Rout' to 'ricker-spect.Rout.save' ... OK
  Running 'ricker.R'
  Comparing 'ricker.Rout' to 'ricker.Rout.save' ...99,107c99,107
< SHRINK            45 -18.987087 -19.858312
< LO-REDUCTION      47 -19.288693 -19.858312
< LO-REDUCTION      49 -19.711127 -19.858312
< LO-REDUCTION      51 -19.779225 -19.858312
< SHRINK            56 -19.098736 -19.858312
< LO-REDUCTION      58 -19.213348 -19.858312
< LO-REDUCTION      60 -19.230757 -19.858312
< SHRINK            65 -19.572673 -19.858312
< HI-REDUCTION      67 -19.622339 -19.858312
---
> SHRINK            45 -18.987087 -19.858319
> LO-REDUCTION      47 -19.288693 -19.858319
> LO-REDUCTION      49 -19.711127 -19.858319
> LO-REDUCTION      51 -19.779236 -19.858319
> SHRINK            56 -19.098736 -19.858319
> LO-REDUCTION      58 -19.213348 -19.858319
> LO-REDUCTION      60 -19.230757 -19.858319
> SHRINK            65 -19.572673 -19.858319
> HI-REDUCTION      67 -19.622339 -19.858319
111,112c111,112
< LO-REDUCTION      78 -19.622472 -19.883729
< LO-REDUCTION      80 -19.692347 -19.883729
---
> LO-REDUCTION      78 -19.622452 -19.883729
> LO-REDUCTION      80 -19.692344 -19.883729
119c119
< SHRINK           103 -19.279000 -19.883729
---
> SHRINK           103 -19.279074 -19.883729
130c130
< SHRINK           140 -19.318169 -20.036526
---
> SHRINK           140 -19.318310 -20.036526
132,133c132,133
< LO-REDUCTION     144 -19.539170 -20.036526
< SHRINK           149 -19.499303 -20.036526
---
> LO-REDUCTION     144 -19.541768 -20.036526
> SHRINK           149 -19.499454 -20.036526
136,212c136,204
< LO-REDUCTION     155 -19.842293 -20.036526
< HI-REDUCTION     157 -19.857050 -20.036526
< SHRINK           162 -19.619339 -20.036526
< LO-REDUCTION     164 -19.714203 -20.036526
< LO-REDUCTION     166 -19.899421 -20.036526
< SHRINK           171 -19.494082 -20.036526
< LO-REDUCTION     173 -19.656942 -20.039593
< LO-REDUCTION     175 -19.793674 -20.039593
< REFLECTION       177 -19.803800 -20.057243
< HI-REDUCTION     179 -19.811405 -20.057243
< SHRINK           184 -19.651680 -20.057243
< LO-REDUCTION     186 -19.705462 -20.057243
< LO-REDUCTION     188 -19.743525 -20.057243
< SHRINK           193 -19.556960 -20.057243
< LO-REDUCTION     195 -19.597290 -20.057243
< LO-REDUCTION     197 -19.783177 -20.057243
< LO-REDUCTION     199 -19.862732 -20.057243
< LO-REDUCTION     201 -19.880573 -20.057243
< SHRINK           206 -19.634931 -20.057243
< LO-REDUCTION     208 -19.689080 -20.057243
< LO-REDUCTION     210 -19.794176 -20.057243
< HI-REDUCTION     212 -19.885080 -20.057243
< LO-REDUCTION     214 -19.899959 -20.057243
< SHRINK           219 -19.593439 -20.057243
< LO-REDUCTION     221 -19.594954 -20.057243
< LO-REDUCTION     223 -19.961413 -20.057243
< SHRINK           228 -19.818816 -20.057243
< HI-REDUCTION     230 -19.877654 -20.057243
< SHRINK           235 -19.797069 -20.057243
< LO-REDUCTION     237 -19.841876 -20.115805
< LO-REDUCTION     239 -19.892766 -20.115805
< SHRINK           244 -19.867279 -20.115805
< HI-REDUCTION     246 -19.934675 -20.237392
< SHRINK           251 -20.008773 -20.237392
< REFLECTION       253 -20.036489 -20.259433
< HI-REDUCTION     255 -20.087695 -20.259433
< LO-REDUCTION     257 -20.207204 -20.259433
< SHRINK           262 -19.984461 -20.259433
< SHRINK           267 -19.984814 -20.259433
< SHRINK           272 -19.845300 -20.259433
< LO-REDUCTION     274 -19.889364 -20.259433
< LO-REDUCTION     276 -19.999567 -20.259433
< HI-REDUCTION     278 -20.006472 -20.259433
< LO-REDUCTION     280 -20.137998 -20.259433
< HI-REDUCTION     282 -20.141151 -20.259433
< HI-REDUCTION     284 -20.146834 -20.259433
< SHRINK           289 -19.906087 -20.259433
< LO-REDUCTION     291 -20.123761 -20.268866
< LO-REDUCTION     293 -20.151617 -20.268866
< LO-REDUCTION     295 -20.192722 -20.268866
< SHRINK           300 -20.129055 -20.268866
< HI-REDUCTION     302 -20.148408 -20.268866
< LO-REDUCTION     304 -20.153190 -20.268866
< REFLECTION       306 -20.232254 -20.340117
< HI-REDUCTION     308 -20.236442 -20.340117
< HI-REDUCTION     310 -20.253389 -20.340117
< HI-REDUCTION     312 -20.268866 -20.392599
< LO-REDUCTION     314 -20.272843 -20.392599
< HI-REDUCTION     316 -20.309205 -20.392599
< SHRINK           321 -20.220777 -20.392599
< REFLECTION       323 -20.275127 -20.403755
< LO-REDUCTION     325 -20.302912 -20.403755
< LO-REDUCTION     327 -20.303946 -20.403755
< HI-REDUCTION     329 -20.348576 -20.403755
< SHRINK           334 -20.263196 -20.403755
< LO-REDUCTION     336 -20.301491 -20.403755
< LO-REDUCTION     338 -20.323156 -20.405032
< LO-REDUCTION     340 -20.358182 -20.405032
< SHRINK           345 -20.301587 -20.405032
< HI-REDUCTION     347 -20.332192 -20.405032
< SHRINK           352 -20.344506 -20.409312
< HI-REDUCTION     354 -20.394435 -20.463644
< LO-REDUCTION     356 -20.405032 -20.463644
< LO-REDUCTION     358 -20.409312 -20.463644
< LO-REDUCTION     360 -20.436627 -20.463644
< SHRINK           365 -20.408946 -20.463644
< SHRINK           370 -20.408946 -20.463644
---
> LO-REDUCTION     155 -19.842500 -20.036526
> SHRINK           160 -19.714203 -20.036526
> LO-REDUCTION     162 -19.900941 -20.036526
> SHRINK           167 -19.494052 -20.036526
> LO-REDUCTION     169 -19.557532 -20.036526
> LO-REDUCTION     171 -19.635954 -20.036526
> SHRINK           176 -19.571857 -20.036526
> HI-REDUCTION     178 -19.633935 -20.036526
> LO-REDUCTION     180 -19.773673 -20.036526
> SHRINK           185 -19.580741 -20.036526
> LO-REDUCTION     187 -19.713589 -20.036526
> SHRINK           192 -19.778851 -20.075344
> LO-REDUCTION     194 -19.920306 -20.075344
> SHRINK           199 -19.253544 -20.075344
> LO-REDUCTION     201 -19.563461 -20.075344
> LO-REDUCTION     203 -19.657461 -20.075344
> SHRINK           208 -19.386987 -20.075344
> LO-REDUCTION     210 -19.445799 -20.075344
> LO-REDUCTION     212 -19.595884 -20.075344
> SHRINK           217 -19.582926 -20.151824
> LO-REDUCTION     219 -19.753819 -20.151824
> LO-REDUCTION     221 -19.772159 -20.151824
> LO-REDUCTION     223 -19.782335 -20.151824
> SHRINK           228 -19.596088 -20.151824
> LO-REDUCTION     230 -19.681504 -20.151824
> SHRINK           235 -19.609725 -20.151824
> HI-REDUCTION     237 -19.615594 -20.151824
> HI-REDUCTION     239 -19.651915 -20.151824
> LO-REDUCTION     241 -19.694368 -20.151824
> LO-REDUCTION     243 -19.769449 -20.151824
> HI-REDUCTION     245 -19.782970 -20.151824
> SHRINK           250 -19.592628 -20.151824
> LO-REDUCTION     252 -19.877327 -20.151824
> HI-REDUCTION     254 -19.966120 -20.151824
> SHRINK           259 -19.757861 -20.151824
> LO-REDUCTION     261 -19.978390 -20.151824
> SHRINK           266 -19.866279 -20.151824
> HI-REDUCTION     268 -20.048979 -20.151824
> LO-REDUCTION     270 -20.073212 -20.164817
> HI-REDUCTION     272 -20.082314 -20.265947
> LO-REDUCTION     274 -20.151824 -20.265947
> SHRINK           279 -20.086588 -20.265947
> SHRINK           284 -20.054913 -20.265947
> REFLECTION       286 -20.079536 -20.312392
> LO-REDUCTION     288 -20.216102 -20.312392
> SHRINK           293 -20.153482 -20.312392
> SHRINK           298 -20.097052 -20.312392
> LO-REDUCTION     300 -20.118531 -20.312392
> LO-REDUCTION     302 -20.165018 -20.312392
> LO-REDUCTION     304 -20.176834 -20.312392
> SHRINK           309 -20.130573 -20.312392
> LO-REDUCTION     311 -20.175138 -20.312392
> HI-REDUCTION     313 -20.232404 -20.312392
> SHRINK           318 -20.158381 -20.340133
> LO-REDUCTION     320 -20.250809 -20.340133
> SHRINK           325 -20.236229 -20.340133
> LO-REDUCTION     327 -20.270202 -20.340133
> LO-REDUCTION     329 -20.313522 -20.340133
> SHRINK           334 -20.301190 -20.340133
> LO-REDUCTION     336 -20.320514 -20.340133
> SHRINK           341 -20.309539 -20.340133
> LO-REDUCTION     343 -20.328223 -20.340133
> SHRINK           348 -20.316445 -20.341834
> LO-REDUCTION     350 -20.337619 -20.341834
> HI-REDUCTION     352 -20.340133 -20.341834
> HI-REDUCTION     354 -20.341082 -20.341834
> SHRINK           359 -20.341834 -20.343672
> SHRINK           364 -20.341834 -20.343672
> SHRINK           369 -20.341834 -20.343672
215c207
<     372 function evaluations used
---
>     371 function evaluations used
242,244c234,236
< log.r           3.0    3.8    3.77    3.74
< log.sigma       0.0   -1.2   -1.66   -1.12
< log.phi         3.0    2.3    2.33    2.41
---
> log.r           3.0    3.8    3.79    3.74
> log.sigma       0.0   -1.2   -1.74   -1.12
> log.phi         3.0    2.3    2.32    2.41
247,248c239,240
< loglik       -230.9 -139.5 -137.06 -143.86
< synth.loglik  -12.3   17.5   18.01   20.46
---
> loglik       -230.9 -139.5 -137.35 -143.33
> synth.loglik  -12.3   17.5   16.47   20.34
  Running 'rw2.R'
  Comparing 'rw2.Rout' to 'rw2.Rout.save' ... OK
  Running 'sir.R'
  Comparing 'sir.Rout' to 'sir.Rout.save' ... OK
  Running 'skeleton.R'
  Comparing 'skeleton.Rout' to 'skeleton.Rout.save' ... OK
  Running 'steps.R'
  Comparing 'steps.Rout' to 'steps.Rout.save' ... OK
  Running 'synlik.R'
  Comparing 'synlik.Rout' to 'synlik.Rout.save' ... OK
  Running 'verhulst.R'
  Comparing 'verhulst.Rout' to 'verhulst.Rout.save' ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... OK
* checking re-building of vignettes ... OK
* checking PDF version of manual ... OK