* using log directory 'd:/Rcompile/CRANpkg/local/2.15/pomp.Rcheck'
* using R version 2.15.0 (2012-03-30)
* using platform: x86_64-pc-mingw32 (64-bit)
* using session charset: ISO8859-1
* checking for file 'pomp/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'pomp' version '0.42-4'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... 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 compiled code ... OK
* checking sizes of PDF files under 'inst/doc' ... OK
* checking installed files from '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 'bbs.R'
  Comparing 'bbs.Rout' to 'bbs.Rout.save' ... OK
  Running 'blowflies.R'
  Comparing 'blowflies.Rout' to 'blowflies.Rout.save' ... OK
  Running 'dacca.R'
  Comparing 'dacca.Rout' to 'dacca.Rout.save' ... OK
  Running 'dimchecks.R'
  Comparing 'dimchecks.Rout' to 'dimchecks.Rout.save' ... OK
  Running 'fhn.R'
  Comparing 'fhn.Rout' to 'fhn.Rout.save' ...99,100c99,100
< V -1.3052973  1.273969824
< R -0.5591607 -0.006907855
---
> V -1.3052919  1.27398107
> R -0.5591608 -0.00692014
105,106c105,106
< V -1.4459105 1.19168398
< R -0.5707826 0.02733687
---
> V -1.4459045 1.19170161
> R -0.5707824 0.02732499
111,112c111,112
< V -1.4714085 1.32435379
< R -0.5861065 0.06165475
---
> 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' ... OK
  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' ... OK
  Running 'ou2-kalman.R'
  Comparing 'ou2-kalman.Rout' to 'ou2-kalman.Rout.save' ... OK
  Running 'ou2-mif-fp.R'
  Comparing 'ou2-mif-fp.Rout' to 'ou2-mif-fp.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] 99.89722
---
> [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 'partrans.R'
  Comparing 'partrans.Rout' to 'partrans.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-bsmc.R'
  Comparing 'ricker-bsmc.Rout' to 'ricker-bsmc.Rout.save' ...29c29
<  3.841075 -1.806405 
---
>  3.890965 -1.766350 
33c33
< 46.4890685  0.1645358 10.0000000  7.0000000  0.0000000 
---
> 50.0502049  0.1702842 10.0000000  7.0000000  0.0000000 
  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
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
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
230c230
< [1] 15.39317
---
> [1] 15.31774
373c373
<  39.47310  -9.04665 -18.05277 
---
> 24.879460 -5.950185 -2.211594 
384c384
<      1      0      0 
---
>   1.00   0.00   0.32 
388c388
< 0.001998002 0.001998002 0.001998002 
---
> 0.001998002 0.001998002 0.641358641 
391c391
< [1] -48.29627
---
> [1] -56.62876
419c419
<   0.591   0.067   0.315   0.907   0.144   0.658 
---
>   0.592   0.067   0.315   0.907   0.144   0.658 
423c423
< 0.8191808 0.1358641 0.6313686 0.1878122 0.2897103 0.6853147 
---
> 0.8171828 0.1358641 0.6313686 0.1878122 0.2897103 0.6853147 
426c426
< [1] -12.45567
---
> [1] -12.45474
454c454
<   0.151   0.317   0.896   0.143   0.653 
---
>   0.152   0.317   0.896   0.143   0.653 
458c458
< 0.3036963 0.6353646 0.2097902 0.2877123 0.6953047 
---
> 0.3056943 0.6353646 0.2097902 0.2877123 0.6953047 
461c461
< [1] 5.174442
---
> [1] 5.174849
498c498
<    0.591    0.591    0.067    0.315    0.106    0.133 
---
>    0.592    0.592    0.067    0.315    0.105    0.133 
502c502
< 0.8191808 0.8191808 0.1358641 0.6313686 0.2137862 0.2677323 
---
> 0.8171828 0.8171828 0.1358641 0.6313686 0.2117882 0.2677323 
505c505
< [1] 31.76948
---
> [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' ...40,45c40,45
< 138  4.0116554  0.05723792   3   45
< 141  4.2498660  0.26933885   3   46
< 144  2.9297800  0.07790589   3   47
< 147  7.1173170  0.01738347   3   48
< 150  0.2364335 -0.08730222   3   49
< 153 18.9815336  0.82198849   3   50
---
> 138  4.0116869  0.05723792   3   45
> 141  4.2497654  0.26933885   3   46
> 144  2.9300053  0.07790589   3   47
> 147  7.1162605  0.01738347   3   48
> 150  0.2366483 -0.08730222   3   49
> 153 18.9946973  0.82198849   3   50
59c59
< 153 217   3   50
---
> 153 218   3   50
  Running 'rw2.R'
  Comparing 'rw2.Rout' to 'rw2.Rout.save' ...375c375
< [1] 8.881784e-16
---
> [1] 1.110223e-16
  Running 'sir.R'
  Comparing 'sir.Rout' to 'sir.Rout.save' ...546c546
< [1] 5.329e-15
---
> [1] 7.105e-15
548c548
< [1] 3.638e-12
---
> [1] 7.276e-12
  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 'bbs.R'
  Comparing 'bbs.Rout' to 'bbs.Rout.save' ... OK
  Running 'blowflies.R'
  Comparing 'blowflies.Rout' to 'blowflies.Rout.save' ... OK
  Running 'dacca.R'
  Comparing 'dacca.Rout' to 'dacca.Rout.save' ... OK
  Running 'dimchecks.R'
  Comparing 'dimchecks.Rout' to 'dimchecks.Rout.save' ... OK
  Running 'fhn.R'
  Comparing 'fhn.Rout' to 'fhn.Rout.save' ...99,100c99,100
< V -1.3052943  1.274026725
< R -0.5591645 -0.006983435
---
> V -1.3052919  1.27398107
> R -0.5591608 -0.00692014
105,106c105,106
< V -1.4459072 1.19176249
< R -0.5707861 0.02726337
---
> V -1.4459045 1.19170161
> R -0.5707824 0.02732499
111,112c111,112
< V -1.4714051 1.32444545
< R -0.5861097 0.06158375
---
> 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' ... OK
  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' ... OK
  Running 'ou2-kalman.R'
  Comparing 'ou2-kalman.Rout' to 'ou2-kalman.Rout.save' ... OK
  Running 'ou2-mif-fp.R'
  Comparing 'ou2-mif-fp.Rout' to 'ou2-mif-fp.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] 94.80102
---
> [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 'partrans.R'
  Comparing 'partrans.Rout' to 'partrans.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-bsmc.R'
  Comparing 'ricker-bsmc.Rout' to 'ricker-bsmc.Rout.save' ...29c29
<  3.887454 -1.721606 
---
>  3.890965 -1.766350 
33c33
< 48.7113263  0.1800624 10.0000000  7.0000000  0.0000000 
---
> 50.0502049  0.1702842 10.0000000  7.0000000  0.0000000 
  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 
258c258
<  1.000000e+00 -3.470661e-18 -1.108330e-18 
---
> 1.000000e+00 2.308125e-18 9.896164e-19 
505c505
< [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' ... OK
  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 ... SKIPPED
* checking PDF version of manual ... OK