* using log directory 'd:/Rcompile/CRANpkg/local/2.15/mcmc.Rcheck'
* using R version 2.15.0 (2012-03-30)
* using platform: x86_64-pc-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'mcmc/DESCRIPTION' ... OK
* this is package 'mcmc' version '0.8'
* 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 'mcmc' 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 use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking sizes of PDF files under 'inst/doc' ... NOTE
  'qpdf' made some significant size reductions:
     compacted 'demo.pdf' from 1014Kb to 280Kb
  consider running tools::compactPDF() on these files
* checking installed files from 'inst/doc' ... NOTE
The following files should probably not be installed:
  'Makefile', 'bfst.tex', 'debug.tex', 'demo.tex', 'metrop.tex',
  'temper.tex'

Consider the use of a .Rinstignore file: see 'Writing R Extensions',
or move the vignette sources from 'inst/doc' to 'vignettes'.
* 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 'circle.R'
  Comparing 'circle.Rout' to 'circle.Rout.save' ... OK
  Running 'initseq.R'
  Comparing 'initseq.Rout' to 'initseq.Rout.save' ...40c40,41
< Iso 0.0-10
---
> Iso 0.0-8 
> Note: This package now has a NAMESPACE.
  Running 'logit.R'
  Comparing 'logit.Rout' to 'logit.Rout.save' ... OK
  Running 'logitbat.R'
  Comparing 'logitbat.Rout' to 'logitbat.Rout.save' ... OK
  Running 'logitfun.R'
  Comparing 'logitfun.Rout' to 'logitfun.Rout.save' ... OK
  Running 'logitfunarg.R'
  Comparing 'logitfunarg.Rout' to 'logitfunarg.Rout.save' ... OK
  Running 'logitidx.R'
  Comparing 'logitidx.Rout' to 'logitidx.Rout.save' ... OK
  Running 'logitlogidx.R'
  Comparing 'logitlogidx.Rout' to 'logitlogidx.Rout.save' ... OK
  Running 'logitmat.R'
  Comparing 'logitmat.Rout' to 'logitmat.Rout.save' ... OK
  Running 'logitnegidx.R'
  Comparing 'logitnegidx.Rout' to 'logitnegidx.Rout.save' ... OK
  Running 'logitsub.R'
  Comparing 'logitsub.Rout' to 'logitsub.Rout.save' ... OK
  Running 'logitsubbat.R'
  Comparing 'logitsubbat.Rout' to 'logitsubbat.Rout.save' ... OK
  Running 'logitvec.R'
  Comparing 'logitvec.Rout' to 'logitvec.Rout.save' ... OK
  Running 'saveseed.R'
  Comparing 'saveseed.Rout' to 'saveseed.Rout.save' ... OK
  Running 'temp-par-witch.R'
  Comparing 'temp-par-witch.Rout' to 'temp-par-witch.Rout.save' ...50c50
< [1] 0.6516291 0.3924419 0.3464789 0.2084433 0.1928375 0.5874317
---
> [1] 0.6335878 0.4974359 0.3245383 0.6022099 0.6129870 0.5913706
54,59c54,59
< [1,]        NA 0.6650943 0.4607843        NA        NA        NA
< [2,] 0.6346154        NA 0.5396825 0.2983871        NA        NA
< [3,] 0.4795918 0.5714286        NA 0.4148936 0.1030928        NA
< [4,]        NA 0.1980198 0.3193277        NA 0.2621359 0.3137255
< [5,]        NA        NA 0.1870504 0.2608696        NA 0.2615385
< [6,]        NA        NA        NA 0.3333333 0.3173653        NA
---
> [1,]        NA 0.7050691 0.5497382        NA        NA        NA
> [2,] 0.7522936        NA 0.5547445 0.6287879        NA        NA
> [3,] 0.5794393 0.5865385        NA 0.5308642 0.5476190        NA
> [4,]        NA 0.6666667 0.5505618        NA 0.8271605 0.6836735
> [5,]        NA        NA 0.5438596 0.8925620        NA 0.8373984
> [6,]        NA        NA        NA 0.8390805 0.9022989        NA
75c75
< [1] 0.5492308 0.4800000 0.5569231 0.7692308 0.9246154 0.7707692
---
> [1] 0.54923077 0.40923077 0.39538462 0.09692308 0.12923077 0.60000000
77c77
< [1] 0.03584574 0.05019272 0.05510132 0.04774849 0.02586413 0.05737443
---
> [1] 0.03482043 0.04817350 0.05463694 0.02855536 0.02113093 0.05130821
88,93c88,93
< [1,] 0.5033010 0.01344527
< [2,] 0.5122330 0.02468881
< [3,] 0.4968932 0.03692207
< [4,] 0.5283495 0.04713313
< [5,] 0.4582524 0.04742925
< [6,] 0.4192233 0.05931187
---
> [1,] 0.5231068 0.01389634
> [2,] 0.5361165 0.02213288
> [3,] 0.4904854 0.03961204
> [4,] 0.5652427 0.04909165
> [5,] 0.4056311 0.05106757
> [6,] 0.2450485 0.05108284
  Running 'temp-par.R'
  Comparing 'temp-par.Rout' to 'temp-par.Rout.save' ...19c19
< -2.0371  -0.6337   0.2394   0.6685   1.9599  
---
> -2.0371  -0.6337   0.2394   0.6686   1.9599  
32,34c32,34
<     Null deviance: 134.602  on 99  degrees of freedom
< Residual deviance:  86.439  on 96  degrees of freedom
< AIC: 94.439
---
>     Null deviance: 134.60  on 99  degrees of freedom
> Residual deviance:  86.44  on 96  degrees of freedom
> AIC: 94.44
  Running 'temp-ser-witch.R'
  Comparing 'temp-ser-witch.Rout' to 'temp-ser-witch.Rout.save' ... OK
  Running 'temp-ser.R'
  Comparing 'temp-ser.Rout' to 'temp-ser.Rout.save' ...19c19
< -2.0371  -0.6337   0.2394   0.6685   1.9599  
---
> -2.0371  -0.6337   0.2394   0.6686   1.9599  
32,34c32,34
<     Null deviance: 134.602  on 99  degrees of freedom
< Residual deviance:  86.439  on 96  degrees of freedom
< AIC: 94.439
---
>     Null deviance: 134.60  on 99  degrees of freedom
> Residual deviance:  86.44  on 96  degrees of freedom
> AIC: 94.44
** running tests for arch 'x64' OK
  Running 'circle.R'
  Comparing 'circle.Rout' to 'circle.Rout.save' ... OK
  Running 'initseq.R'
  Comparing 'initseq.Rout' to 'initseq.Rout.save' ...40c40,41
< Iso 0.0-10
---
> Iso 0.0-8 
> Note: This package now has a NAMESPACE.
  Running 'logit.R'
  Comparing 'logit.Rout' to 'logit.Rout.save' ...67c67
< [1] 8.235190e-06 5.499507e-06 6.082246e-06
---
> [1] 8.242296e-06 5.499507e-06 6.082246e-06
  Running 'logitbat.R'
  Comparing 'logitbat.Rout' to 'logitbat.Rout.save' ... OK
  Running 'logitfun.R'
  Comparing 'logitfun.Rout' to 'logitfun.Rout.save' ... OK
  Running 'logitfunarg.R'
  Comparing 'logitfunarg.Rout' to 'logitfunarg.Rout.save' ... OK
  Running 'logitidx.R'
  Comparing 'logitidx.Rout' to 'logitidx.Rout.save' ... OK
  Running 'logitlogidx.R'
  Comparing 'logitlogidx.Rout' to 'logitlogidx.Rout.save' ... OK
  Running 'logitmat.R'
  Comparing 'logitmat.Rout' to 'logitmat.Rout.save' ... OK
  Running 'logitnegidx.R'
  Comparing 'logitnegidx.Rout' to 'logitnegidx.Rout.save' ... OK
  Running 'logitsub.R'
  Comparing 'logitsub.Rout' to 'logitsub.Rout.save' ... OK
  Running 'logitsubbat.R'
  Comparing 'logitsubbat.Rout' to 'logitsubbat.Rout.save' ... OK
  Running 'logitvec.R'
  Comparing 'logitvec.Rout' to 'logitvec.Rout.save' ... OK
  Running 'saveseed.R'
  Comparing 'saveseed.Rout' to 'saveseed.Rout.save' ... OK
  Running 'temp-par-witch.R'
  Comparing 'temp-par-witch.Rout' to 'temp-par-witch.Rout.save' ... OK
  Running 'temp-par.R'
  Comparing 'temp-par.Rout' to 'temp-par.Rout.save' ...19c19
< -2.0371  -0.6337   0.2394   0.6685   1.9599  
---
> -2.0371  -0.6337   0.2394   0.6686   1.9599  
32,34c32,34
<     Null deviance: 134.602  on 99  degrees of freedom
< Residual deviance:  86.439  on 96  degrees of freedom
< AIC: 94.439
---
>     Null deviance: 134.60  on 99  degrees of freedom
> Residual deviance:  86.44  on 96  degrees of freedom
> AIC: 94.44
  Running 'temp-ser-witch.R'
  Comparing 'temp-ser-witch.Rout' to 'temp-ser-witch.Rout.save' ... OK
  Running 'temp-ser.R'
  Comparing 'temp-ser.Rout' to 'temp-ser.Rout.save' ...19c19
< -2.0371  -0.6337   0.2394   0.6685   1.9599  
---
> -2.0371  -0.6337   0.2394   0.6686   1.9599  
32,34c32,34
<     Null deviance: 134.602  on 99  degrees of freedom
< Residual deviance:  86.439  on 96  degrees of freedom
< AIC: 94.439
---
>     Null deviance: 134.60  on 99  degrees of freedom
> Residual deviance:  86.44  on 96  degrees of freedom
> AIC: 94.44
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK
NOTE: There were 2 notes.
See
  'd:/Rcompile/CRANpkg/local/2.15/mcmc.Rcheck/00check.log'
for details.
* using check arguments '--no-vignettes'