- using R version 2.14.1 Patched (2012-02-05 r58287)
- using platform: i686-pc-linux-gnu (32-bit)
- using session charset: UTF-8
- 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 for executable files ... 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 for sufficient/correct file permissions ... 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
- 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’ ... OK
- checking examples ... OK
- checking for unstated dependencies in tests ... OK
- checking tests ... 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
- 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