* using log directory 'd:/Rcompile/CRANpkg/local/2.15/Biograph.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 'Biograph/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'Biograph' version '2.0'
* 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 'Biograph' 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 ... NOTE
Biograph.long : <anonymous>: no visible binding for global variable
  'ncovariates'
Biograph.long : <anonymous>: no visible binding for global variable
  'namstates'
Biograph.long: no visible binding for global variable 'ncovariates'
Biograph.msm: no visible binding for global variable 'ncovariates'
Biograph.msm : <anonymous>: no visible binding for global variable
  'namstates'
Biograph.msm: no visible binding for global variable 'namstates'
Biograph.mstate: no visible binding for global variable 'numstates'
Biograph.mstate: no visible binding for global variable 'namstates'
Biograph.mstate : <anonymous>: no visible binding for global variable
  'namstates'
Biograph.mvna: no visible binding for global variable 'namstates'
Biograph.mvna : <anonymous>: no visible binding for global variable
  'namstates'
ChangeObservationWindow.e: no visible binding for global variable
  'namstates'
ChangeObservationWindow.t: no visible binding for global variable
  'namstates'
ChangeObservationWindow.t: no visible binding for global variable
  'format.in'
Cumrates: no visible binding for global variable 'namstates'
Cumrates: no visible binding for global variable 'format.in'
Cumrates: no visible binding for global variable 'iagehigh'
Cumrates: no visible binding for global variable 'numstates'
Lexis.lines: no visible binding for global variable 'namstates'
Lexis.lines: no visible binding for global variable 'Tstart'
Lexis.lines: no visible binding for global variable 'Tstarta'
Lexis.lines: no visible binding for global variable 'state'
Lexis.lines: no visible binding for global variable 'ID'
Lexis.lines: no visible binding for global variable 'locIDx'
Lexis.lines: no visible binding for global variable 'locIDy'
LexisOccExp: no visible binding for global variable 'namstates'
LexisOccExp: no visible binding for global variable 'Dlong2'
Lexislines.episodes: no visible binding for global variable 'namstates'
Lexislines.episodes: no visible binding for global variable 'DES'
Lexislines.episodes: no visible binding for global variable 'TstopY'
Lexislines.episodes: no visible binding for global variable 'Tstopage'
Lexislines.episodes: no visible binding for global variable 'lex.id'
MSLT.S: no visible binding for global variable 'numstates'
MSLT.e: no visible binding for global variable 'numstates'
Occup: no visible binding for global variable 'iagehigh'
Occup: no visible binding for global variable 'iagelow'
Occup: no visible binding for global variable 'namage'
Occup: no visible binding for global variable 'numstates'
Occup: no visible binding for global variable 'namstates'
OverviewEpisodes: no visible binding for global variable 'namstates'
OverviewEpisodes: no visible binding for global variable 'numstates'
OverviewTransitions: no visible binding for global variable 'namstates'
OverviewTransitions: no visible binding for global variable 'iagelow'
OverviewTransitions: no visible binding for global variable 'iagehigh'
OverviewTransitions: no visible binding for global variable 'numstates'
OverviewTransitions: no visible binding for global variable 'nage'
Parameters: no visible binding for global variable 'numstates'
Parameters: no visible binding for global variable 'nsample'
Parameters: no visible binding for global variable 'nage'
RateTable: no visible binding for global variable 'iagelow'
RateTable: no visible binding for global variable 'iagehigh'
RateTable: no visible binding for global variable 'numstates'
RateTable: no visible binding for global variable 'namstates'
RateTable: no visible binding for global variable 'nage'
Rates.ac: no visible binding for global variable 'numstates'
Rates.ac: no visible binding for global variable 'namage'
Rates.ac: no visible binding for global variable 'namstates'
SamplePath: no visible binding for global variable 'namstates'
Sequences.ind: no visible binding for global variable 'namstates'
Trans: no visible binding for global variable 'namstates'
Trans: no visible binding for global variable 'format.in'
Trans: no visible binding for global variable 'iagelow'
Trans: no visible binding for global variable 'iagehigh'
Trans: no visible binding for global variable 'numstates'
Trans: no visible binding for global variable 'nage'
TransitionAB: no visible binding for global variable 'namstates'
YearTrans: no visible binding for global variable 'format.in'
check.par: no visible binding for global variable 'namstates'
check.par: no visible binding for global variable 'iagelow'
check.par: no visible binding for global variable 'iagehigh'
plot.MSLT.S: no visible binding for global variable 'iagelow'
plot.MSLT.S: no visible binding for global variable 'iagehigh'
plot.MSLT.S: no visible binding for global variable 'numstates'
plot.MSLT.S: no visible binding for global variable 'namstates'
plot.MSLT.S: no visible binding for global variable 'state'
plot.occup.S: no visible binding for global variable 'numstates'
plot.occup.S: no visible binding for global variable 'namage'
plot.occup.S: no visible binding for global variable 'state'
transitions: no visible binding for global variable 'numstates'
* 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ...
** running examples for arch 'i386' ... ERROR
Running examples in 'Biograph-Ex.R' failed
The error most likely occurred in:

> ### Name: Lexis.points
> ### Title: Plot observations in Lexis diagram
> ### Aliases: Lexis.points
> 
> ### ** Examples
> 
> #  Example 1: ages at labour market entry, by sex
>   data(GLHS)
>   #y <- Parameters(GLHS)
>   z <- Lexis.points (Bdata=GLHS,transition="NJ",title="Date and age at labour market entry by sex and cohort",cov="sex",group="cohort",legend.pos=c(0.5,2.2),pdf=FALSE)
[1] "check.par: the function checks whether \"format.date\" is present (attribute of Biograph object) and all parameters are defined (by function Parameters) "
[1] ". . . . Running function Parameters . . . . "
[1] Number of states = 2
[1] Names of the states =  N                      J                     
[1] To change the sequence of states, type: <namstates <- c(...)> after calling Parameters
[1] "Exploring types of transitions"
[1] "check.par: the function checks whether \"format.date\" is present (attribute of Biograph object) and all parameters are defined (by function Parameters) "
[1] Age profile: Number of individuals with transition NJ is 201
> 
> #  Example 2: ages at first birth among married women, by religious denomination
>   data(NLOG98)
>   y <- Parameters (NLOG98)
[1] ". . . . Running function Parameters . . . . "
[1] "Exploring types of transitions"
>   z <- Lexis.points (Bdata=NLOG98,transition="MK",title="Date and age at first birth (married women) by religion and cohort",cov="kerk",group="cohort",legend.pos=c(0.6,1.6),pdf=FALSE)
[1] "check.par: the function checks whether \"format.date\" is present (attribute of Biograph object) and all parameters are defined (by function Parameters) "
[1] "date.convert: The vector you supplied has no values."
[1] "date.convert: The vector you supplied has no values."
[1] "date.convert: The vector you supplied has no values."
[1] "check.par: the function checks whether \"format.date\" is present (attribute of Biograph object) and all parameters are defined (by function Parameters) "
[1] Age profile: Number of individuals with transition MK is 2994
Error: Insufficient values in manual scale. 5 needed but only 4 provided.
Execution halted
** running examples for arch 'x64' ... ERROR
Running examples in 'Biograph-Ex.R' failed
The error most likely occurred in:

> ### Name: Lexis.points
> ### Title: Plot observations in Lexis diagram
> ### Aliases: Lexis.points
> 
> ### ** Examples
> 
> #  Example 1: ages at labour market entry, by sex
>   data(GLHS)
>   #y <- Parameters(GLHS)
>   z <- Lexis.points (Bdata=GLHS,transition="NJ",title="Date and age at labour market entry by sex and cohort",cov="sex",group="cohort",legend.pos=c(0.5,2.2),pdf=FALSE)
[1] "check.par: the function checks whether \"format.date\" is present (attribute of Biograph object) and all parameters are defined (by function Parameters) "
[1] ". . . . Running function Parameters . . . . "
[1] Number of states = 2
[1] Names of the states =  N                      J                     
[1] To change the sequence of states, type: <namstates <- c(...)> after calling Parameters
[1] "Exploring types of transitions"
[1] "check.par: the function checks whether \"format.date\" is present (attribute of Biograph object) and all parameters are defined (by function Parameters) "
[1] Age profile: Number of individuals with transition NJ is 201
> 
> #  Example 2: ages at first birth among married women, by religious denomination
>   data(NLOG98)
>   y <- Parameters (NLOG98)
[1] ". . . . Running function Parameters . . . . "
[1] "Exploring types of transitions"
>   z <- Lexis.points (Bdata=NLOG98,transition="MK",title="Date and age at first birth (married women) by religion and cohort",cov="kerk",group="cohort",legend.pos=c(0.6,1.6),pdf=FALSE)
[1] "check.par: the function checks whether \"format.date\" is present (attribute of Biograph object) and all parameters are defined (by function Parameters) "
[1] "date.convert: The vector you supplied has no values."
[1] "date.convert: The vector you supplied has no values."
[1] "date.convert: The vector you supplied has no values."
[1] "check.par: the function checks whether \"format.date\" is present (attribute of Biograph object) and all parameters are defined (by function Parameters) "
[1] Age profile: Number of individuals with transition MK is 2994
Error: Insufficient values in manual scale. 5 needed but only 4 provided.
Execution halted