Check results for 'Biograph'

using R Under development (unstable) (2012-05-19 r59366)
using platform: x86_64-unknown-linux-gnu (64-bit)
using session charset: UTF-8
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 for executable files ... 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 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 loading without being on the library search path ... 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 examples ... 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