Check results for 'Biograph'

using R Under development (unstable) (2012-02-27 r58511)
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 '1.0'
checking package dependencies ... OK
checking if this is a source package ... OK
checking if there is a namespace ... NOTE
As from R 2.14.0 all packages need a namespace.
One will be generated on installation, but it is better to handcraft a
NAMESPACE file: R CMD build will produce a suitable starting point.
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
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 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
AgeTrans: no visible binding for global variable
'date_in_month_or_year'
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 'timeunit'
Biograph.long: no visible binding for global variable 'ncovariates'
Biograph.msm: no visible binding for global variable 'timeunit'
Biograph.msm : <anonymous>: 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 'timeunit'
Biograph.mvna: no visible binding for global variable 'namstates'
Biograph.mvna : <anonymous>: no visible binding for global variable
'namstates'
CMC.ages: no visible binding for global variable 'timeunit'
CMC.years: no visible binding for global variable 'timeunit'
ChangeObservationWindow.e: no visible binding for global variable
'nsample'
ChangeObservationWindow.t: no visible binding for global variable
'timeunit'
Cumrates: no visible binding for global variable 'namstates'
Cumrates: no visible binding for global variable 'iagehigh'
Cumrates: no visible binding for global variable 'numstates'
Cumrates: no visible binding for global variable 'namage'
GLHS.Biograph: no visible binding for global variable 'rrdat'
LexisOccExp: no visible binding for global variable
'date_in_month_or_year'
Lexislines.episodes: no visible binding for global variable 'survey'
Lexislines.episodes: no visible binding for global variable 'timeunit'
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.S.plot: no visible binding for global variable 'namstates'
MSLT.S.plot: 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: warning in vector(mod = "numeric", length = 400): partial
argument match of 'mod' to 'mode'
Occup: 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 'namstates'
OverviewTransitions: no visible binding for global variable
'date_in_month_or_year'
OverviewTransitions: no visible binding for global variable 'nage'
Parameters: no visible binding for '<<-' assignment to 'nsample'
Parameters: no visible binding for global variable 'numstates'
Parameters: no visible binding for global variable 'namstates'
Parameters: no visible binding for global variable 'nsample'
Parameters: no visible binding for '<<-' assignment to 'iagelow'
Parameters: no visible binding for '<<-' assignment to 'iagehigh'
Parameters: no visible binding for '<<-' assignment to 'nage'
Parameters: no visible binding for global variable 'iagehigh'
Parameters: no visible binding for global variable 'iagelow'
Parameters: no visible binding for '<<-' assignment to 'namage'
Parameters: no visible binding for '<<-' assignment to 'ncovariates'
Parameters: no visible binding for '<<-' assignment to 'ncmc_tr'
Parameters: no visible binding for '<<-' assignment to 'maxtrans'
Parameters: no visible binding for global variable 'ncmc_tr'
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: no visible binding for global variable 'numstates'
Rates: no visible binding for global variable 'namage'
Rates: no visible binding for global variable 'namstates'
StackGraph: no visible binding for global variable 'numstates'
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 'namstates'
Trans: no visible binding for global variable 'date_in_month_or_year'
Trans: no visible binding for global variable 'nage'
TransitionAB: no visible binding for global variable
'date_in_month_or_year'
YearTrans: no visible binding for global variable
'date_in_month_or_year'
p.OverviewEpisodes: no visible binding for global variable 'timeunit'
p.OverviewEpisodes: no visible binding for global variable 'numstates'
p.OverviewEpisodes: no visible binding for global variable 'namstates'
p.SamplePath: warning in vector(mod = "numeric", length = nss1):
partial argument match of 'mod' to 'mode'
p.SamplePath: warning in vector(mod = "numeric", length = nss): partial
argument match of 'mod' to 'mode'
p.SamplePath: no visible binding for global variable 'namstates'
p.Trans: no visible binding for global variable 'numstates'
p.Trans: no visible binding for global variable 'namstates'
statesequence.ind: no visible binding for global variable 'namstates'
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 ... WARNING
'library' or 'require' call not declared from: 'mstate'
checking contents of 'data' directory ... OK
checking data for non-ASCII characters ... OK
checking data for ASCII and uncompressed saves ... OK
checking examples ...
** running examples for arch 'i386' ... ERROR
Running examples in 'Biograph-Ex.R' failed
The error most likely occurred in:

> ### Name: Biograph.mstate
> ### Title: Biograph to mstate object of class "msdata"
> ### Aliases: Biograph.mstate
> ### Keywords: msdata remove.intrastate
>
> ### ** Examples
>
> data (GLHS)
> D <- Biograph.mstate (GLHS)
[1] "Biograph first runs 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] Number of feasible transitions = 3
[1] " Biograph.mstate: calls function Remove_intrastate . . . "
[1] . . . . . . Removes intrastate transitions . . . .
[1] . . . . Intrastate transitions removed. Running 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] Number of feasible transitions = 2
[1] A new Biograph object without intrastate transitions is returned.
[1] . . . . . Creating long format . . . . . .
[1] . . . . . running reshape . . . . .
[1] . . . . Adjusting long format . . . .
> # Function events of mstate package
> library (mstate)
Error in library(mstate) : there is no package called 'mstate'
Execution halted
** running examples for arch 'x64' ... ERROR
Running examples in 'Biograph-Ex.R' failed
The error most likely occurred in:

> ### Name: Biograph.mstate
> ### Title: Biograph to mstate object of class "msdata"
> ### Aliases: Biograph.mstate
> ### Keywords: msdata remove.intrastate
>
> ### ** Examples
>
> data (GLHS)
> D <- Biograph.mstate (GLHS)
[1] "Biograph first runs 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] Number of feasible transitions = 3
[1] " Biograph.mstate: calls function Remove_intrastate . . . "
[1] . . . . . . Removes intrastate transitions . . . .
[1] . . . . Intrastate transitions removed. Running 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] Number of feasible transitions = 2
[1] A new Biograph object without intrastate transitions is returned.
[1] . . . . . Creating long format . . . . . .
[1] . . . . . running reshape . . . . .
[1] . . . . Adjusting long format . . . .
> # Function events of mstate package
> library (mstate)
Error in library(mstate) : there is no package called 'mstate'
Execution halted