CRAN Package Check Results for Package compeir

Last updated on 2020-03-02 10:52:43 CET.

Check Details

Version: 1.0
Check: R code for possible problems
Result: NOTE
    CIFplot: no visible global function definition for 'plot'
    CIFplot: no visible global function definition for 'gray'
    CIFplot: no visible global function definition for 'lines'
    iprop: no visible global function definition for 'qnorm'
    irates: no visible global function definition for 'qnorm'
    irates.ratio: no visible global function definition for 'qnorm'
    Undefined global functions or variables:
     gray lines plot qnorm
    Consider adding
     importFrom("grDevices", "gray")
     importFrom("graphics", "lines", "plot")
     importFrom("stats", "qnorm")
    to your NAMESPACE file.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-ix86+x86_64, r-devel-windows-ix86+x86_64-gcc8, r-patched-linux-x86_64, r-patched-solaris-x86, r-release-linux-x86_64, r-release-windows-ix86+x86_64, r-release-osx-x86_64, r-oldrel-windows-ix86+x86_64, r-oldrel-osx-x86_64

Version: 1.0
Check: Rd line widths
Result: NOTE
    Rd file 'CIFplot.Rd':
     \usage lines wider than 90 characters:
     CIFplot(x, event.code = NULL, covar.code = NULL, indiv.times = NULL, indiv.events = NULL, indiv.covar = NULL,
    
    Rd file 'irates.Rd':
     \usage lines wider than 90 characters:
     irates(data, time.code = NULL, no.event.code = NULL, no.event.lab = NULL, event.lab = NULL, covar.lab = NULL,
    
    Rd file 'plot.irates.Rd':
     \usage lines wider than 90 characters:
     plot(x, covar.code = NULL, full.sample = FALSE, n.row = 1, viewport.size = list(w = 3.5, h = 2.5),
     box.size = list(w = NULL, h = NULL), dist = 0.5, irates.vbw = NULL, arrow.maxlwd = 10, display.digits = 2, cex = 0.9, show.values = TRU ... [TRUNCATED]
    
    Rd file 'print.iprop.Rd':
     \usage lines wider than 90 characters:
     print(x, event.code = NULL, covar.code = NULL, full.sample = FALSE, display.digits = 4, ...)
    
    Rd file 'print.irates.Rd':
     \usage lines wider than 90 characters:
     print(x, event.code = NULL, covar.code = NULL, full.sample = FALSE, display.digits = 4, ...)
    
    These lines will be truncated in the PDF manual.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-patched-linux-x86_64, r-release-linux-x86_64

Version: 1.0
Check: examples
Result: ERROR
    Running examples in 'compeir-Ex.R' failed
    The error most likely occurred in:
    
    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### Name: CIFplot
    > ### Title: Plotting estimates of the cumulative incidence function
    > ### Aliases: CIFplot
    >
    > ### ** Examples
    >
    > ### Example data.frame with aggregated count data
    > dat <- data.frame(
    + times = c(7948,2899),
    + no.event = c(6,8),
    + event.1 = c(589,68),
    + event.2 = c(55,21),
    + row.names = c("covar0","covar1"))
    >
    > ### Compute irates object from dat
    > ir <- irates(dat)
    >
    > ### Compute the cumulative incidence function from irates object
    > ### here: timespan is specified by xlim (default: xlim = c(0,30))
    > CIFplot(x = ir)
    >
    >
    > ### sir.adm: Individual patient data
    > data(sir.adm)
    >
    > ### aggregate data
    > agg.sir.adm <- data.reshape(
    + times = sir.adm$time,
    + events = sir.adm$status,
    + covar = sir.adm$pneu,
    + no.event.code= "0")
    >
    > ### Plot parametric and non-parametric CIF estimates
    > CIFplot(
    + x = irates(agg.sir.adm),
    + indiv.times = sir.adm$time,
    + indiv.events = sir.adm$status,
    + indiv.covar = sir.adm$pneu)
    Error in object$n.risk[, trs.sep[i, 1]] : subscript out of bounds
    Calls: CIFplot ... summary -> summary.etm -> ci.transfo -> lapply -> FUN
    Execution halted
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Version: 1.0
Check: package dependencies
Result: WARN
    Requires orphaned package: ‘etm’
Flavor: r-devel-linux-x86_64-fedora-clang