CRAN Package Check Results for Package JPSurv

Last updated on 2018-06-17 19:49:45 CEST.

Check Details

Version: 1.0.1
Check: S3 generic/method consistency
Result: NOTE
    Found the following apparent S3 methods exported but not registered:
     plot.joinpoint predict.joinpoint print.joinpoint summary.joinpoint
    See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
    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-patched-solaris-x86, r-release-linux-x86_64

Version: 1.0.1
Check: R code for possible problems
Result: NOTE
    CoxFit : GetEstimate: no visible global function definition for ‘lm’
    CoxFit : GetEstimate: no visible global function definition for ‘vcov’
    CoxModel_Year: no visible global function definition for ‘model.frame’
    CoxModel_Year: no visible global function definition for ‘model.matrix’
    joinpoint: no visible global function definition for ‘as.formula’
    joinpoint: no visible global function definition for ‘model.frame’
    joinpoint: no visible global function definition for ‘model.matrix’
    joinpoint : plot.surv: no visible global function definition for
     ‘predict’
    joinpoint : plot.surv: no visible global function definition for ‘plot’
    joinpoint : plot.surv: no visible global function definition for
     ‘lines’
    joinpoint : plot.surv: no visible global function definition for
     ‘legend’
    read.seerstat: no visible global function definition for ‘read.table’
    Undefined global functions or variables:
     as.formula legend lines lm model.frame model.matrix plot predict
     read.table vcov
    Consider adding
     importFrom("graphics", "legend", "lines", "plot")
     importFrom("stats", "as.formula", "lm", "model.frame", "model.matrix",
     "predict", "vcov")
     importFrom("utils", "read.table")
    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-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: 1.0.1
Check: Rd line widths
Result: NOTE
    Rd file 'aapc.Rd':
     \examples lines wider than 100 characters:
     # Fit the survival join point model with zero join points, i.e., fit the proportional hazard relative survival model.
    
    Rd file 'joinpoint.Rd':
     \examples lines wider than 100 characters:
     # Fit the survival join point model with zero join points, i.e., fit the proportional hazard relative survival model.
     fit2 = joinpoint(~Year, data=prostate, Site_and_age_for_total_stage == 18 & Sex == 1, numJPoints = 0);
    
    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: 1.0.1
Check: examples
Result: ERROR
    Running examples in ‘JPSurv-Ex.R’ failed
    The error most likely occurred in:
    
    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### Name: joinpoint
    > ### Title: Fitting a join point relative survival model
    > ### Aliases: joinpoint print.joinpoint plot.joinpoint summary.joinpoint
    >
    > ### ** Examples
    >
    > #load the SEER-9 prostate cancer dataset.
    > data(prostate);
    > # Fit the survival join point model with zero join points, i.e., fit the proportional hazard relative survival model.
    > fit1 = joinpoint(~Year, data=prostate, numJPoints = 0);
    > # Fit the survival join point model on a subset of the dataset.
    > fit2 = joinpoint(~Year, data=prostate, Site_and_age_for_total_stage == 18 & Sex == 1, numJPoints = 0);
    > # Fit the survival join point model for non-SEER*Stat datasets.
    > fit3 = joinpoint(~Alive_at_Start + Died + Lost_to_Followup + Expected_Survival_Interval
    + + Interval + Year, prostate, numJPoints = 0);
    > plot(fit1);
    Error in xy.coords(x, y, xlabel, ylabel, log) :
     'x' is a list, but does not have components 'x' and 'y'
    Calls: plot -> plot.default -> xy.coords
    Execution halted
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-patched-linux-x86_64, r-release-linux-x86_64