CRAN Package Check Results for Package PresenceAbsence

Last updated on 2020-08-07 01:49:55 CEST.

Check Details

Version: 1.1.9
Check: DESCRIPTION meta-information
Result: NOTE
    Malformed Title field: should not end in a period.
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-macos-x86_64, r-release-windows-ix86+x86_64, r-oldrel-macos-x86_64, r-oldrel-windows-ix86+x86_64

Version: 1.1.9
Check: top-level files
Result: NOTE
    Non-standard file/directory found at top level:
     'COPYRIGHTS'
    Copyright information should be in file inst/COPYRIGHTS
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: 1.1.9
Check: R code for possible problems
Result: NOTE
    auc: no visible global function definition for 'var'
    auc.roc.plot: no visible global function definition for 'par'
    auc.roc.plot: no visible global function definition for 'lines'
    auc.roc.plot: no visible global function definition for 'abline'
    auc.roc.plot: no visible global function definition for 'points'
    auc.roc.plot: no visible global function definition for 'text'
    auc.roc.plot: no visible global function definition for 'legend'
    calibration.plot: no visible global function definition for 'qf'
    calibration.plot: no visible global function definition for 'par'
    calibration.plot: no visible global function definition for 'abline'
    calibration.plot: no visible global function definition for 'lines'
    calibration.plot: no visible global function definition for 'points'
    calibration.plot: no visible global function definition for 'text'
    error.threshold.plot: no visible global function definition for 'par'
    error.threshold.plot: no visible global function definition for 'lines'
    error.threshold.plot: no visible global function definition for
     'abline'
    error.threshold.plot: no visible global function definition for
     'points'
    error.threshold.plot: no visible global function definition for
     'legend'
    presence.absence.hist: no visible global function definition for 'hist'
    presence.absence.hist: no visible global function definition for
     'barplot'
    presence.absence.hist: no visible global function definition for 'par'
    presence.absence.hist: no visible global function definition for 'text'
    presence.absence.hist: no visible global function definition for
     'legend'
    presence.absence.hist: no visible global function definition for
     'abline'
    presence.absence.hist: no visible global function definition for
     'points'
    presence.absence.simulation: no visible global function definition for
     'rbinom'
    presence.absence.simulation: no visible global function definition for
     'rbeta'
    presence.absence.summary: no visible global function definition for
     'par'
    presence.absence.summary: no visible global function definition for
     'mtext'
    Undefined global functions or variables:
     abline barplot hist legend lines mtext par points qf rbeta rbinom
     text var
    Consider adding
     importFrom("graphics", "abline", "barplot", "hist", "legend", "lines",
     "mtext", "par", "points", "text")
     importFrom("stats", "qf", "rbeta", "rbinom", "var")
    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-macos-x86_64, r-release-windows-ix86+x86_64

Version: 1.1.9
Check: Rd line widths
Result: NOTE
    Rd file 'auc.roc.plot.Rd':
     \usage lines wider than 90 characters:
     auc.roc.plot(DATA, threshold = 101, find.auc = TRUE, which.model = (1:(ncol(DATA) - 2)), na.rm = FALSE, xlab = "1-Specificity (false po ... [TRUNCATED]
    
    Rd file 'calibration.plot.Rd':
     \usage lines wider than 90 characters:
     calibration.plot(DATA, which.model = 1, na.rm = FALSE, alpha = 0.05, N.bins = 5, xlab = "Predicted Probability of Occurrence", ylab = " ... [TRUNCATED]
    
    Rd file 'cmx.Rd':
     \examples lines wider than 100 characters:
     SIMDATA$Predicted[SIMDATA$Observed==1]<-rnorm(n=length(SIMDATA$Observed[SIMDATA$Observed==1]),mean=.8,sd=.15)
     SIMDATA$Predicted[SIMDATA$Observed==0]<-rnorm(n=length(SIMDATA$Observed[SIMDATA$Observed==0]),mean=.2,sd=.15)
     SIMDATA$Predicted<-(SIMDATA$Predicted-min(SIMDATA$Predicted))/(max(SIMDATA$Predicted)-min(SIMDATA$Predicted))
    
    Rd file 'error.threshold.plot.Rd':
     \usage lines wider than 90 characters:
     error.threshold.plot(DATA, threshold = 101, which.model = 1, na.rm = FALSE, xlab = "Threshold", ylab = "Accuracy Measures", main = NULL ... [TRUNCATED]
     \examples lines wider than 100 characters:
     opt.methods=c("Default", "Sens=Spec", "MinROCdist"), vert.lines=TRUE ... [TRUNCATED]
    
    Rd file 'optimal.thresholds.Rd':
     \usage lines wider than 90 characters:
     optimal.thresholds(DATA = NULL, threshold = 101, which.model = 1:(ncol(DATA)-2), model.names = NULL, na.rm = FALSE, opt.methods = NULL, ... [TRUNCATED]
    
    Rd file 'presence.absence.accuracy.Rd':
     \usage lines wider than 90 characters:
     presence.absence.accuracy(DATA, threshold = 0.5, find.auc = TRUE, st.dev = TRUE, which.model = (1:(ncol(DATA) - 2)), na.rm = FALSE)
    
    Rd file 'presence.absence.hist.Rd':
     \usage lines wider than 90 characters:
     presence.absence.hist(DATA, which.model = 1, na.rm = FALSE, xlab = "predicted probability", ylab = "number of plots", main = NULL, mode ... [TRUNCATED]
    
    Rd file 'presence.absence.simulation.Rd':
     \usage lines wider than 90 characters:
     presence.absence.simulation(n, prevalence, N.models = 1, shape1.absent, shape2.absent, shape1.present, shape2.present)
    
    Rd file 'presence.absence.summary.Rd':
     \usage lines wider than 90 characters:
     presence.absence.summary(DATA, threshold = 101, find.auc = TRUE, which.model = 1, na.rm = FALSE, main = NULL, model.names = NULL, alpha ... [TRUNCATED]
    
    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: 1.1.9
Check: R code for possible problems
Result: NOTE
    auc: no visible global function definition for ‘var’
    auc.roc.plot: no visible global function definition for ‘par’
    auc.roc.plot: no visible global function definition for ‘plot’
    auc.roc.plot: no visible global function definition for ‘lines’
    auc.roc.plot: no visible global function definition for ‘abline’
    auc.roc.plot: no visible global function definition for ‘points’
    auc.roc.plot: no visible global function definition for ‘text’
    auc.roc.plot: no visible global function definition for ‘legend’
    calibration.plot: no visible global function definition for ‘qf’
    calibration.plot: no visible global function definition for ‘par’
    calibration.plot: no visible global function definition for ‘plot’
    calibration.plot: no visible global function definition for ‘abline’
    calibration.plot: no visible global function definition for ‘lines’
    calibration.plot: no visible global function definition for ‘points’
    calibration.plot: no visible global function definition for ‘text’
    error.threshold.plot: no visible global function definition for ‘par’
    error.threshold.plot: no visible global function definition for ‘plot’
    error.threshold.plot: no visible global function definition for ‘lines’
    error.threshold.plot: no visible global function definition for
     ‘abline’
    error.threshold.plot: no visible global function definition for
     ‘points’
    error.threshold.plot: no visible global function definition for
     ‘legend’
    presence.absence.hist: no visible global function definition for ‘hist’
    presence.absence.hist: no visible global function definition for
     ‘barplot’
    presence.absence.hist: no visible global function definition for ‘par’
    presence.absence.hist: no visible global function definition for ‘text’
    presence.absence.hist: no visible global function definition for ‘plot’
    presence.absence.hist: no visible global function definition for
     ‘legend’
    presence.absence.hist: no visible global function definition for
     ‘abline’
    presence.absence.hist: no visible global function definition for
     ‘points’
    presence.absence.simulation: no visible global function definition for
     ‘rbinom’
    presence.absence.simulation: no visible global function definition for
     ‘rbeta’
    presence.absence.summary: no visible global function definition for
     ‘par’
    presence.absence.summary: no visible global function definition for
     ‘mtext’
    Undefined global functions or variables:
     abline barplot hist legend lines mtext par plot points qf rbeta
     rbinom text var
    Consider adding
     importFrom("graphics", "abline", "barplot", "hist", "legend", "lines",
     "mtext", "par", "plot", "points", "text")
     importFrom("stats", "qf", "rbeta", "rbinom", "var")
    to your NAMESPACE file.
Flavors: r-oldrel-macos-x86_64, r-oldrel-windows-ix86+x86_64