Package: CalibrationCurves
Check: examples
New result: ERROR
  Running examples in ‘CalibrationCurves-Ex.R’ failed
  The error most likely occurred in:
  
  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: val.prob.ci.2
  > ### Title: Calibration performance
  > ### Aliases: val.prob.ci.2
  > 
  > ### ** Examples
  > 
  > 
  > # Load package
  > library(CalibrationCurves)
  > set.seed(1783)
  > 
  > # Simulate training data
  > X      = replicate(4, rnorm(5e2))
  > p0true = binomial()$linkinv(cbind(1, X) %*% c(0.1, 0.5, 1.2, -0.75, 0.8))
  > y      = rbinom(5e2, 1, p0true)
  > Df     = data.frame(y, X)
  > 
  > # Fit logistic model
  > FitLog = lrm(y ~ ., Df)
  > 
  > # Simulate validation data
  > Xval   = replicate(4, rnorm(5e2))
  > p0true = binomial()$linkinv(cbind(1, Xval) %*% c(0.1, 0.5, 1.2, -0.75, 0.8))
  > yval   = rbinom(5e2, 1, p0true)
  > Pred   = binomial()$linkinv(cbind(1, Xval) %*% coef(FitLog))
  > 
  > # Default calibration plot
  > val.prob.ci.2(Pred, yval)
  Error in h(simpleError(msg, call)) : 
    error in evaluating the argument 'x' in selecting a method for function 'as.matrix': error in evaluating the argument 'x' in selecting a method for function 'as.matrix': 'a' must be a numeric matrix
  Calls: val.prob.ci.2 ... solve.default -> .handleSimpleError -> h -> .handleSimpleError -> h
  Execution halted

Package: CalibrationCurves
Check: re-building of vignette outputs
New result: ERROR
  Error(s) in re-building vignettes:
    ...
  --- re-building ‘CalibrationCurves.Rmd’ using rmarkdown
  
  Quitting from lines 177-178 [unnamed-chunk-6] (CalibrationCurves.Rmd)
  Error: processing vignette 'CalibrationCurves.Rmd' failed with diagnostics:
  error in evaluating the argument 'x' in selecting a method for function 'as.matrix': error in evaluating the argument 'x' in selecting a method for function 'as.matrix': 'a' must be a numeric matrix
  --- failed re-building ‘CalibrationCurves.Rmd’
  
  SUMMARY: processing the following file failed:
    ‘CalibrationCurves.Rmd’
  
  Error: Vignette re-building failed.
  Execution halted

Package: PResiduals
Check: examples
New result: ERROR
  Running examples in ‘PResiduals-Ex.R’ failed
  The error most likely occurred in:
  
  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: conditional_Spearman
  > ### Title: Conditional Partial Spearman's Rank Correlation
  > ### Aliases: conditional_Spearman
  > 
  > ### ** Examples
  > 
  > data(PResidData)
  > library(rms)
  Loading required package: Hmisc
  
  Attaching package: ‘Hmisc’
  
  The following objects are masked from ‘package:base’:
  
      format.pval, units
  
  > #### fitting cumulative link models for both Y and W
  > result <- conditional_Spearman(c|y~ x + w, conditional.by="w",
  +                                        conditional.method="lm", conditional.formula="~rcs(w)",
  +                                        fit.x="poisson",fit.y="orm",
  +                                        data=PResidData, fisher=TRUE)
  Error in eval(substitute(family)) : object 'link' not found
  Calls: conditional_Spearman -> orm.scores -> orm -> eval -> eval
  Execution halted

Package: rankCorr
Check: examples
New result: ERROR
  Running examples in ‘rankCorr-Ex.R’ failed
  The error most likely occurred in:
  
  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: rankCorrCluster
  > ### Title: Total, between-, and within-cluster Spearman rank correlations
  > ###   for clustered data
  > ### Aliases: rankCorrCluster
  > 
  > ### ** Examples
  > 
  > library(mvtnorm)
  > k <- 50; m <- 5
  > sigma.u <- matrix(c(1, 0.6, 0.6, 4), ncol=2); sigma.e <- matrix(c(1, 0.6, 0.6, 1), ncol=2)
  > u <- rmvnorm(k, c(1, -1), sigma.u)
  > x1 <- matrix(NA, k, m)
  > y1 <- matrix(NA, k, m)
  > for (i in 1:k){
  + r <- rmvnorm(m, c(0, 0), sigma.e)
  + x1[i,] <- u[i, 1] + r[, 1]
  + y1[i,] <- u[i, 2] + r[, 2]
  + }
  > x <- as.vector(t(x1))
  > y <- as.vector(t(y1))
  > cluster <- rep(1:k, each=m)
  > rankCorrCluster(x, y, cluster, link.x = "probit", link.y = "probit",
  + methods_between_corr = "approx")
  Error in eval(substitute(family)) : object 'lnk' not found
  Calls: rankCorrCluster -> scores_presid -> orm -> eval -> eval
  Execution halted