Package check result: ERROR

Check: CRAN incoming feasibility, Result: NOTE
  Maintainer: ‘Yann Richet <yann.richet@irsn.fr>’
  
  New submission
  
  Package was archived on CRAN
  
  Possibly misspelled words in DESCRIPTION:
    Ciyou (47:5)
    Nocedal (47:36)
    Sanderson (45:90)
    Zhu (47:11)
  
  CRAN repository db overrides:
    X-CRAN-Comment: Archived on 2025-06-16 as issues were not corrected
      in time.

Check: tests, Result: ERROR
    Running ‘test-AllKrigingConcistency.R’ [2s/2s]
    Running ‘test-KrigingCopy.R’ [1s/1s]
    Running ‘test-KrigingFit.R’ [1s/1s]
    Running ‘test-KrigingLeaveOneOut.R’ [2s/2s]
    Running ‘test-KrigingLeaveOneOut_3d.R’ [1s/1s]
    Running ‘test-KrigingLogLik.R’ [2s/2s]
    Running ‘test-KrigingLogLikGradHess.R’ [5s/5s]
    Running ‘test-KrigingMethods.R’ [2s/2s]
    Running ‘test-KrigingPredict.R’ [8s/8s]
    Running ‘test-KrigingSimulate.R’ [1s/1s]
    Running ‘test-KrigingUpdate.R’ [1s/1s]
    Running ‘test-KrigingUpdateSimulate.R’ [2s/2s]
    Running ‘test-LinearAlgebra.R’ [1s/1s]
    Running ‘test-NoiseKrigingFit.R’ [1s/1s]
    Running ‘test-NoiseKrigingLogLik.R’ [2s/2s]
    Running ‘test-NoiseKrigingMethods.R’ [2s/2s]
    Running ‘test-NoiseKrigingPredict.R’ [6s/6s]
    Running ‘test-NoiseKrigingSimulate.R’ [3s/3s]
    Running ‘test-NoiseKrigingUpdate.R’ [1s/1s]
    Running ‘test-NoiseKrigingUpdateSimulate.R’ [2s/2s]
    Running ‘test-NuggetKrigingFit.R’ [1s/1s]
    Running ‘test-NuggetKrigingLogLik.R’ [3s/3s]
    Running ‘test-NuggetKrigingLogMargPost.R’ [5s/5s]
    Running ‘test-NuggetKrigingMethods.R’ [2s/2s]
    Running ‘test-NuggetKrigingPredict.R’ [5s/5s]
    Running ‘test-NuggetKrigingSimulate.R’ [1s/1s]
    Running ‘test-NuggetKrigingUpdate.R’ [1s/1s]
    Running ‘test-NuggetKrigingUpdateSimulate.R’ [2s/2s]
    Running ‘test-RobustGaSP-Nugget.R’ [0s/0s]
    Running ‘test-RobustGaSP.R’ [1s/1s]
    Running ‘test-RobustGaSPtrendlinear.R’ [1s/1s]
    Running ‘test-RobustGaSPvsKrigingLMP.R’ [1s/1s]
    Running ‘test-RobustGaSPvsNuggetKrigingLMP.R’ [0s/0s]
    Running ‘test-SaveLoad.R’ [1s/1s]
    Running ‘test-asDiceKriging.R’ [6s/6s]
    Running ‘test-estimnone.R’ [1s/1s]
    Running ‘test-normalize.R’ [2s/2s]
    Running ‘test-rlibkriging-demo.R’ [1s/1s]
    Running ‘test-unstableLL.R’ [1s/1s]
  Running the tests in ‘tests/test-KrigingFit.R’ failed.
  Complete output:
    > library(testthat)
    >  Sys.setenv('OMP_THREAD_LIMIT'=2)
    >  library(rlibkriging)
    
    Attaching package: 'rlibkriging'
    
    The following objects are masked from 'package:base':
    
        load, save
    
    > 
    > context("Fit: 1D")
    > 
    > f = function(x) 1-1/2*(sin(12*x)/(1+x)+2*cos(7*x)*x^5+0.7)
    > n <- 5
    > set.seed(123)
    > X <- as.matrix(runif(n))
    > y = f(X)
    > k = NULL
    > r = NULL
    > k = DiceKriging::km(design=X,response=y,covtype = "gauss",control = list(trace=F))
    > r <- Kriging(y, X, "gauss")
    > 
    > ll = Vectorize(function(x) logLikelihoodFun(r,x)$logLikelihood)
    > plot(ll,xlim=c(0.000001,10))
    >   for (x in seq(0.000001,10,,11)){
    +     envx = new.env()
    +     ll2x = logLikelihoodFun(r,x)$logLikelihood
    +     gll2x = logLikelihoodFun(r,x,return_grad = T)$logLikelihoodGrad
    +     arrows(x,ll2x,x+.1,ll2x+.1*gll2x,col='red')
    +   }
    > 
    > theta_ref = optimize(ll,interval=c(0.001,2),maximum=T)$maximum
    > abline(v=theta_ref,col='black')
    > abline(v=as.list(r)$theta,col='red')
    > abline(v=k@covariance@range.val,col='blue')
    > 
    > test_that(desc="Fit: 1D / fit of theta by DiceKriging is right",
    +           expect_equal(theta_ref, k@covariance@range.val, tol= 1e-3))
    Test passed 😸
    > 
    > test_that(desc="Fit: 1D / fit of theta by libKriging is right",
    +           expect_equal(array(theta_ref), array(as.list(r)$theta), tol= 0.01))
    Test passed 🥳
    > 
    > #############################################################
    > 
    > context("Fit: 2D (Branin)")
    > 
    > f = function(X) apply(X,1,DiceKriging::branin)
    > n <- 15
    > set.seed(1234)
    > X <- cbind(runif(n),runif(n))
    > y = f(X)
    > k = NULL
    > r = NULL
    > k = DiceKriging::km(design=X,response=y,covtype = "gauss",control = list(trace=F),parinit = c(.2,.5))
    > r <- Kriging(y, X, "gauss", parameters=list(theta=matrix(c(.2,.5),ncol=2)))
    > 
    > ll = function(X) {if (!is.matrix(X)) X = matrix(X,ncol=2);
    +                   # print(dim(X));
    +                   apply(X,1,
    +                     function(x) {
    +                       # print(dim(x))
    +                       #print(matrix(unlist(x),ncol=2));
    +                       y=-logLikelihoodFun(r,matrix(unlist(x),ncol=2))$logLikelihood
    +                       #print(y);
    +                       y})}
    > #DiceView::contourview(ll,xlim=c(0.01,2),ylim=c(0.01,2))
    > x=seq(0.01,2,,5)
    > contour(x,x,matrix(ll(as.matrix(expand.grid(x,x))),nrow=length(x)),nlevels = 30)
    > 
    > theta_ref = optim(par=matrix(c(.2,.5),ncol=2),ll,lower=c(0.01,0.01),upper=c(2,2),method="L-BFGS-B")$par
    > points(theta_ref,col='black')
    > points(as.list(r)$theta[1],as.list(r)$theta[2],col='red')
    > points(k@covariance@range.val[1],k@covariance@range.val[2],col='blue')
    > 
    > test_that(desc="Fit: 2D (Branin) / fit of theta 2D is _quite_ the same that DiceKriging one",
    +           expect_equal(ll(array(as.list(r)$theta)), ll(k@covariance@range.val), tol=1e-1))
    Test passed 😸
    > 
    > 
    > 
    > #############################################################
    > 
    > context("Fit: 2D (Branin) multistart")
    > 
    > f = function(X) apply(X,1,DiceKriging::branin)
    > n <- 15
    > set.seed(1234)
    > X <- cbind(runif(n),runif(n))
    > y = f(X)
    > k = NULL
    > r = NULL
    > 
    > parinit = matrix(runif(10*ncol(X)),ncol=ncol(X))
    > k <- tryCatch( # needed to catch warning due to %dopar% usage when using multistart
    +     withCallingHandlers(
    +       {
    +         error_text <- "No error."
    +         DiceKriging::km(design=X,response=y,covtype = "gauss",multistart = 10, parinit=parinit,control = list(trace=F))
    +       },
    +       warning = function(e) {
    +         error_text <<- trimws(paste0("WARNING: ", e))
    +         invokeRestart("muffleWarning")
    +       }
    +     ),
    +     error = function(e) {
    +       return(list(value = NA, error_text = trimws(paste0("ERROR: ", e))))
    +     },
    +     finally = {
    +     }
    +   )
    > r <- Kriging(y, X, "gauss", parameters=list(theta=parinit))
    > l = as.list(r)
    > 
    > # save(list=ls(),file="fit-2d-multistart.Rdata")
    > 
    > ll = function(X) {if (!is.matrix(X)) X = matrix(X,ncol=2);
    + # print(dim(X));
    + apply(X,1,
    +       function(x) {
    +         # print(dim(x))
    +         #print(matrix(unlist(x),ncol=2));
    +         y=-logLikelihoodFun(r,matrix(unlist(x),ncol=2))$logLikelihood
    +         #print(y);
    +         y})}
    > #DiceView::contourview(ll,xlim=c(0.01,2),ylim=c(0.01,2))
    > x=seq(0.01,2,,5)
    > contour(x,x,matrix(ll(as.matrix(expand.grid(x,x))),nrow=length(x)),nlevels = 30)
    > 
    > theta_ref = optim(par=matrix(c(.2,.5),ncol=2),ll,lower=c(0.01,0.01),upper=c(2,2),method="L-BFGS-B")$par
    > points(theta_ref,col='black')
    > points(as.list(r)$theta[1],as.list(r)$theta[2],col='red')
    > points(k@covariance@range.val[1],k@covariance@range.val[2],col='blue')
    Error in k@covariance : 
      no applicable method for `@` applied to an object of class "list"
    Calls: points
    Execution halted
  Running the tests in ‘tests/test-NoiseKrigingFit.R’ failed.
  Complete output:
    > library(testthat)
    >  Sys.setenv('OMP_THREAD_LIMIT'=2)
    >  library(rlibkriging)
    
    Attaching package: 'rlibkriging'
    
    The following objects are masked from 'package:base':
    
        load, save
    
    > 
    > ##library(rlibkriging, lib.loc="bindings/R/Rlibs")
    > ##library(testthat)
    > 
    > context("Fit: 1D")
    > 
    > f = function(x) 1-1/2*(sin(12*x)/(1+x)+2*cos(7*x)*x^5+0.7)
    > n <- 5
    > set.seed(123)
    > X <- as.matrix(runif(n))
    > y = f(X) + 0.1*rnorm(nrow(X))
    > k = NULL
    > r = NULL
    > k = DiceKriging::km(design=X,response=y,noise.var=rep(0.1^2,nrow(X)),covtype = "gauss",control = list(trace=F),nugget.estim=F,optim.method='BFGS',multistart = 20)
    Error in f(model, envir = envir.logLik) : Package "foreach" not found
    Calls: <Anonymous> -> f
    Execution halted
  Running the tests in ‘tests/test-NuggetKrigingFit.R’ failed.
  Complete output:
    > library(testthat)
    >  Sys.setenv('OMP_THREAD_LIMIT'=2)
    >  library(rlibkriging)
    
    Attaching package: 'rlibkriging'
    
    The following objects are masked from 'package:base':
    
        load, save
    
    > 
    > ##library(rlibkriging, lib.loc="bindings/R/Rlibs")
    > ##library(testthat)
    > 
    > context("Fit: 1D")
    > 
    > f = function(x) 1-1/2*(sin(12*x)/(1+x)+2*cos(7*x)*x^5+0.7)
    > n <- 5
    > set.seed(123)
    > X <- as.matrix(runif(n))
    > y = f(X)
    > k = NULL
    > r = NULL
    > k = DiceKriging::km(design=X,response=y,covtype = "gauss",control = list(trace=F),nugget.estim=T,optim.method='BFGS',multistart = 20)
    Error in f(model, envir = envir.logLik) : Package "foreach" not found
    Calls: <Anonymous> -> f
    Execution halted
  Running the tests in ‘tests/test-RobustGaSP-Nugget.R’ failed.
  Complete output:
    > library(testthat)
    >  Sys.setenv('OMP_THREAD_LIMIT'=2)
    >  library(rlibkriging)
    
    Attaching package: 'rlibkriging'
    
    The following objects are masked from 'package:base':
    
        load, save
    
    > 
    > ##library(rlibkriging, lib.loc="bindings/R/Rlibs")
    > ##library(testthat)
    > 
    > if(!requireNamespace('RobustGaSP', quietly = TRUE)) {
    +   skip('RobustGaSP not available')
    + }
    Error: Reason: RobustGaSP not available
    Execution halted
  Running the tests in ‘tests/test-RobustGaSP.R’ failed.
  Complete output:
    > library(testthat)
    >  Sys.setenv('OMP_THREAD_LIMIT'=2)
    >  library(rlibkriging)
    
    Attaching package: 'rlibkriging'
    
    The following objects are masked from 'package:base':
    
        load, save
    
    > 
    > ##library(rlibkriging, lib.loc="bindings/R/Rlibs")
    > ##library(testthat)
    > 
    > if(!requireNamespace('RobustGaSP', quietly = TRUE)) {
    +   skip('RobustGaSP not available')
    + }
    Error: Reason: RobustGaSP not available
    Execution halted
  Running the tests in ‘tests/test-RobustGaSPtrendlinear.R’ failed.
  Complete output:
    > library(testthat)
    >  Sys.setenv('OMP_THREAD_LIMIT'=2)
    >  library(rlibkriging)
    
    Attaching package: 'rlibkriging'
    
    The following objects are masked from 'package:base':
    
        load, save
    
    > 
    > ##library(testthat)
    >  Sys.setenv('OMP_THREAD_LIMIT'=2)
    > #library(rlibkriging)
    > 
    > if(!requireNamespace('RobustGaSP', quietly = TRUE)) {
    +   skip('RobustGaSP not available')
    + }
    Error: Reason: RobustGaSP not available
    Execution halted
  Running the tests in ‘tests/test-RobustGaSPvsKrigingLMP.R’ failed.
  Complete output:
    > library(testthat)
    >  Sys.setenv('OMP_THREAD_LIMIT'=2)
    >  library(rlibkriging)
    
    Attaching package: 'rlibkriging'
    
    The following objects are masked from 'package:base':
    
        load, save
    
    > 
    > kernel_type = function(kernel) {
    +   if (kernel=="matern3_2") return("matern_3_2")
    +   if (kernel=="matern5_2") return("matern_5_2")
    +   stop(paste0("Cannot use ",kernel))
    + }
    > kernel_type_num = function(kernel) {
    +   if (kernel=="matern3_2") return(2)
    +   if (kernel=="matern5_2") return(3)
    +   stop(paste0("Cannot use ",kernel))
    + }
    > 
    > for (kernel in c("matern5_2","matern3_2")) {
    +   context(paste0("Check Marginal Posterior for kernel ",kernel))
    +   
    +   f = function(x) 1-1/2*(sin(12*x)/(1+x)+2*cos(7*x)*x^5+0.7)
    +   plot(f)
    +   n <- 5
    +   set.seed(123)
    +   X <- as.matrix(runif(n))
    +   y = f(X)
    +   points(X,y)
    + 
    +   k = RobustGaSP::rgasp(design=X,response=y,kernel_type=kernel_type(kernel))
    + 
    +   lmp = function(theta) {
    +     #cat("theta: ",theta,"\n")
    +     lml = RobustGaSP::log_marginal_lik(param=log(1/theta),nugget=k@nugget,nugget_est=k@nugget.est,
    +       R0=k@R0,X=k@X,zero_mean=k@zero_mean,output=k@output,kernel_type=kernel_type_num(kernel),alpha=k@alpha)
    +     #cat("  lml: ",lml,"\n")
    +     larp = RobustGaSP::log_approx_ref_prior(param=log(1/theta),nugget=k@nugget,nugget_est=k@nugget.est,
    +       CL=k@CL,a=0.2,b=1/(length(y))^{1/dim(as.matrix(X))[2]}*(0.2+dim(as.matrix(X))[2]))
    +     #cat("  larp: ",larp,"\n")
    +     return(lml+larp)
    +   }
    + 
    +   plot(Vectorize(lmp),ylab="LMP",xlab="theta",xlim=c(0.01,2),ylim=c(-5,5))
    +   abline(v=1/k@beta_hat)
    + 
    +   lmp_deriv = function(theta) {
    +     #cat("theta: ",theta,"\n")
    +     lml_d = RobustGaSP::log_marginal_lik_deriv(param=log(1/theta),nugget=k@nugget,nugget_est=k@nugget.est,
    +       R0=k@R0,X=k@X,zero_mean=k@zero_mean,output=k@output,kernel_type=kernel_type_num(kernel),alpha=k@alpha)
    +     #cat("  lml_d: ",lml_d,"\n")
    +     larp_d = RobustGaSP::log_approx_ref_prior_deriv(param=log(1/theta),nugget=k@nugget,nugget_est=k@nugget.est,
    +       CL=k@CL,a=0.2,b=1/(length(y))^{1/dim(as.matrix(X))[2]}*(0.2+dim(as.matrix(X))[2]))
    +     #cat("  larp_d: ",larp_d,"\n")
    +     return((lml_d + larp_d)* 1/theta * (-1/theta))
    +   }
    + 
    +   for (x in seq(0.01,2,,11)){
    +     arrows(x,lmp(x),x+.1,lmp(x)+.1*lmp_deriv(x))
    +   }
    + 
    +   #library(rlibkriging)
    +   r <- Kriging(y, X, kernel, objective="LMP")
    +   ## Should be equal:
    +   #lmp(1.0); lmp_deriv(1.0);
    +   #logMargPostFun(r,1.0,return_grad = T)
    +   #lmp(0.1); lmp_deriv(0.1);
    +   #logMargPostFun(r,0.1,return_grad = T)
    +   #ll2 = function(theta) logMargPostFun(r,theta)$logMargPost
    +   # plot(Vectorize(ll2),col='red',add=T,xlim=c(0.01,2)) # FIXME fails with "error: chol(): decomposition failed"
    +   for (x in seq(0.01,2,,11)){
    +     ll2x = logMargPostFun(r,x)$logMargPost
    +     gll2x = logMargPostFun(r,x,return_grad = T)$logMargPostGrad
    +     arrows(x,ll2x,x+.1,ll2x+.1*gll2x,col='red')
    +   }
    +   
    +   precision <- 1e-8  # the following tests should work with it, since the computations are analytical
    +   x=.5
    +   test_that(desc="logMargPost is the same that RobustGaSP one", 
    +             expect_equal(logMargPostFun(r,x)$logMargPost[1],lmp(x),tolerance = precision))
    +   
    +   test_that(desc="logMargPost Grad is the same that RobustGaSP one", 
    +             expect_equal(logMargPostFun(r,x,return_grad = T)$logMargPostGrad[1],lmp_deriv(x),tolerance= precision))
    + }
    Error in loadNamespace(x) : there is no package called 'RobustGaSP'
    Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
    Execution halted
  Running the tests in ‘tests/test-RobustGaSPvsNuggetKrigingLMP.R’ failed.
  Complete output:
    > library(testthat)
    >  Sys.setenv('OMP_THREAD_LIMIT'=2)
    >  library(rlibkriging)
    
    Attaching package: 'rlibkriging'
    
    The following objects are masked from 'package:base':
    
        load, save
    
    > 
    > if(!requireNamespace('RobustGaSP', quietly = TRUE)) {
    +   skip('RobustGaSP not available')
    + }
    Error: Reason: RobustGaSP not available
    Execution halted