* using log directory ‘/data/gannet/ripley/R/packages/tests-devel/kergp.Rcheck’
* using R Under development (unstable) (2025-02-15 r87723)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3)
    GNU Fortran (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3)
* running under: Fedora Linux 40 (Workstation Edition)
* using session charset: UTF-8
* using option ‘--no-stop-on-test-error’
* checking for file ‘kergp/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘kergp’ version ‘0.5.8’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘kergp’ can be installed ... [25s/32s] OK
See 'https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-fedora-gcc/kergp-00install.html' for details.
* used C compiler: ‘gcc (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3)’
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [32s/40s] OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... OK
* checking compiled code ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking examples ... [31s/37s] ERROR
Running examples in ‘kergp-Ex.R’ failed
The error most likely occurred in:

> ### Name: gp
> ### Title: Gaussian Process Model
> ### Aliases: gp
> 
> ### ** Examples
> 
> ## ==================================================================
> ## Example 1. Data sampled from a GP model with a known covTS object
> ## ==================================================================
> set.seed(1234)
> myCov <- covTS(inputs = c("Temp", "Humid"),
+                kernel = "k1Matern5_2",
+                dep = c(range = "input"),
+                value = c(range = 0.4))
> ## change coefficients (variances)
> coef(myCov) <- c(0.5, 0.8, 2, 16)
> d <- myCov@d; n <- 20
> ## design matrix
> X <- matrix(runif(n*d), nrow = n, ncol = d)
> colnames(X) <- inputNames(myCov)
> ## generate the GP realization
> myGp <- gp(formula = y ~ 1, data = data.frame(y = rep(0, n), X), 
+             cov = myCov, estim = FALSE,
+             beta = 10, varNoise = 0.05)
> y <- simulate(myGp, cond = FALSE)$sim
Loading required package: MASS
> 
> ## parIni: add noise to true parameters
> parCovIni <- coef(myCov)
> parCovIni[] <- 0.9 * parCovIni[] +  0.1 * runif(length(parCovIni))
> coefLower(myCov) <- rep(1e-2, 4)
> coefUpper(myCov) <- c(5, 5, 20, 20)
> est <- gp(y ~ 1, data = data.frame(y = y, X),
+           cov = myCov, 
+           noise = TRUE,
+           varNoiseLower = 1e-2,
+           varNoiseIni = 1.0,
+           parCovIni = parCovIni) 
Warning in nloptr.add.default.options(opts.user = opts, x0 = x0, num_constraints_ineq = num_constraints_ineq,  :
  No termination criterion specified, using default(relative x-tolerance = 1e-04)
Error in fitList[[bestIndex]] : 
  attempt to select less than one element in get1index
Error in gp(y ~ 1, data = data.frame(y = y, X), cov = myCov, noise = TRUE,  : 
  Maximum Likelihood error
Execution halted
* checking PDF version of manual ... [14s/17s] OK
* checking HTML version of manual ... [10s/14s] OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 1 ERROR