- 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 the install log 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