* using log directory ‘/data/gannet/ripley/R/packages/tests-devel/DiceOptim.Rcheck’ * using R Under development (unstable) (2024-04-05 r86344) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc-13 (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Fedora Linux 36 (Workstation Edition) * using session charset: UTF-8 * using option ‘--no-stop-on-test-error’ * checking for file ‘DiceOptim/DESCRIPTION’ ... OK * this is package ‘DiceOptim’ version ‘2.1.1’ * package encoding: UTF-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 ‘DiceOptim’ can be installed ... [16s/19s] OK See 'https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-fedora-gcc/DiceOptim-00install.html' for details. * used C compiler: ‘gcc-13 (GCC) 13.2.0’ * 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 ... [33s/42s] OK * checking Rd files ... NOTE checkRd: (-1) EGO.cst.Rd:71: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) EGO.cst.Rd:72: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) EGO.cst.Rd:73: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) EGO.cst.Rd:74: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) EGO.cst.Rd:75: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) EGO.cst.Rd:76: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) EGO.cst.Rd:77: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) crit_AL.Rd:28: Lost braces in \itemize; meant \describe ? checkRd: (-1) crit_AL.Rd:29: Lost braces in \itemize; meant \describe ? checkRd: (-1) crit_AL.Rd:30: Lost braces in \itemize; meant \describe ? checkRd: (-1) crit_AL.Rd:31: Lost braces in \itemize; meant \describe ? checkRd: (-1) crit_AL.Rd:32: Lost braces in \itemize; meant \describe ? checkRd: (-1) crit_AL.Rd:33: Lost braces in \itemize; meant \describe ? checkRd: (-1) critcst_optimizer.Rd:48: Lost braces in \itemize; meant \describe ? checkRd: (-1) critcst_optimizer.Rd:49: Lost braces in \itemize; meant \describe ? checkRd: (-1) easyEGO.Rd:60: Lost braces 60 | \item \code{trace}{: between -1 and 3} | ^ checkRd: (-1) easyEGO.Rd:61: Lost braces 61 | \item \code{seed}{: to fix the seed of the run} | ^ checkRd: (-1) easyEGO.Rd:62: Lost braces 62 | \item \code{cov.reestim}{: Boolean, if TRUE (default) the covariance parameters are re-estimated at each iteration} | ^ checkRd: (-1) easyEGO.Rd:63: Lost braces 63 | \item \code{model.trend}{: trend for the GP model} | ^ checkRd: (-1) easyEGO.Rd:64: Lost braces 64 | \item \code{lb, ub}{: lower and upper bounds for the GP covariance ranges} | ^ checkRd: (-1) easyEGO.Rd:65: Lost braces 65 | \item \code{nugget}{: optional nugget effect} | ^ checkRd: (-1) easyEGO.Rd:66: Lost braces 66 | \item \code{covtype}{: covariance of the GP model (default "matern5_2")} | ^ checkRd: (-1) easyEGO.Rd:67: Lost braces 67 | \item \code{optim.method}{: optimisation of the GP hyperparameters (default "BFGS")} | ^ checkRd: (-1) easyEGO.Rd:68: Lost braces 68 | \item \code{multistart}{: number of restarts of BFGS} | ^ checkRd: (-1) easyEGO.Rd:69: Lost braces 69 | \item \code{gpmean.trick, gpmean.freq}{: Boolean and integer, resp., for the gpmean trick} | ^ checkRd: (-1) easyEGO.Rd:70: Lost braces 70 | \item \code{scaling}{: Boolean, activates input scaling} | ^ checkRd: (-1) easyEGO.Rd:71: Lost braces 71 | \item \code{warping}{: Boolean, activates output warping} | ^ checkRd: (-1) easyEGO.Rd:72: Lost braces 72 | \item \code{TR}{: Boolean, activates TREGO instead of EGO} | ^ checkRd: (-1) easyEGO.Rd:73: Lost braces 73 | \item \code{trcontrol}{: list of parameters of the trust region, see \code{\link[DiceOptim]{TREGO.nsteps}}} | ^ checkRd: (-1) easyEGO.Rd:74: Lost braces 74 | \item \code{always.sample}{: Boolean, activates force observation even if it leads to poor conditioning} | ^ checkRd: (-1) easyEGO.Rd:43: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) easyEGO.Rd:44: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) easyEGO.Rd:45: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) easyEGO.Rd:46: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) easyEGO.Rd:47: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) easyEGO.Rd:48: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) easyEGO.cst.Rd:74-75: Lost braces 74 | \item \code{method}{: choice of constrained improvement function: "\code{AL}", "\code{EFI}" or "\code{SUR}" | ^ checkRd: (-1) easyEGO.cst.Rd:76: Lost braces 76 | \item \code{trace}{: if positive, tracing information on the progress of the optimization is produced.} | ^ checkRd: (-1) easyEGO.cst.Rd:77-78: Lost braces 77 | \item \code{inneroptim}{: choice of the inner optimization algorithm: "\code{genoud}" or "\code{random}" | ^ checkRd: (-1) easyEGO.cst.Rd:79: Lost braces 79 | \item \code{maxit}{: maximum number of iterations of the inner loop. } | ^ checkRd: (-1) easyEGO.cst.Rd:80: Lost braces 80 | \item \code{seed}{: to fix the random variable generator} | ^ checkRd: (-1) easyEGO.cst.Rd:54: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) easyEGO.cst.Rd:55: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) easyEGO.cst.Rd:56-57: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) integration_design_cst.Rd:61: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) integration_design_cst.Rd:62-63: Lost braces in \itemize; \value handles \item{}{} directly * 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 pragmas in C/C++ headers and code ... OK * checking compilation flags used ... OK * checking compiled code ... OK * checking examples ... [34s/43s] OK * checking PDF version of manual ... [14s/21s] OK * checking HTML version of manual ... OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 1 NOTE