* using log directory ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/DiceOptim.Rcheck’
* using R Under development (unstable) (2025-02-23 r87804)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 19.1.7 (1+b1)
    Debian flang-new version 19.1.7 (1+b1)
* running under: Debian GNU/Linux trixie/sid
* using session charset: UTF-8
* 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 serialization versions ... OK
* checking whether package ‘DiceOptim’ can be installed ... OK
See 'https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-debian-clang/DiceOptim-00install.html' for details.
* used C compiler: ‘Debian clang version 19.1.7 (1+b1)’
* checking package directory ... OK
* checking for future file timestamps ... 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 ... [0s/0s] OK
* checking whether the package can be loaded with stated dependencies ... [0s/1s] OK
* checking whether the package can be unloaded cleanly ... [0s/1s] OK
* checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the namespace can be unloaded cleanly ... [0s/1s] OK
* checking loading without being on the library search path ... [0s/1s] 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 ... [23s/30s] OK
* checking Rd files ... [1s/1s] 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 ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  max_qEI.Rd: genoud
  qEGO.nsteps.Rd: genoud
  sampleFromEI.Rd: km
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 ... [23s/30s] OK
Examples with CPU (user + system) or elapsed time > 5s
             user system elapsed
qEGO.nsteps 4.787  0.007   5.721
* checking PDF version of manual ... [9s/12s] OK
* checking HTML version of manual ... [4s/5s] OK
* checking for non-standard things in the check directory ... OK
* DONE
Status: 2 NOTEs