* using log directory ‘/data/gannet/ripley/R/packages/tests-clang/Phase12Compare.Rcheck’ * using R Under development (unstable) (2024-04-24 r86484) * using platform: x86_64-pc-linux-gnu * R was compiled by clang version 18.1.4 flang-new version 18.1.4 * running under: Fedora Linux 36 (Workstation Edition) * using session charset: UTF-8 * using option ‘--no-stop-on-test-error’ * checking for file ‘Phase12Compare/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘Phase12Compare’ version ‘1.5’ * 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 ‘Phase12Compare’ can be installed ... [69s/76s] OK See 'https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-fedora-clang/Phase12Compare-00install.html' for details. * used C++ compiler: ‘clang version 18.1.4’ * checking installed package size ... OK * 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 ... [12s/16s] OK * checking Rd files ... NOTE checkRd: (-1) GetEfftoxContour.Rd:37: Lost braces; missing escapes or markup? 37 | \item{Contour}{Contour vector for desirability function. Contains in order: (pi_{1,E},pi_{2,T},pi_{3,E},pi_{4,T}).} | ^ checkRd: (-1) GetEfftoxContour.Rd:37: Lost braces; missing escapes or markup? 37 | \item{Contour}{Contour vector for desirability function. Contains in order: (pi_{1,E},pi_{2,T},pi_{3,E},pi_{4,T}).} | ^ checkRd: (-1) GetEfftoxContour.Rd:37: Lost braces; missing escapes or markup? 37 | \item{Contour}{Contour vector for desirability function. Contains in order: (pi_{1,E},pi_{2,T},pi_{3,E},pi_{4,T}).} | ^ checkRd: (-1) GetEfftoxContour.Rd:37: Lost braces; missing escapes or markup? 37 | \item{Contour}{Contour vector for desirability function. Contains in order: (pi_{1,E},pi_{2,T},pi_{3,E},pi_{4,T}).} | ^ checkRd: (-1) GetEfftoxContour.Rd:47: Lost braces; missing escapes or markup? 47 | \item{HypermeansEFF}{Hypermeans for the Efftox model. In order, entries are hypermeans for (beta_{0,E},beta_{1,E},beta_{2,E},beta_{0,T},beta_{1,T},psi).} | ^ checkRd: (-1) GetEfftoxContour.Rd:47: Lost braces; missing escapes or markup? 47 | \item{HypermeansEFF}{Hypermeans for the Efftox model. In order, entries are hypermeans for (beta_{0,E},beta_{1,E},beta_{2,E},beta_{0,T},beta_{1,T},psi).} | ^ checkRd: (-1) GetEfftoxContour.Rd:47: Lost braces; missing escapes or markup? 47 | \item{HypermeansEFF}{Hypermeans for the Efftox model. In order, entries are hypermeans for (beta_{0,E},beta_{1,E},beta_{2,E},beta_{0,T},beta_{1,T},psi).} | ^ checkRd: (-1) GetEfftoxContour.Rd:47: Lost braces; missing escapes or markup? 47 | \item{HypermeansEFF}{Hypermeans for the Efftox model. In order, entries are hypermeans for (beta_{0,E},beta_{1,E},beta_{2,E},beta_{0,T},beta_{1,T},psi).} | ^ checkRd: (-1) GetEfftoxContour.Rd:47: Lost braces; missing escapes or markup? 47 | \item{HypermeansEFF}{Hypermeans for the Efftox model. In order, entries are hypermeans for (beta_{0,E},beta_{1,E},beta_{2,E},beta_{0,T},beta_{1,T},psi).} | ^ checkRd: (-1) GetEfftoxContour.Rd:49: Lost braces; missing escapes or markup? 49 | \item{HypervarsEFF}{Hypervariances for the Efftox model. In order, entries are hypervariances for (beta_{0,E},beta_{1,E},beta_{2,E},beta_{0,T},beta_{1,T},psi).} | ^ checkRd: (-1) GetEfftoxContour.Rd:49: Lost braces; missing escapes or markup? 49 | \item{HypervarsEFF}{Hypervariances for the Efftox model. In order, entries are hypervariances for (beta_{0,E},beta_{1,E},beta_{2,E},beta_{0,T},beta_{1,T},psi).} | ^ checkRd: (-1) GetEfftoxContour.Rd:49: Lost braces; missing escapes or markup? 49 | \item{HypervarsEFF}{Hypervariances for the Efftox model. In order, entries are hypervariances for (beta_{0,E},beta_{1,E},beta_{2,E},beta_{0,T},beta_{1,T},psi).} | ^ checkRd: (-1) GetEfftoxContour.Rd:49: Lost braces; missing escapes or markup? 49 | \item{HypervarsEFF}{Hypervariances for the Efftox model. In order, entries are hypervariances for (beta_{0,E},beta_{1,E},beta_{2,E},beta_{0,T},beta_{1,T},psi).} | ^ checkRd: (-1) GetEfftoxContour.Rd:49: Lost braces; missing escapes or markup? 49 | \item{HypervarsEFF}{Hypervariances for the Efftox model. In order, entries are hypervariances for (beta_{0,E},beta_{1,E},beta_{2,E},beta_{0,T},beta_{1,T},psi).} | ^ checkRd: (-1) GetEfftoxUt.Rd:47: Lost braces; missing escapes or markup? 47 | \item{HypermeansEFF}{Hypermeans for the Efftox model. In order, entries are hypermeans for (beta_{0,E},beta_{1,E},beta_{2,E},beta_{0,T},beta_{1,T},psi).} | ^ checkRd: (-1) GetEfftoxUt.Rd:47: Lost braces; missing escapes or markup? 47 | \item{HypermeansEFF}{Hypermeans for the Efftox model. In order, entries are hypermeans for (beta_{0,E},beta_{1,E},beta_{2,E},beta_{0,T},beta_{1,T},psi).} | ^ checkRd: (-1) GetEfftoxUt.Rd:47: Lost braces; missing escapes or markup? 47 | \item{HypermeansEFF}{Hypermeans for the Efftox model. In order, entries are hypermeans for (beta_{0,E},beta_{1,E},beta_{2,E},beta_{0,T},beta_{1,T},psi).} | ^ checkRd: (-1) GetEfftoxUt.Rd:47: Lost braces; missing escapes or markup? 47 | \item{HypermeansEFF}{Hypermeans for the Efftox model. In order, entries are hypermeans for (beta_{0,E},beta_{1,E},beta_{2,E},beta_{0,T},beta_{1,T},psi).} | ^ checkRd: (-1) GetEfftoxUt.Rd:47: Lost braces; missing escapes or markup? 47 | \item{HypermeansEFF}{Hypermeans for the Efftox model. In order, entries are hypermeans for (beta_{0,E},beta_{1,E},beta_{2,E},beta_{0,T},beta_{1,T},psi).} | ^ checkRd: (-1) GetEfftoxUt.Rd:49: Lost braces; missing escapes or markup? 49 | \item{HypervarsEFF}{Hypervariances for the Efftox model. In order, entries are hypervariances for (beta_{0,E},beta_{1,E},beta_{2,E},beta_{0,T},beta_{1,T},psi).} | ^ checkRd: (-1) GetEfftoxUt.Rd:49: Lost braces; missing escapes or markup? 49 | \item{HypervarsEFF}{Hypervariances for the Efftox model. In order, entries are hypervariances for (beta_{0,E},beta_{1,E},beta_{2,E},beta_{0,T},beta_{1,T},psi).} | ^ checkRd: (-1) GetEfftoxUt.Rd:49: Lost braces; missing escapes or markup? 49 | \item{HypervarsEFF}{Hypervariances for the Efftox model. In order, entries are hypervariances for (beta_{0,E},beta_{1,E},beta_{2,E},beta_{0,T},beta_{1,T},psi).} | ^ checkRd: (-1) GetEfftoxUt.Rd:49: Lost braces; missing escapes or markup? 49 | \item{HypervarsEFF}{Hypervariances for the Efftox model. In order, entries are hypervariances for (beta_{0,E},beta_{1,E},beta_{2,E},beta_{0,T},beta_{1,T},psi).} | ^ checkRd: (-1) GetEfftoxUt.Rd:49: Lost braces; missing escapes or markup? 49 | \item{HypervarsEFF}{Hypervariances for the Efftox model. In order, entries are hypervariances for (beta_{0,E},beta_{1,E},beta_{2,E},beta_{0,T},beta_{1,T},psi).} | ^ checkRd: (-1) GetSpsoContour.Rd:35: Lost braces; missing escapes or markup? 35 | \item{Contour}{Contour vector for desirability function. Contains in order: (pi_{1,E},pi_{2,T},pi_{3,E},pi_{4,T}).} | ^ checkRd: (-1) GetSpsoContour.Rd:35: Lost braces; missing escapes or markup? 35 | \item{Contour}{Contour vector for desirability function. Contains in order: (pi_{1,E},pi_{2,T},pi_{3,E},pi_{4,T}).} | ^ checkRd: (-1) GetSpsoContour.Rd:35: Lost braces; missing escapes or markup? 35 | \item{Contour}{Contour vector for desirability function. Contains in order: (pi_{1,E},pi_{2,T},pi_{3,E},pi_{4,T}).} | ^ checkRd: (-1) GetSpsoContour.Rd:35: Lost braces; missing escapes or markup? 35 | \item{Contour}{Contour vector for desirability function. Contains in order: (pi_{1,E},pi_{2,T},pi_{3,E},pi_{4,T}).} | ^ checkRd: (-1) SimEfftoxContour.Rd:39: Lost braces; missing escapes or markup? 39 | \item{Contour}{Contour vector for desirability function. Contains in order: (pi_{1,E},pi_{2,T},pi_{3,E},pi_{4,T}).} | ^ checkRd: (-1) SimEfftoxContour.Rd:39: Lost braces; missing escapes or markup? 39 | \item{Contour}{Contour vector for desirability function. Contains in order: (pi_{1,E},pi_{2,T},pi_{3,E},pi_{4,T}).} | ^ checkRd: (-1) SimEfftoxContour.Rd:39: Lost braces; missing escapes or markup? 39 | \item{Contour}{Contour vector for desirability function. Contains in order: (pi_{1,E},pi_{2,T},pi_{3,E},pi_{4,T}).} | ^ checkRd: (-1) SimEfftoxContour.Rd:39: Lost braces; missing escapes or markup? 39 | \item{Contour}{Contour vector for desirability function. Contains in order: (pi_{1,E},pi_{2,T},pi_{3,E},pi_{4,T}).} | ^ checkRd: (-1) SimEfftoxContour.Rd:49: Lost braces; missing escapes or markup? 49 | \item{HypermeansEFF}{Hypermeans for the Efftox model. In order, entries are hypermeans for (beta_{0,E},beta_{1,E},beta_{2,E},beta_{0,T},beta_{1,T},psi).} | ^ checkRd: (-1) SimEfftoxContour.Rd:49: Lost braces; missing escapes or markup? 49 | \item{HypermeansEFF}{Hypermeans for the Efftox model. In order, entries are hypermeans for (beta_{0,E},beta_{1,E},beta_{2,E},beta_{0,T},beta_{1,T},psi).} | ^ checkRd: (-1) SimEfftoxContour.Rd:49: Lost braces; missing escapes or markup? 49 | \item{HypermeansEFF}{Hypermeans for the Efftox model. In order, entries are hypermeans for (beta_{0,E},beta_{1,E},beta_{2,E},beta_{0,T},beta_{1,T},psi).} | ^ checkRd: (-1) SimEfftoxContour.Rd:49: Lost braces; missing escapes or markup? 49 | \item{HypermeansEFF}{Hypermeans for the Efftox model. In order, entries are hypermeans for (beta_{0,E},beta_{1,E},beta_{2,E},beta_{0,T},beta_{1,T},psi).} | ^ checkRd: (-1) SimEfftoxContour.Rd:49: Lost braces; missing escapes or markup? 49 | \item{HypermeansEFF}{Hypermeans for the Efftox model. In order, entries are hypermeans for (beta_{0,E},beta_{1,E},beta_{2,E},beta_{0,T},beta_{1,T},psi).} | ^ checkRd: (-1) SimEfftoxContour.Rd:51: Lost braces; missing escapes or markup? 51 | \item{HypervarsEFF}{Hypervariances for the Efftox model. In order, entries are hypervariances for (beta_{0,E},beta_{1,E},beta_{2,E},beta_{0,T},beta_{1,T},psi).} | ^ checkRd: (-1) SimEfftoxContour.Rd:51: Lost braces; missing escapes or markup? 51 | \item{HypervarsEFF}{Hypervariances for the Efftox model. In order, entries are hypervariances for (beta_{0,E},beta_{1,E},beta_{2,E},beta_{0,T},beta_{1,T},psi).} | ^ checkRd: (-1) SimEfftoxContour.Rd:51: Lost braces; missing escapes or markup? 51 | \item{HypervarsEFF}{Hypervariances for the Efftox model. In order, entries are hypervariances for (beta_{0,E},beta_{1,E},beta_{2,E},beta_{0,T},beta_{1,T},psi).} | ^ checkRd: (-1) SimEfftoxContour.Rd:51: Lost braces; missing escapes or markup? 51 | \item{HypervarsEFF}{Hypervariances for the Efftox model. In order, entries are hypervariances for (beta_{0,E},beta_{1,E},beta_{2,E},beta_{0,T},beta_{1,T},psi).} | ^ checkRd: (-1) SimEfftoxContour.Rd:51: Lost braces; missing escapes or markup? 51 | \item{HypervarsEFF}{Hypervariances for the Efftox model. In order, entries are hypervariances for (beta_{0,E},beta_{1,E},beta_{2,E},beta_{0,T},beta_{1,T},psi).} | ^ checkRd: (-1) SimEfftoxUt.Rd:49: Lost braces; missing escapes or markup? 49 | \item{HypermeansEFF}{Hypermeans for the Efftox model. In order, entries are hypermeans for (beta_{0,E},beta_{1,E},beta_{2,E},beta_{0,T},beta_{1,T},psi).} | ^ checkRd: (-1) SimEfftoxUt.Rd:49: Lost braces; missing escapes or markup? 49 | \item{HypermeansEFF}{Hypermeans for the Efftox model. In order, entries are hypermeans for (beta_{0,E},beta_{1,E},beta_{2,E},beta_{0,T},beta_{1,T},psi).} | ^ checkRd: (-1) SimEfftoxUt.Rd:49: Lost braces; missing escapes or markup? 49 | \item{HypermeansEFF}{Hypermeans for the Efftox model. In order, entries are hypermeans for (beta_{0,E},beta_{1,E},beta_{2,E},beta_{0,T},beta_{1,T},psi).} | ^ checkRd: (-1) SimEfftoxUt.Rd:49: Lost braces; missing escapes or markup? 49 | \item{HypermeansEFF}{Hypermeans for the Efftox model. In order, entries are hypermeans for (beta_{0,E},beta_{1,E},beta_{2,E},beta_{0,T},beta_{1,T},psi).} | ^ checkRd: (-1) SimEfftoxUt.Rd:49: Lost braces; missing escapes or markup? 49 | \item{HypermeansEFF}{Hypermeans for the Efftox model. In order, entries are hypermeans for (beta_{0,E},beta_{1,E},beta_{2,E},beta_{0,T},beta_{1,T},psi).} | ^ checkRd: (-1) SimEfftoxUt.Rd:51: Lost braces; missing escapes or markup? 51 | \item{HypervarsEFF}{Hypervariances for the Efftox model. In order, entries are hypervariances for (beta_{0,E},beta_{1,E},beta_{2,E},beta_{0,T},beta_{1,T},psi).} | ^ checkRd: (-1) SimEfftoxUt.Rd:51: Lost braces; missing escapes or markup? 51 | \item{HypervarsEFF}{Hypervariances for the Efftox model. In order, entries are hypervariances for (beta_{0,E},beta_{1,E},beta_{2,E},beta_{0,T},beta_{1,T},psi).} | ^ checkRd: (-1) SimEfftoxUt.Rd:51: Lost braces; missing escapes or markup? 51 | \item{HypervarsEFF}{Hypervariances for the Efftox model. In order, entries are hypervariances for (beta_{0,E},beta_{1,E},beta_{2,E},beta_{0,T},beta_{1,T},psi).} | ^ checkRd: (-1) SimEfftoxUt.Rd:51: Lost braces; missing escapes or markup? 51 | \item{HypervarsEFF}{Hypervariances for the Efftox model. In order, entries are hypervariances for (beta_{0,E},beta_{1,E},beta_{2,E},beta_{0,T},beta_{1,T},psi).} | ^ checkRd: (-1) SimEfftoxUt.Rd:51: Lost braces; missing escapes or markup? 51 | \item{HypervarsEFF}{Hypervariances for the Efftox model. In order, entries are hypervariances for (beta_{0,E},beta_{1,E},beta_{2,E},beta_{0,T},beta_{1,T},psi).} | ^ checkRd: (-1) SimSpsoContour.Rd:37: Lost braces; missing escapes or markup? 37 | \item{Contour}{Contour vector for desirability function. Contains in order: (pi_{1,E},pi_{2,T},pi_{3,E},pi_{4,T}).} | ^ checkRd: (-1) SimSpsoContour.Rd:37: Lost braces; missing escapes or markup? 37 | \item{Contour}{Contour vector for desirability function. Contains in order: (pi_{1,E},pi_{2,T},pi_{3,E},pi_{4,T}).} | ^ checkRd: (-1) SimSpsoContour.Rd:37: Lost braces; missing escapes or markup? 37 | \item{Contour}{Contour vector for desirability function. Contains in order: (pi_{1,E},pi_{2,T},pi_{3,E},pi_{4,T}).} | ^ checkRd: (-1) SimSpsoContour.Rd:37: Lost braces; missing escapes or markup? 37 | \item{Contour}{Contour vector for desirability function. Contains in order: (pi_{1,E},pi_{2,T},pi_{3,E},pi_{4,T}).} | ^ * 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 ... [8s/10s] OK * checking PDF version of manual ... [8s/13s] 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