* using log directory ‘/data/blackswan/ripley/R/packages/tests-devel/osDesign.Rcheck’ * using R Under development (unstable) (2025-11-17 r89032) * 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 * checking for file ‘osDesign/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘osDesign’ version ‘1.8’ * 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 ‘osDesign’ can be installed ... 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 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 ... [13s/13s] OK * checking Rd files ... NOTE checkRd: (-1) ccPower.Rd:57: Lost braces; missing escapes or markup? 57 | The correspondence between \code{betaTruth} and \code{X}, specifically the ordering of elements, is based on successive use of \code{\link{factor}} to each column of \code{X} which is expanded via the \code{expandX} argument. Each exposure that is expanded must conform to a {0, 1, 2, ...} integer-based coding convention. | ^ checkRd: (-1) ccSim.Rd:70: Lost braces in \itemize; meant \describe ? checkRd: (-1) ccSim.Rd:71: Lost braces in \itemize; meant \describe ? checkRd: (-1) ccSim.Rd:72: Lost braces in \itemize; meant \describe ? checkRd: (-1) ccSim.Rd:73: Lost braces in \itemize; meant \describe ? checkRd: (-1) ccSim.Rd:74: Lost braces in \itemize; meant \describe ? checkRd: (-1) ccSim.Rd:78: Lost braces; missing escapes or markup? 78 | The correspondence between \code{betaTruth} and \code{X}, specifically the ordering of elements, is based on successive use of \code{\link{factor}} to each column of \code{X} which is expanded via the \code{expandX} argument. Each exposure that is expanded must conform to a {0, 1, 2, ...} integer-based coding convention. | ^ checkRd: (-1) phaseI.Rd:55: Lost braces; missing escapes or markup? 55 | The correspondence between \code{betaTruth} and \code{X}, specifically the ordering of elements, is based on successive use of \code{\link{factor}} to each column of \code{X} which is expanded via the \code{expandX} argument. Each exposure that is expanded must conform to a {0, 1, 2, ...} integer-based coding convention. | ^ checkRd: (-1) tpsPower.Rd:67: Lost braces in \itemize; meant \describe ? checkRd: (-1) tpsPower.Rd:68: Lost braces in \itemize; meant \describe ? checkRd: (-1) tpsPower.Rd:69: Lost braces in \itemize; meant \describe ? checkRd: (-1) tpsPower.Rd:70: Lost braces in \itemize; meant \describe ? checkRd: (-1) tpsPower.Rd:71: Lost braces in \itemize; meant \describe ? checkRd: (-1) tpsPower.Rd:77: Lost braces; missing escapes or markup? 77 | The correspondence between \code{betaTruth} and \code{X}, specifically the ordering of elements, is based on successive use of \code{\link{factor}} to each column of \code{X} which is expanded via the \code{expandX} argument. Each exposure that is expanded must conform to a {0, 1, 2, ...} integer-based coding convention. | ^ checkRd: (-1) tpsSim.Rd:86: Lost braces in \itemize; meant \describe ? checkRd: (-1) tpsSim.Rd:87: Lost braces in \itemize; meant \describe ? checkRd: (-1) tpsSim.Rd:88: Lost braces in \itemize; meant \describe ? checkRd: (-1) tpsSim.Rd:89: Lost braces in \itemize; meant \describe ? checkRd: (-1) tpsSim.Rd:90: Lost braces in \itemize; meant \describe ? checkRd: (-1) tpsSim.Rd:96: Lost braces in \itemize; meant \describe ? checkRd: (-1) tpsSim.Rd:97: Lost braces in \itemize; meant \describe ? checkRd: (-1) tpsSim.Rd:98: Lost braces in \itemize; meant \describe ? checkRd: (-1) tpsSim.Rd:99: Lost braces in \itemize; meant \describe ? checkRd: (-1) tpsSim.Rd:100: Lost braces in \itemize; meant \describe ? checkRd: (-1) tpsSim.Rd:101: Lost braces in \itemize; meant \describe ? checkRd: (-1) tpsSim.Rd:102: Lost braces in \itemize; meant \describe ? checkRd: (-1) tpsSim.Rd:103: Lost braces in \itemize; meant \describe ? checkRd: (-1) tpsSim.Rd:107: Lost braces; missing escapes or markup? 107 | The correspondence between \code{betaTruth} and \code{X}, specifically the ordering of elements, is based on successive use of \code{\link{factor}} to each column of \code{X} which is expanded via the \code{expandX} argument. Each exposure that is expanded must conform to a {0, 1, 2, ...} integer-based coding convention. | ^ * 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 contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking examples ... [18s/19s] OK * checking examples with --run-donttest ... [30m/31m] ERROR Running examples in ‘osDesign-Ex.R’ failed The error most likely occurred in: > ### Name: plotPower > ### Title: Plot function for power, based on two-phase and case-control > ### design > ### Aliases: plotPower > > ### ** Examples > > ## > data(Ohio) > > ## > XM <- cbind(Int=1, Ohio[,1:3]) > fitM <- glm(cbind(Death, N-Death) ~ factor(Age) + Sex + Race, data=Ohio, + family=binomial) > betaNamesM <- c("Int", "Age1", "Age2", "Sex", "Race") > > ## Power for the TPS design where phase I stratification is based on Age > ## > newBetaM <- fitM$coef > newBetaM[2:3] <- newBetaM[2:3] / 2 > ## > ## No test: > powerRaceTPS <- tpsPower(B=10000, betaTruth=fitM$coef, X=XM, N=Ohio$N, + strata=4, + nII=seq(from=100, to=1000, by=100), + betaNames=c("Int", "Age1", "Age2", "Sex", "Race"), monitor=1000) Warning: glm.fit: algorithm did not converge Warning: glm.fit: algorithm did not converge Warning: glm.fit: algorithm did not converge Warning: glm.fit: algorithm did not converge Warning: glm.fit: algorithm did not converge * checking PDF version of manual ... OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * checking for new files in some other directories ... OK * DONE Status: 1 ERROR, 1 NOTE See ‘/data/blackswan/ripley/R/packages/tests-devel/osDesign.Rcheck/00check.log’ for details. Command exited with non-zero status 1 Time 32:16.53, 1752.78 + 120.60