* using log directory ‘/srv/hornik/tmp/CRAN/Surrogate.Rcheck’ * using R Under development (unstable) (2024-02-17 r85935) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 17.0.6 (5) Debian flang-new version 17.0.6 (5) * running under: Debian GNU/Linux trixie/sid * using session charset: UTF-8 * checking for file ‘Surrogate/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘Surrogate’ version ‘3.2.2’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [5s/5s] NOTE Maintainer: ‘Wim Van Der Elst ’ Possibly misspelled words in DESCRIPTION: BOF (26:59, 27:15, 27:27) Baekeland (27:68) Biologicals (27:55) GlaxoSmithKline (27:39) Hasselt (26:67) Mandaat (28:3) OCPO (27:31) Size of tarball: 5534512 bytes * 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 ‘Surrogate’ can be installed ... [17s/17s] OK * 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 R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... [1s/1s] OK * checking whether the package can be loaded with stated dependencies ... [1s/1s] OK * checking whether the package can be unloaded cleanly ... [1s/1s] OK * checking whether the namespace can be loaded with stated dependencies ... [1s/1s] OK * checking whether the namespace can be unloaded cleanly ... [1s/1s] OK * checking loading without being on the library search path ... [1s/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 ... [38s/38s] OK * checking Rd files ... [1s/1s] NOTE checkRd: (-1) ICA.BinBin.Grid.Sample.Rd:20: Lost braces; missing escapes or markup? 20 | \item{Volume.Perc}{Note that the marginals that are observable in the data set a number of restrictions on the unidentified correlations. For example, under montonicity for \eqn{S} and \eqn{T}, it holds that \eqn{\pi_{0111}<=min(\pi_{0\cdot1\cdot}, \pi_{\cdot1\cdot1})} and \eqn{\pi_{1100}<=min(\pi_{1\cdot0\cdot}, \pi_{\cdot1\cdot0})}. For example, when \eqn{min(\pi_{0\cdot1\cdot}, \pi_{\cdot1\cdot1})=0.10} and \eqn{min(\pi_{1\cdot0\cdot}, \pi_{\cdot1\cdot0})=0.08}, then all valid \eqn{\pi_{0111}<=0.10} and all valid \eqn{\pi_{1100}<=0.08}. The argument \code{Volume.Perc} specifies the fraction of the 'volume' of the paramater space that is explored. This volume is computed based on the grids G={0, 0.01, ..., maximum possible value for the counterfactual probability at hand}. E.g., in the previous example, the 'volume' of the parameter space would be \eqn{11*9=99}, and when e.g., the argument \code{Volume.Perc=1} is used a total of \eqn{99} runs will be conducted. Notice that when monotonicity is not assumed, relatively high values of \code{Volume.Perc} will lead to a large number of runs and consequently a long analysis time.} | ^ checkRd: (-1) ICA.BinBin.Grid.Sample.Uncert.Rd:20: Lost braces; missing escapes or markup? 20 | \item{Volume.Perc}{Note that the marginals that are observable in the data set a number of restrictions on the unidentified correlations. For example, under montonicity for \eqn{S} and \eqn{T}, it holds that \eqn{\pi_{0111}<=min(\pi_{0\cdot1\cdot}, \pi_{\cdot1\cdot1})} and \eqn{\pi_{1100}<=min(\pi_{1\cdot0\cdot}, \pi_{\cdot1\cdot0})}. For example, when \eqn{min(\pi_{0\cdot1\cdot}, \pi_{\cdot1\cdot1})=0.10} and \eqn{min(\pi_{1\cdot0\cdot}, \pi_{\cdot1\cdot0})=0.08}, then all valid \eqn{\pi_{0111}<=0.10} and all valid \eqn{\pi_{1100}<=0.08}. The argument \code{Volume.Perc} specifies the fraction of the 'volume' of the paramater space that is explored. This volume is computed based on the grids G={0, 0.01, ..., maximum possible value for the counterfactual probability at hand}. E.g., in the previous example, the 'volume' of the parameter space would be \eqn{11*9=99}, and when e.g., the argument \code{Volume.Perc=1} is used a total of \eqn{99} runs will be conducted. Notice that when monotonicity is not assumed, relatively high values of \code{Volume.Perc} will lead to a large number of runs and consequently a long analysis time.} | ^ checkRd: (-1) ICABinBin.Rd:22: Lost braces; missing escapes or markup? 22 | \item{Volume.Perc}{Note that the marginals that are observable in the data set a number of restrictions on the unidentified correlations. For example, under montonicity for \eqn{S} and \eqn{T}, it holds that \eqn{\pi_{0111}<=min(\pi_{0\cdot1\cdot}, \pi_{\cdot1\cdot1})} and \eqn{\pi_{1100}<=min(\pi_{1\cdot0\cdot}, \pi_{\cdot1\cdot0})}. For example, when \eqn{min(\pi_{0\cdot1\cdot}, \pi_{\cdot1\cdot1})=0.10} and \eqn{min(\pi_{1\cdot0\cdot}, \pi_{\cdot1\cdot0})=0.08}, then all valid \eqn{\pi_{0111}<=0.10} and all valid \eqn{\pi_{1100}<=0.08}. The argument \code{Volume.Perc} specifies the fraction of the 'volume' of the paramater space that is explored. This volume is computed based on the grids G={0, 0.01, ..., maximum possible value for the counterfactual probability at hand}. E.g., in the previous example, the 'volume' of the parameter space would be \eqn{11*9=99}, and when e.g., the argument \code{Volume.Perc=1} is used a total of \eqn{99} runs will be conducted for each given value of \code{Sum_Pi_f}. Notice that when monotonicity is not assumed, relatively high values of \code{Volume.Perc} will lead to a large number of runs and consequently a long analysis time.} | ^ checkRd: (-1) MICA.Sample.ContCont.Rd:47-51: Lost braces 47 | \bold{Notes}{ | ^ checkRd: (-1) MICAContCont.Rd:42-46: Lost braces 42 | \bold{Notes}{ | ^ * 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 ... [0s/0s] OK * checking data for ASCII and uncompressed saves ... OK * checking examples ... [39s/39s] OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... [74s/74s] OK Running ‘testthat.R’ [74s/74s] * checking PDF version of manual ... [7s/7s] OK * checking HTML version of manual ... [6s/6s] OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 2 NOTEs