* using log directory ‘/srv/hornik/tmp/CRAN/Rsmlx.Rcheck’ * using R Under development (unstable) (2023-10-16 r85339) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 16.0.6 (15) GNU Fortran (Debian 13.2.0-4) 13.2.0 * running under: Debian GNU/Linux trixie/sid * using session charset: UTF-8 * checking for file ‘Rsmlx/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘Rsmlx’ version ‘2023.1.3’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [3s/5s] Note_to_CRAN_maintainers Maintainer: ‘Frano Mihaljevic ’ * 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 ‘Rsmlx’ can be installed ... [7s/7s] 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 ... [0s/0s] OK * checking whether the package can be unloaded cleanly ... [0s/0s] OK * checking whether the namespace can be loaded with stated dependencies ... [0s/0s] 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 whether startup messages can be suppressed ... [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 ... [16s/16s] OK * checking Rd files ... [0s/0s] NOTE checkRd: (-1) buildAll.Rd:68: Lost braces 68 | \item{center.covariate}{TRUE/{FALSE} center the covariates of the final model (default=FALSE)} | ^ checkRd: (-1) buildAll.Rd:70: Lost braces 70 | \item{criterion}{penalization criterion to optimize c("AIC", "BIC", {"BICc"}, gamma)} | ^ checkRd: (-1) buildAll.Rd:72: Lost braces 72 | \item{linearization}{TRUE/{FALSE} whether the computation of the likelihood is based on a linearization of the model (default=FALSE, deprecated)} | ^ checkRd: (-1) buildAll.Rd:78: Lost braces 78 | \item{direction}{method for covariate search c({"full"}, "both", "backward", "forward"), (default="full" or "both")} | ^ checkRd: (-1) buildAll.Rd:86: Lost braces 86 | \item{seq.cov}{TRUE/{FALSE} whether the covariate model is built before the correlation model} | ^ checkRd: (-1) buildVar.Rd:41: Lost braces 41 | \item{criterion}{penalization criterion to optimize c("AIC", "BIC", {"BICc"}, gamma)} | ^ checkRd: (-1) buildVar.Rd:43: Lost braces 43 | \item{linearization}{TRUE/{FALSE} whether the computation of the likelihood is based on a linearization of the model (default=FALSE)} | ^ checkRd: (-1) buildmlx.Rd:56: Lost braces 56 | \item{center.covariate}{TRUE/{FALSE} center the covariates of the final model (default=FALSE)} | ^ checkRd: (-1) buildmlx.Rd:58: Lost braces 58 | \item{criterion}{penalization criterion to optimize c("AIC", "BIC", {"BICc"}, gamma)} | ^ checkRd: (-1) buildmlx.Rd:60: Lost braces 60 | \item{linearization}{TRUE/{FALSE} whether the computation of the likelihood is based on a linearization of the model (default=FALSE)} | ^ checkRd: (-1) buildmlx.Rd:66: Lost braces 66 | \item{direction}{method for covariate search c({"full"}, "both", "backward", "forward"), (default="full" or "both")} | ^ checkRd: (-1) buildmlx.Rd:78: Lost braces 78 | \item{seq.cov}{TRUE/{FALSE} whether the covariate model is built before the correlation model} | ^ checkRd: (-1) confintmlx.Rd:23: Lost braces 23 | \item{method}{method c({"fim"}, "proflike", "bootstrap")} | ^ checkRd: (-1) confintmlx.Rd:39: Lost braces 39 | \item \code{print} {TRUE}/FALSE display the results (default=TRUE) | ^ checkRd: (-1) pkbuild.Rd:30: Lost braces 30 | \item{stat}{({FALSE}, TRUE): the statistical model is also built (using buildmlx)} | ^ checkRd: (-1) pkbuild.Rd:32: Lost braces 32 | \item{param}{({"clearance"}, "rate", "both): parameterization} | ^ checkRd: (-1) pkbuild.Rd:37: Lost braces 37 | \item{MM}{({FALSE}, TRUE): tested models include or not Michaelis Menten elimination models} | ^ checkRd: (-1) pkbuild.Rd:39: Lost braces 39 | \item{linearization}{TRUE/{FALSE} whether the computation of the likelihood is based on a linearization of the model (default=FALSE)} | ^ checkRd: (-1) pkbuild.Rd:41: Lost braces 41 | \item{criterion}{penalization criterion to optimize c("AIC", "BIC", {"BICc"}, gamma)} | ^ checkRd: (-1) testmlx.Rd:23: Lost braces 23 | \item{adjust}{method to take into account the dependency of MCMC sample c({"edf"},"BH")} | ^ checkRd: (-1) writeDataSmlx.Rd:22: Lost braces 22 | It must be one of {"\\t", " ", ";", ","}} | ^ checkRd: (-1) writeDataSmlx.Rd:25: Lost braces 25 | It must be one of {"csv", "txt"} | ^ * 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 LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking examples ... [1s/1s] OK * checking PDF version of manual ... [3s/3s] OK * checking HTML version of manual ... [0s/0s] OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 1 NOTE