* using log directory ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/BWGS.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 ‘BWGS/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘BWGS’ version ‘0.2.1’ * 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 whether package ‘BWGS’ can be installed ... OK See 'https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-debian-clang/BWGS-00install.html' for details. * 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 ... [2s/2s] OK * checking whether the package can be loaded with stated dependencies ... [2s/2s] OK * checking whether the package can be unloaded cleanly ... [2s/2s] OK * checking whether the namespace can be loaded with stated dependencies ... [2s/3s] OK * checking whether the namespace can be unloaded cleanly ... [2s/3s] OK * checking loading without being on the library search path ... [2s/3s] 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 ... [17s/20s] OK * checking Rd files ... [0s/1s] NOTE checkRd: (-1) bwgs.cv.Rd:27: Lost braces; missing escapes or markup? 27 | \item{geno}{Matrix (n x m) of genotypes for the training population: n lines with m markers. Genotypes should be coded {-1, 0, 1}. Missing data are allowed and coded as NA.} | ^ checkRd: (-1) bwgs.cv.Rd:59: Lost braces; missing escapes or markup? 59 | \item{r2}{Coefficient of linkage disequilibrium (LD). Setting 0<r2<1 if the genotypic reduction method is in {LD or ANO+LD }.} | ^ checkRd: (-1) bwgs.predict.Rd:25: Lost braces; missing escapes or markup? 25 | \item{geno_train}{Matrix (n x m) of genotypes for the training population: n lines with m markers. Genotypes should be coded as {-1, 0, 1, NA}. Missing data are allowed and coded as NA.} | ^ checkRd: (-1) bwgs.predict.Rd:29: Lost braces; missing escapes or markup? 29 | \item{geno_target}{Matrix (z x m) of genotypes for the target population: z lines with the same m markers as in geno_train. Genotypes should be coded as {-1, 0, 1, NA}. Missing data are allowed and coded as NA. Other arguments are identical to those of bwgs.cv, except pop_reduct_method, nTimes and nFolds, since the prediction is run only once, using the whole training population for model estimation, then applied to the target population.} | ^ checkRd: (-1) bwgs.predict.Rd:49: Lost braces; missing escapes or markup? 49 | \item{r2}{Coefficient of linkage disequilibrium (LD). Setting 0<r2<1 if the genotypic reduction method is in {LD or ANO+LD }.} | ^ * 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/1s] OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking examples ... [2s/3s] OK * checking PDF version of manual ... [4s/6s] OK * checking HTML version of manual ... [0s/1s] OK * checking for non-standard things in the check directory ... OK * DONE Status: 1 NOTE