* 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