* using log directory ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/plink.Rcheck’ * using R Under development (unstable) (2024-04-27 r86487) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 18.1.4 (1) Debian flang-new version 18.1.4 (1) * running under: Debian GNU/Linux trixie/sid * using session charset: UTF-8 * checking for file ‘plink/DESCRIPTION’ ... OK * this is package ‘plink’ version ‘1.5-1’ * 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 ‘plink’ can be installed ... OK See 'https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-debian-clang/plink-00install.html' for details. * checking package directory ... OK * checking for future file timestamps ... OK * checking ‘build’ 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 ... [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 ... [44s/51s] OK * checking Rd files ... [1s/1s] NOTE checkRd: (-1) as.weight.Rd:56-60: Lost braces in \itemize; meant \describe ? checkRd: (-1) as.weight.Rd:62-63: Lost braces in \itemize; meant \describe ? checkRd: (-1) as.weight.Rd:65-66: Lost braces in \itemize; meant \describe ? checkRd: (-1) as.weight.Rd:68-70: Lost braces in \itemize; meant \describe ? checkRd: (-1) as.weight.Rd:72-73: Lost braces in \itemize; meant \describe ? checkRd: (-1) as.weight.Rd:78-80: Lost braces in \itemize; meant \describe ? checkRd: (-1) as.weight.Rd:82-83: Lost braces in \itemize; meant \describe ? checkRd: (-1) as.weight.Rd:85-92: Lost braces in \itemize; meant \describe ? checkRd: (-1) as.weight.Rd:94-96: Lost braces in \itemize; meant \describe ? checkRd: (-1) as.weight.Rd:98-104: Lost braces in \itemize; meant \describe ? checkRd: (-1) plink-package.Rd:13-37: Lost braces in \itemize; meant \describe ? checkRd: (-1) plink-package.Rd:18: Lost braces in \itemize; meant \describe ? checkRd: (-1) plink-package.Rd:19: Lost braces in \itemize; meant \describe ? checkRd: (-1) plink-package.Rd:20: Lost braces in \itemize; meant \describe ? checkRd: (-1) plink-package.Rd:21: Lost braces in \itemize; meant \describe ? checkRd: (-1) plink-package.Rd:22: Lost braces in \itemize; meant \describe ? checkRd: (-1) plink-package.Rd:23: Lost braces in \itemize; meant \describe ? checkRd: (-1) plink-package.Rd:24: Lost braces in \itemize; meant \describe ? checkRd: (-1) plink-package.Rd:25: Lost braces in \itemize; meant \describe ? checkRd: (-1) plink-package.Rd:27: Lost braces in \itemize; meant \describe ? checkRd: (-1) plink-package.Rd:28: Lost braces in \itemize; meant \describe ? checkRd: (-1) plink-package.Rd:29: Lost braces in \itemize; meant \describe ? checkRd: (-1) plink-package.Rd:30: Lost braces in \itemize; meant \describe ? checkRd: (-1) plink-package.Rd:31: Lost braces in \itemize; meant \describe ? checkRd: (-1) plink-package.Rd:32: Lost braces in \itemize; meant \describe ? checkRd: (-1) plink-package.Rd:33: Lost braces in \itemize; meant \describe ? checkRd: (-1) plink-package.Rd:34: Lost braces in \itemize; meant \describe ? checkRd: (-1) plink-package.Rd:39-81: Lost braces in \itemize; meant \describe ? checkRd: (-1) plink-package.Rd:44: Lost braces in \itemize; meant \describe ? checkRd: (-1) plink-package.Rd:45-46: Lost braces in \itemize; meant \describe ? checkRd: (-1) plink-package.Rd:47: Lost braces in \itemize; meant \describe ? checkRd: (-1) plink-package.Rd:48: Lost braces in \itemize; meant \describe ? checkRd: (-1) plink-package.Rd:54: Lost braces in \itemize; meant \describe ? checkRd: (-1) plink-package.Rd:55: Lost braces in \itemize; meant \describe ? checkRd: (-1) plink-package.Rd:56: Lost braces in \itemize; meant \describe ? checkRd: (-1) plink-package.Rd:57: Lost braces in \itemize; meant \describe ? checkRd: (-1) plink-package.Rd:63: Lost braces in \itemize; meant \describe ? checkRd: (-1) plink-package.Rd:64: Lost braces in \itemize; meant \describe ? checkRd: (-1) plink-package.Rd:65-66: Lost braces in \itemize; meant \describe ? checkRd: (-1) plink-package.Rd:71-72: Lost braces in \itemize; meant \describe ? checkRd: (-1) plink-package.Rd:73-74: Lost braces in \itemize; meant \describe ? checkRd: (-1) plink-package.Rd:75-76: Lost braces in \itemize; meant \describe ? checkRd: (-1) plink-package.Rd:83: Lost braces in \itemize; meant \describe ? checkRd: (-1) plink-package.Rd:85-86: Lost braces in \itemize; meant \describe ? checkRd: (-1) plink-package.Rd:88-89: Lost braces in \itemize; meant \describe ? checkRd: (-1) plink-package.Rd:91-93: Lost braces in \itemize; meant \describe ? checkRd: (-1) plink-package.Rd:95-98: Lost braces in \itemize; meant \describe ? checkRd: (-1) plink-package.Rd:100: Lost braces in \itemize; meant \describe ? * 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 sizes of PDF files under ‘inst/doc’ ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... [25s/30s] OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed plot.irt.prob 4.944 0.020 5.959 plink-methods 4.343 0.004 5.043 * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [22s/28s] OK * checking PDF version of manual ... [9s/10s] OK * checking HTML version of manual ... [4s/6s] OK * checking for non-standard things in the check directory ... OK * DONE Status: 1 NOTE