* using log directory ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/mrMLM.Rcheck’
* using R Under development (unstable) (2024-04-29 r86495)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc-13 (Debian 13.2.0-23) 13.2.0
    GNU Fortran (Debian 13.2.0-23) 13.2.0
* running under: Debian GNU/Linux trixie/sid
* using session charset: UTF-8
* checking for file ‘mrMLM/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘mrMLM’ version ‘5.0.1’
* 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 whether package ‘mrMLM’ can be installed ... OK
See 'https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-debian-gcc/mrMLM-00install.html' for details.
* used C++ compiler: ‘g++-13 (Debian 13.2.0-23) 13.2.0’
* 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/4s] OK
* checking whether the package can be loaded with stated dependencies ... [2s/4s] OK
* checking whether the package can be unloaded cleanly ... [2s/4s] OK
* checking whether the namespace can be loaded with stated dependencies ... [2s/4s] OK
* checking whether the namespace can be unloaded cleanly ... [2s/4s] OK
* checking loading without being on the library search path ... [2s/4s] 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 ... [65s/108s] OK
* checking Rd files ... [0s/1s] NOTE
checkRd: (-1) MultiManhattan.Rd:33: Lost braces; missing escapes or markup?
    33 |         \item{LogTimes}{Magnification of {-log10(P-value)}; the default is
       |                                          ^
checkRd: (-1) MultiManhattan.Rd:35: Lost braces; missing escapes or markup?
    35 |     \item{LODTimes}{Magnification of {LOD score}; the default is 1.2.}
       |                                      ^
* 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 data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... OK
* checking compiled code ... OK
* checking examples ... [20s/63s] OK
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
MultiManhattan 4.761  0.221   6.208
pLARmEB        2.136  0.084  11.991
mrMLM          1.957  0.057   8.122
pKWmEB         1.896  0.072   8.031
FASTmrEMMA     1.332  0.304   5.808
FASTmrMLM      1.556  0.010   7.334
ISIS           1.499  0.031   5.542
mrMLMFun       1.152  0.055   6.019
* checking PDF version of manual ... [5s/12s] OK
* checking HTML version of manual ... [1s/2s] OK
* checking for non-standard things in the check directory ... OK
* DONE
Status: 1 NOTE