* using log directory ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/MXM.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 ‘MXM/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MXM’ version ‘1.5.5’
* 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 ‘MXM’ can be installed ... OK
See 'https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-debian-gcc/MXM-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 ... [5s/7s] OK
* checking whether the package can be loaded with stated dependencies ... [4s/7s] OK
* checking whether the package can be unloaded cleanly ... [4s/5s] OK
* checking whether the namespace can be loaded with stated dependencies ... [4s/7s] OK
* checking whether the namespace can be unloaded cleanly ... [5s/7s] OK
* checking loading without being on the library search path ... [5s/8s] 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 ... [220s/364s] OK
* checking Rd files ... [2s/3s] NOTE
checkRd: (-1) bbc.Rd:39: Lost braces
    39 | The "nbdev.mxm" (negative binomial deviance) is missing. For more information on these see \code{\link{cv.ses}}. bold{Note} that they come with "".
       |                                                                                                                      ^
checkRd: (-1) cv.fbed.lmm.reg.Rd:32: Lost braces; missing escapes or markup?
    32 | The folds of the data to use (a list generated by the function generateCVRuns {TunePareto}). If NULL the folds are created internally with the same function.
       |                                                                               ^
checkRd: (-1) cv.gomp.Rd:29: Lost braces; missing escapes or markup?
    29 | The folds of the data to use (a list generated by the function generateCVRuns {TunePareto}). If NULL the folds are created internally with the same function.
       |                                                                               ^
checkRd: (-1) cv.ses.Rd:94: Lost braces; missing escapes or markup?
    94 | The folds of the data to use (a list generated by the function generateCVRuns {TunePareto}). If NULL the folds are created internally with the same function.
       |                                                                               ^
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [29s/53s] OK
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
bn.skel.utils 3.237  0.019   5.823
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [45s/97s] OK
* checking PDF version of manual ... [14s/25s] OK
* checking HTML version of manual ... [7s/15s] OK
* checking for non-standard things in the check directory ... OK
* DONE
Status: 1 NOTE