* using log directory ‘/srv/hornik/tmp/CRAN/qape.Rcheck’
* using R Under development (unstable) (2024-02-21 r85960)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 17.0.6 (5)
    Debian flang-new version 17.0.6 (5)
* running under: Debian GNU/Linux trixie/sid
* using session charset: UTF-8
* checking for file ‘qape/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘qape’ version ‘2.2’
* checking CRAN incoming feasibility ... [3s/3s] NOTE
Maintainer: ‘Alicja Wolny-Dominiak <alicja.wolny-dominiak@ue.katowice.pl>’

Possibly misspelled words in DESCRIPTION:
  EBLUP (11:211)
  Ypop (11:173)
* 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 ‘qape’ can be installed ... [6s/6s] OK
* 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 R 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 ... [11s/11s] NOTE
Found if() conditions comparing class() to string:
File ‘qape/R/bootPar.R’: if (class(predictor) != "EBLUP" & class(predictor) != "plugInLMM" & class(predictor) != "ebpLMMne") ...
File ‘qape/R/bootParFuture.R’: if (class(predictor) != "EBLUP" & class(predictor) != "plugInLMM" & class(predictor) != "ebpLMMne") ...
File ‘qape/R/bootParFutureCor.R’: if (class(predictor) != "EBLUP" & class(predictor) != "plugInLMM" & class(predictor) != "ebpLMMne") ...
File ‘qape/R/bootParMis.R’: if (class(predictorLMM) != "plugInLMM" | class(predictorLMMmis) != "plugInLMM") ...
File ‘qape/R/bootRes.R’: if (class(predictor) != "EBLUP" & class(predictor) != "plugInLMM" & class(predictor) != "ebpLMMne") ...
File ‘qape/R/bootResFuture.R’: if (class(predictor) != "EBLUP" & class(predictor) != "plugInLMM" & class(predictor) != "ebpLMMne") ...
File ‘qape/R/bootResMis.R’: if (class(predictorLMM) != "plugInLMM" | class(predictorLMMmis) != "plugInLMM") ...
File ‘qape/R/corrRanef.R’: if (class(obj) != "try-error") ...
File ‘qape/R/doubleBoot.R’: if (class(predictor) != "EBLUP" & class(predictor) != "plugInLMM" & class(predictor) != "ebpLMMne") ...
File ‘qape/R/doubleBootFuture.R’: if (class(predictor) != "EBLUP" & class(predictor) != "plugInLMM" & class(predictor) != "ebpLMMne") ...
File ‘qape/R/doubleBootMis.R’: if (class(predictorLMM) != "plugInLMM" | class(predictorLMMmis) != "plugInLMM") ...
File ‘qape/R/mcBootMis.R’: if (class(predictorLMM) != "plugInLMM" | class(predictorLMMmis) != "plugInLMM") ...
File ‘qape/R/mcLMMmis.R’: if (class(predictorLMM) != "plugInLMM" | class(predictorLMMmis) != "plugInLMM" | class(predictorLMM2) != "plugInLMM") ...
Use inherits() (or maybe is()) instead.
* checking Rd files ... [0s/0s] NOTE
checkRd: (-1) srswrRe.Rd:10: Lost braces
    10 |   \item{listRanef}{{\emph{ranef(model)}} object where {\emph{model}} is an { \emph{lmer}} object.}
       |                                                                            ^
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'bootParMis.Rd':
  \examples lines wider than 100 characters:
     predictorLMMmis <- plugInLMM(YS, fixed.part, random.part.mis, reg, con, weights, backTrans, thetaFun)

Rd file 'bootResMis.Rd':
  \examples lines wider than 100 characters:
     predictorLMMmis <- plugInLMM(YS, fixed.part, random.part.mis, reg, con, weights, backTrans, thetaFun)

Rd file 'doubleBootMis.Rd':
  \examples lines wider than 100 characters:
     predictorLMMmis <- plugInLMM(YS, fixed.part, random.part.mis, reg, con, weights, backTrans, thetaFun)

Rd file 'mcLMMmis.Rd':
  \examples lines wider than 100 characters:
     predictorLMMmis <- plugInLMM(YS, fixed.part, random.part, reg, con, weights.mis, backTrans, thetaFun)

These lines will be truncated in the PDF manual.
* 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/0s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking examples ... [29s/29s] NOTE
Examples with CPU (user + system) or elapsed time > 5s
            user system elapsed
mcBootMis 12.234  0.164  12.399
* checking PDF version of manual ... [3s/3s] OK
* checking HTML version of manual ... [1s/1s] OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 5 NOTEs