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### Running command:
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###   /home/biocbuild/R/R/bin/R CMD check --install=check:RUVcorr.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings RUVcorr_1.38.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/RUVcorr.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14)
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RUVcorr/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RUVcorr’ version ‘1.38.0’
* checking package namespace information ... NOTE
Found export directives that require package ‘methods’:
  ‘exportClasses’ ‘exportMethods’
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains ‘methods’.
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘RUVcorr’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... 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 ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... WARNING
Warning: S4 exports specified in 'NAMESPACE' but not defined in package ‘RUVcorr’
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... 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 ... OK
* checking Rd files ... NOTE
checkRd: (-1) calculateThreshold.Rd:48: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) calculateThreshold.Rd:49: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) calculateThreshold.Rd:50: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) findWeights.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) findWeights.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simulateGEdata.Rd:54: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simulateGEdata.Rd:55: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simulateGEdata.Rd:56: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simulateGEdata.Rd:57: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simulateGEdata.Rd:58: Lost braces in \itemize; \value handles \item{}{} directly
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... NOTE
Documented arguments not in \usage in Rd file 'findIQR.Rd':
  ‘Vector’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                          user system elapsed
calculateThreshold      27.182  0.036  27.086
plotThreshold           27.149  0.008  27.033
plot.optimizeParameters 24.682  0.004  23.978
ECDFPlot                15.473  0.056  15.281
prioritise              15.154  0.024  15.030
wcor                    14.980  0.026  14.857
findWeights             14.764  0.012  14.622
simulateGEdata          14.552  0.000  14.309
optimizeParameters      14.144  0.008  13.483
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/RUVcorr.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/R/R/bin/R CMD INSTALL RUVcorr
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* installing to library ‘/home/biocbuild/R/R-4.4.1/site-library’
* installing *source* package ‘RUVcorr’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (RUVcorr)