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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_1.41.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/RUVcorr.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RUVcorr/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RUVcorr’ version ‘1.41.0’
* 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
plotThreshold           23.868  0.032  23.958
calculateThreshold      23.665  0.016  23.735
plot.optimizeParameters 19.871  0.012  19.917
prioritise              13.117  0.020  13.164
wcor                    12.964  0.012  12.997
ECDFPlot                12.707  0.032  12.760
findWeights             12.723  0.000  12.746
simulateGEdata          11.395  0.000  11.413
optimizeParameters      11.346  0.000  11.367
* 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-3.22-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-4.5.0/site-library’
* installing *source* package ‘RUVcorr’ ...
** this is package ‘RUVcorr’ version ‘1.41.0’
** 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)