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### Running command:
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###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:qmtools.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings qmtools_1.11.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/qmtools.Rcheck’
* using R Under development (unstable) (2024-10-21 r87258)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘qmtools/DESCRIPTION’ ... OK
* this is package ‘qmtools’ version ‘1.11.0’
* package encoding: UTF-8
* 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 hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘qmtools’ 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 ... OK
* 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 ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  clusterFeatures.Rd: SummarizedExperiment-class
  compareSamples.Rd: SummarizedExperiment-class
  faahko_se.Rd: SummarizedExperiment-class
  imputeIntensity.Rd: SummarizedExperiment-class
  imputeKNN.Rd: SummarizedExperiment-class
  normalizeIntensity.Rd: SummarizedExperiment-class
  normalizePQN.Rd: SummarizedExperiment-class
  plotBox.Rd: SummarizedExperiment-class
  plotCorr.Rd: SummarizedExperiment-class
  plotMiss.Rd: SummarizedExperiment, SummarizedExperiment-class
  plotRTgroup.Rd: SummarizedExperiment-class
  reduceFeatures.Rd: SummarizedExperiment-class
  reducePCA.Rd: SummarizedExperiment-class
  reducePLSDA.Rd: SummarizedExperiment-class
  reduceTSNE.Rd: SummarizedExperiment-class
  removeBlankRatio.Rd: SummarizedExperiment-class
  removeFeatures.Rd: SummarizedExperiment-class
  removeICC.Rd: SummarizedExperiment-class
  removeMiss.Rd: SummarizedExperiment-class
  removeRSD.Rd: SummarizedExperiment-class
  scaleCols.Rd: SummarizedExperiment-class
  scaleRows.Rd: SummarizedExperiment-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
          user system elapsed
plotMiss 7.323  0.027   7.357
plotCorr 6.086  0.049   6.136
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/qmtools.Rcheck/00check.log’
for details.