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### Running command:
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###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:batchCorr.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings batchCorr_0.99.8.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/batchCorr.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.2 LTS
* using session charset: UTF-8
* checking for file ‘batchCorr/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘batchCorr’ version ‘0.99.8’
* 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 ‘batchCorr’ 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 ... 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 ... 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
correctDrift 93.015  1.473  56.167
mergeBatches 90.393  1.444  53.733
* 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: OK

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### Running command:
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###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL batchCorr
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* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘batchCorr’ ...
** this is package ‘batchCorr’ version ‘0.99.8’
** using staged installation
** R
** data
** 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 (batchCorr)

R version 4.5.1 (2025-06-13) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(batchCorr)
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

The following objects are masked from 'package:matrixStats':

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: generics

Attaching package: 'generics'

The following objects are masked from 'package:base':

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
    unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:utils':

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: Seqinfo
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'Biobase'

The following object is masked from 'package:MatrixGenerics':

    rowMedians

The following objects are masked from 'package:matrixStats':

    anyMissing, rowMedians

> data("ThreeBatchData")
> test_check("batchCorr")
Mclust 
Missing BIC values for some model(s). You may want to check which models have missing BIC values and/or try again.
Missing BIC values for some model(s). You may want to check which models have missing BIC values and/or try again.
Missing BIC values for some model(s). You may want to check which models have missing BIC values and/or try again.
Missing BIC values for some model(s). You may want to check which models have missing BIC values and/or try again.
Missing BIC values for some model(s). You may want to check which models have missing BIC values and/or try again.
Missing BIC values for some model(s). You may want to check which models have missing BIC values and/or try again.
Missing BIC values for some model(s). You may want to check which models have missing BIC values and/or try again.
Missing BIC values for some model(s). You may want to check which models have missing BIC values and/or try again.
Missing BIC values for some model(s). You may want to check which models have missing BIC values and/or try again.
Missing BIC values for some model(s). You may want to check which models have missing BIC values and/or try again.
Missing BIC values for some model(s). You may want to check which models have missing BIC values and/or try again.
MClust final model with 11 clusters and VEE geometry.
BIC performed in 27.645 seconds and clustering in 0.537999999999997 seconds.
Calculation of QC drift profiles performed.

Drift correction of 10 out of 11 clusters
using QC samples only.

Corrected peak table in $TestFeatsCorr


Filtering by QC CV < 0.3 -> 778 features out of 995 kept in the peak table. 

Peak table in $TestFeatsFinal, final variables in $finalVars
            and cluster info in $actionInfo.
Mclust 
Missing BIC values for some model(s). You may want to check which models have missing BIC values and/or try again.
Missing BIC values for some model(s). You may want to check which models have missing BIC values and/or try again.
Missing BIC values for some model(s). You may want to check which models have missing BIC values and/or try again.
Missing BIC values for some model(s). You may want to check which models have missing BIC values and/or try again.
Missing BIC values for some model(s). You may want to check which models have missing BIC values and/or try again.
Missing BIC values for some model(s). You may want to check which models have missing BIC values and/or try again.
Missing BIC values for some model(s). You may want to check which models have missing BIC values and/or try again.
Missing BIC values for some model(s). You may want to check which models have missing BIC values and/or try again.
Missing BIC values for some model(s). You may want to check which models have missing BIC values and/or try again.
Missing BIC values for some model(s). You may want to check which models have missing BIC values and/or try again.
Missing BIC values for some model(s). You may want to check which models have missing BIC values and/or try again.
Missing BIC values for some model(s). You may want to check which models have missing BIC values and/or try again.
Missing BIC values for some model(s). You may want to check which models have missing BIC values and/or try again.
Missing BIC values for some model(s). You may want to check which models have missing BIC values and/or try again.
Missing BIC values for some model(s). You may want to check which models have missing BIC values and/or try again.
Missing BIC values for some model(s). You may want to check which models have missing BIC values and/or try again.
MClust final model with 8 clusters and VVE geometry.
BIC performed in 21.424 seconds and clustering in 4.554 seconds.
Calculation of QC drift profiles performed.

Drift correction of 5 out of 8 clusters

Corrected peak table in $TestFeatsCorr


Filtering by QC CV < 0.3 -> 706 features out of 997 kept in the peak table. 

Peak table in $TestFeatsFinal, final variables in $finalVars
            and cluster info in $actionInfo.
Mclust 
Missing BIC values for some model(s). You may want to check which models have missing BIC values and/or try again.
Missing BIC values for some model(s). You may want to check which models have missing BIC values and/or try again.
Missing BIC values for some model(s). You may want to check which models have missing BIC values and/or try again.
Missing BIC values for some model(s). You may want to check which models have missing BIC values and/or try again.
Missing BIC values for some model(s). You may want to check which models have missing BIC values and/or try again.
MClust final model with 5 clusters and VVE geometry.
BIC performed in 6.141 seconds and clustering in 4.02500000000001 seconds.
Calculation of QC drift profiles performed.
Calculation of QC drift profiles performed.

Drift correction of 4 out of 5 clusters
using QC samples only.

Corrected peak table in $TestFeatsCorr


Filtering by QC CV < 0.3 -> 771 features out of 995 kept in the peak table. 

Peak table in $TestFeatsFinal, final variables in $finalVars
            and cluster info in $actionInfo.
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 56 ]
> 
> proc.time()
   user  system elapsed 
123.630   3.212  78.828