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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:OUTRIDER.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings OUTRIDER_1.27.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/OUTRIDER.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘OUTRIDER/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OUTRIDER’ version ‘1.27.2’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 22 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* 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 ‘OUTRIDER’ can be installed ... OK
* used C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
* used SDK: ‘MacOSX11.3.1.sdk’
* 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 dependencies in R code ... NOTE
Unexported object imported by a ':::' call: 'ggbio:::.buildFacetsFromArgs'
  See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  'checkOutriderDataSet'
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
estimateBestQ: no visible binding for global variable ‘oht’
plotEncDimSearch.OUTRIDER: no visible binding for global variable ‘oht’
plotEncDimSearch.OUTRIDER: no visible binding for global variable
  ‘singular_values’
plotEncDimSearch,OutriderDataSet: no visible binding for global
  variable ‘oht’
plotEncDimSearch,OutriderDataSet: no visible binding for global
  variable ‘singular_values’
Undefined global functions or variables:
  oht singular_values
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Non-topic package-anchored link(s) in Rd file 'getter_setter_functions.Rd':
  ‘[DESeq2]{estimateDispersions}’

Non-topic package-anchored link(s) in Rd file 'sizeFactors.Rd':
  ‘[DESeq2]{estimateSizeFactors}’

See section 'Cross-references' in the 'Writing R Extensions' manual.
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘OUTRIDER-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotAberrantPerSample
> ### Title: Visualization functions for OUTRIDER
> ### Aliases: plotAberrantPerSample plotCountCorHeatmap plotManhattan
> ###   plotEncDimSearch plotQQ plotVolcano plotFunction plotFunctions
> ###   plotExpectedVsObservedCounts plotExpressionRank
> ###   plotCountGeneSampleHeatmap plotFPKM plotDispEsts plotPowerAnalysis
> ###   plotExpressedGenes plotSizeFactors plotVolcano,OutriderDataSet-method
> ###   plotQQ,OutriderDataSet-method
> ###   plotCountCorHeatmap,OutriderDataSet-method
> ###   plotAberrantPerSample,OutriderDataSet-method
> ###   plotDispEsts,OutriderDataSet-method
> ###   plotEncDimSearch,OutriderDataSet-method
> ###   plotManhattan,OutriderDataSet-method
> 
> ### ** Examples
> 
> ods <- makeExampleOutriderDataSet(dataset="Kremer")
> implementation <- 'autoencoder'
> ## Don't show: 
>     # reduce the object size to speed up the calculations
>     ods <- ods[1:400,1:80]
>     implementation <- 'pca'
> ## End(Don't show)
> 
> mcols(ods)$basepairs <- 300 # assign pseudo gene length for filtering
> ods <- filterExpression(ods)
16 genes are filtered out. This is 4.78% of the genes.
> # restrict FDR correction to set of genes of interest per sample
> genesOfInterest <- list(MUC1372 = c("ATPIF1", "UROD", "YBX1", 
+                                      sample(rownames(ods), 25)),
+                         MUC1360 = sample(rownames(ods), 50),
+                         MUC1350 = sample(rownames(ods), 75),
+                         X76619 = sample(rownames(ods), 20),
+                         X74172 = sample(rownames(ods), 150))
> ods <- OUTRIDER(ods, implementation=implementation, subsets=list("exampleGenes"=genesOfInterest))
Fri Sep 12 20:51:26 2025: SizeFactor estimation ...
Fri Sep 12 20:51:26 2025: Controlling for confounders ...
Optimal encoding dimension: 12 
Using estimated q with: 12
Fri Sep 12 20:51:26 2025: Using the pca implementation for controlling.
Fri Sep 12 20:51:26 2025: Used the pca implementation for controlling.
Fri Sep 12 20:51:26 2025: Fitting the data ...
Fri Sep 12 20:51:26 2025: P-value calculation ...
Fri Sep 12 20:51:26 2025: Zscore calculation ...
> 
> plotAberrantPerSample(ods)
Warning in scale_y_log10(limits = c(oneOffset, NA)) :
  log-10 transformation introduced infinite values.
Warning: Removed 74 rows containing missing values or values outside the scale range
(`geom_bar()`).
> plotAberrantPerSample(ods, subsetName="exampleGenes")
Warning in scale_y_log10(limits = c(oneOffset, NA)) :
  log-10 transformation introduced infinite values.
Warning: Removed 4 rows containing missing values or values outside the scale range
(`geom_bar()`).
> 
> plotVolcano(ods, 49)
> plotVolcano(ods, 'MUC1365', basePlot=TRUE)
> plotVolcano(ods, 'MUC1351', basePlot=TRUE, xaxis="log2fc", label=c("NBPF16"))
Warning in .local(object, ...) : Did not find gene(s) NBPF16 to label.
> plotVolcano(ods, 'MUC1372', basePlot=TRUE, subsetName="exampleGenes")
> 
> plotExpressionRank(ods, 35)
> plotExpressionRank(ods, 35, subsetName="exampleGenes")
> plotExpressionRank(ods, "NDUFS5", normalized=FALSE, label="MUC1372",
+     log=FALSE, main="Over expression outlier", basePlot=TRUE)
> 
> plotQQ(ods, 149)
Warning in text.default(x, y, ...) :
  conversion failure on 'CI (α = 0.05)' in 'mbcsToSbcs': for α (U+03B1)
> plotQQ(ods, 149, subsetName="exampleGenes")
Warning in text.default(x, y, ...) :
  conversion failure on 'CI (α = 0.05)' in 'mbcsToSbcs': for α (U+03B1)
> plotQQ(ods, global=TRUE, outlierRatio=0.001)
Warning in text.default(x, y, ...) :
  conversion failure on 'CI (α = 0.05)' in 'mbcsToSbcs': for α (U+03B1)
> 
> plotExpectedVsObservedCounts(ods, 149)
> plotExpectedVsObservedCounts(ods, "ATAD3C", basePlot=TRUE)
> plotExpectedVsObservedCounts(ods, "UROD", subsetName="exampleGenes")
> 
> plotExpressedGenes(ods)
> 
> sex <- sample(c("female", "male"), dim(ods)[2], replace=TRUE)
> colData(ods)$Sex <- sex
> ods <- plotCountCorHeatmap(ods, nColCluster=4, normalized=FALSE)
> ods <- plotCountCorHeatmap(ods, colGroup="Sex", colColSet="Set1")
> table(colData(ods)$clusterNumber_4)

 1  2  3  4 
17 15 17 31 
> 
> plotCountGeneSampleHeatmap(ods, normalized=FALSE)
> plotCountGeneSampleHeatmap(ods, rowGroups="theta", 
+         rowColSet=list(c("white", "darkgreen")))
> 
> plotSizeFactors(ods)
> 
> mcols(ods)$basepairs <- 1
> mcols(ods)$passedFilter <- rowMeans(counts(ods)) > 10
> plotFPKM(ods)
2850 sample-gene combinations are zero. This is 11.2% of the data
Warning in fortify(data, ...) : Arguments in `...` must be used.
✖ Problematic argument:
• alpha = 0.5
ℹ Did you misspell an argument name?
> 
> plotDispEsts(ods, compareDisp=FALSE)
> 
> plotPowerAnalysis(ods)
Warning: Removed 23097 rows containing non-finite outside the scale range
(`stat_smooth()`).
Warning: Removed 3 rows containing missing values or values outside the scale range
(`geom_smooth()`).
> 
> ## Not run: 
> ##D # for speed reasons we only search for 5 different dimensions
> ##D ods <- estimateBestQ(ods, useOHT=FALSE, params=c(3, 10, 20, 35, 50), 
> ##D         implementation=implementation)
> ##D plotEncDimSearch(ods)
> ## End(Not run)
> 
> # To show the pvalues of a sample in a manhattan plot, rowRanges(ods) must 
> # contain the genomic position of each feature or a GRanges object must 
> # be provided 
> ## Not run: 
> ##D # in case rowRanges(ods) is a GRangesList, run this first once to speed up:
> ##D rowRanges(ods) <- unlist(endoapply(rowRanges(ods), range))
> ## End(Not run)
> gr <- GRanges(
+          seqnames=sample(paste0("chr", 1:22), nrow(ods), replace=TRUE),
+          ranges=IRanges(start=runif(nrow(ods), min=0, max=1e5), width=100))
> plotManhattan(ods, "MUC1350", value="pvalue", featureRanges=gr)
Loading required namespace: ggbio
Error:
! The `facets` argument of `facet_grid()` was deprecated in ggplot2
  2.2.0 and is now defunct.
ℹ Please use the `rows` argument instead.
Backtrace:
     ▆
  1. ├─OUTRIDER::plotManhattan(ods, "MUC1350", value = "pvalue", featureRanges = gr)
  2. └─OUTRIDER::plotManhattan(ods, "MUC1350", value = "pvalue", featureRanges = gr)
  3.   └─OUTRIDER (local) .local(object, ...)
  4.     └─OUTRIDER:::plotGrandLinear.adapted(...)
  5.       ├─base::do.call(ggbio::autoplot, c(list(aes.res), args.non))
  6.       ├─ggplot2 (local) `<stndrdGn>`(...)
  7.       └─ggbio (local) `<stndrdGn>`(...)
  8.         └─ggbio (local) .local(object, ...)
  9.           └─ggbio:::.buildFacetsFromArgs(object, args.facets)
 10.             ├─BiocGenerics::do.call(facet_grid, args.facets)
 11.             ├─base::do.call(facet_grid, args.facets)
 12.             └─ggplot2 (local) `<fn>`(scales = "fixed", facets = ~seqnames)
 13.               └─lifecycle::deprecate_stop("2.2.0", "facet_grid(facets)", "facet_grid(rows)")
 14.                 └─lifecycle:::deprecate_stop0(msg)
 15.                   └─rlang::cnd_signal(...)
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
          user system elapsed
OUTRIDER 4.315  1.126    4.98
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
    8.       ├─base::do.call(ggbio::autoplot, c(list(aes.res), args.non))
    9.       ├─ggplot2 (local) `<stndrdGn>`(...)
   10.       └─ggbio (local) `<stndrdGn>`(...)
   11.         └─ggbio (local) .local(object, ...)
   12.           └─ggbio:::.buildFacetsFromArgs(object, args.facets)
   13.             ├─BiocGenerics::do.call(facet_grid, args.facets)
   14.             ├─base::do.call(facet_grid, args.facets)
   15.             └─ggplot2 (local) `<fn>`(scales = "fixed", facets = ~seqnames)
   16.               └─lifecycle::deprecate_stop("2.2.0", "facet_grid(facets)", "facet_grid(rows)")
   17.                 └─lifecycle:::deprecate_stop0(msg)
   18.                   └─rlang::cnd_signal(...)
  
  [ FAIL 1 | WARN 12 | SKIP 0 | PASS 128 ]
  Error: Test failures
  Execution halted
* 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: 2 ERRORs, 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.22-bioc/meat/OUTRIDER.Rcheck/00check.log’
for details.