##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:OUTRIDER.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings OUTRIDER_1.27.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/OUTRIDER.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 ‘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: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’
* 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 ... 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 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 10:18:42 2025: SizeFactor estimation ...
Fri Sep 12 10:18:42 2025: Controlling for confounders ...
Optimal encoding dimension: 12 
Using estimated q with: 12
Fri Sep 12 10:18:42 2025: Using the pca implementation for controlling.
Fri Sep 12 10:18:43 2025: Used the pca implementation for controlling.
Fri Sep 12 10:18:43 2025: Fitting the data ...
Fri Sep 12 10:18:44 2025: P-value calculation ...
Fri Sep 12 10:18:44 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
estimateBestQ           16.975  0.903  19.175
OUTRIDER                12.828  2.993  17.265
computePvalues           2.973  2.618   4.758
getter_setter_functions  4.616  0.190   6.887
* 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
  ‘/home/biocbuild/bbs-3.22-bioc/meat/OUTRIDER.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL OUTRIDER
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’
* installing *source* package ‘OUTRIDER’ ...
** this is package ‘OUTRIDER’ version ‘1.27.2’
** using staged installation
** libs
using C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0/site-library/RcppArmadillo/include' -I/usr/local/include   -fopenmp -DARMA_DONT_USE_OPENMP -fPIC  -g -O2  -Wall -Werror=format-security  -c RcppExports.cpp -o RcppExports.o
In file included from /home/biocbuild/R/R-4.5.0/site-library/RcppArmadillo/include/RcppArmadillo.h:29,
                 from RcppExports.cpp:4:
/home/biocbuild/R/R-4.5.0/site-library/RcppArmadillo/include/RcppArmadillo/version/arma.h:71:153: note: ‘#pragma message: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.’
   71 |         #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.")
      |                                                                                                                                                         ^
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0/site-library/RcppArmadillo/include' -I/usr/local/include   -fopenmp -DARMA_DONT_USE_OPENMP -fPIC  -g -O2  -Wall -Werror=format-security  -c loss_n_gradient_functions.cpp -o loss_n_gradient_functions.o
In file included from /home/biocbuild/R/R-4.5.0/site-library/RcppArmadillo/include/RcppArmadillo.h:29,
                 from loss_n_gradient_functions.cpp:4:
/home/biocbuild/R/R-4.5.0/site-library/RcppArmadillo/include/RcppArmadillo/version/arma.h:71:153: note: ‘#pragma message: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.’
   71 |         #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.")
      |                                                                                                                                                         ^
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -shared -L/home/biocbuild/R/R-4.5.0/lib -L/usr/local/lib -o OUTRIDER.so RcppExports.o loss_n_gradient_functions.o -fopenmp -lopenblas -lgfortran -lm -L/home/biocbuild/R/R-4.5.0/lib -lR
installing to /home/biocbuild/R/R-4.5.0/site-library/00LOCK-OUTRIDER/00new/OUTRIDER/libs
** 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
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (OUTRIDER)

R version 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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(OUTRIDER)
Loading required package: BiocParallel
Loading required package: GenomicFeatures
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
Loading required package: stats4

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: GenomicRanges
Loading required package: AnnotationDbi
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")'.

Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'matrixStats'

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

    anyMissing, rowMedians


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

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

    rowMedians

Loading required package: data.table

Attaching package: 'data.table'

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

    shift

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

    shift

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

    shift

The following objects are masked from 'package:S4Vectors':

    first, second

> 
> register(SerialParam())
> 
> test_check("OUTRIDER")
[1] "Tue Sep  9 09:47:29 2025: Initial PCA loss: 6.26163874597201"
[1] "Tue Sep  9 09:47:31 2025: Iteration: 1 loss: 4.61274364487784"
[1] "Tue Sep  9 09:47:32 2025: Iteration: 2 loss: 4.54597124864171"
[1] "Tue Sep  9 09:47:32 2025: Iteration: 3 loss: 4.51903738160059"
[1] "Tue Sep  9 09:47:33 2025: Iteration: 4 loss: 4.50456127540118"
[1] "Tue Sep  9 09:47:34 2025: Iteration: 5 loss: 4.48974111339921"
[1] "Tue Sep  9 09:47:35 2025: Iteration: 6 loss: 4.47737785451903"
Time difference of 5.673723 secs
[1] "Tue Sep  9 09:47:35 2025: 6 Final nb-AE loss: 4.47737785451903"
[1] "Tue Sep  9 09:47:37 2025: Initial PCA loss: 6.26163874597201"
[1] "Tue Sep  9 09:47:39 2025: Iteration: 1 loss: 4.61274364487784"
[1] "Tue Sep  9 09:47:40 2025: Iteration: 2 loss: 4.54597124864171"
[1] "Tue Sep  9 09:47:41 2025: Iteration: 3 loss: 4.51903738160059"
[1] "Tue Sep  9 09:47:42 2025: Iteration: 4 loss: 4.50456127540118"
[1] "Tue Sep  9 09:47:42 2025: Iteration: 5 loss: 4.48974111339921"
[1] "Tue Sep  9 09:47:43 2025: Iteration: 6 loss: 4.47737785451903"
Time difference of 5.73945 secs
[1] "Tue Sep  9 09:47:43 2025: 6 Final nb-AE loss: 4.47737785451903"
class: OutriderDataSet
class: RangedSummarizedExperiment 
dim: 100 50 
metadata(1): version
assays(1): counts
rownames(100): ENSG00000223972.4 ENSG00000227232.4 ...
  ENSG00000107404.13 ENSG00000162576.12
rowData names(0):
colnames(50): GTEX.UPK5.0426.SM.3GAEK GTEX.WFG7.2026.SM.3GIL7 ...
  GTEX.11UD2.2526.SM.5CVNU GTEX.13O61.1426.SM.5KM3D
colData names(1): sampleID
[1] "Tue Sep  9 09:47:52 2025: Initial PCA loss: 4.44436014904527"
[1] "Tue Sep  9 09:47:54 2025: Iteration: 1 loss: 4.08076982033188"
[1] "Tue Sep  9 09:47:55 2025: Iteration: 2 loss: 4.06786639700012"
Time difference of 2.040634 secs
[1] "Tue Sep  9 09:47:55 2025: 2 Final nb-AE loss: 4.06786639700012"
[1] "Evaluation loss: 0.241009668112005 for q=3"
[1] "Tue Sep  9 09:47:56 2025: Initial PCA loss: 4.42060196494994"
[1] "Tue Sep  9 09:47:58 2025: Iteration: 1 loss: 4.00353496662085"
[1] "Tue Sep  9 09:47:59 2025: Iteration: 2 loss: 3.98352408629492"
Time difference of 2.06956 secs
[1] "Tue Sep  9 09:47:59 2025: 2 Final nb-AE loss: 3.98352408629492"
[1] "Evaluation loss: 0.286096376334896 for q=4"
[1] "Tue Sep  9 09:48:00 2025: Initial PCA loss: 4.39943903038031"
[1] "Tue Sep  9 09:48:02 2025: Iteration: 1 loss: 3.93057337393919"
[1] "Tue Sep  9 09:48:03 2025: Iteration: 2 loss: 3.90202648797038"
Time difference of 1.928 secs
[1] "Tue Sep  9 09:48:03 2025: 2 Final nb-AE loss: 3.90202648797038"
[1] "Evaluation loss: 0.260278862625752 for q=5"
Optimal encoding dimension: 4 
Optimal encoding dimension: 50 
Optimal encoding dimension: 20 
Optimal encoding dimension: 2 
Optimal encoding dimension: 4 
[1] "Tue Sep  9 09:48:29 2025: Initial PCA loss: 7.16457134714849"
[1] "Tue Sep  9 09:48:31 2025: Iteration: 1 loss: 6.82914904822917"
[1] "Tue Sep  9 09:48:32 2025: Iteration: 2 loss: 6.82749374530494"
Time difference of 2.255547 secs
[1] "Tue Sep  9 09:48:32 2025: 2 Final nb-AE loss: 6.82749374530494"
[ FAIL 0 | WARN 11 | SKIP 0 | PASS 131 ]

[ FAIL 0 | WARN 11 | SKIP 0 | PASS 131 ]
> 
> proc.time()
   user  system elapsed 
107.993   2.433 110.702 

R version 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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(OUTRIDER)
Loading required package: BiocParallel
Loading required package: GenomicFeatures
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
Loading required package: stats4

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: GenomicRanges
Loading required package: AnnotationDbi
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")'.

Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'matrixStats'

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

    anyMissing, rowMedians


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

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

    rowMedians

Loading required package: data.table

Attaching package: 'data.table'

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

    shift

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

    shift

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

    shift

The following objects are masked from 'package:S4Vectors':

    first, second

> 
> register(SerialParam())
> 
> test_check("OUTRIDER")
[1] "Fri Sep 12 10:19:33 2025: Initial PCA loss: 6.02198671707807"
[1] "Fri Sep 12 10:19:34 2025: Iteration: 1 loss: 4.35594779072543"
[1] "Fri Sep 12 10:19:35 2025: Iteration: 2 loss: 4.28577049644644"
[1] "Fri Sep 12 10:19:36 2025: Iteration: 3 loss: 4.26816326810787"
[1] "Fri Sep 12 10:19:37 2025: Iteration: 4 loss: 4.26128703133725"
[1] "Fri Sep 12 10:19:38 2025: Iteration: 5 loss: 4.25751015569151"
[1] "Fri Sep 12 10:19:39 2025: Iteration: 6 loss: 4.25454375893969"
Time difference of 5.760273 secs
[1] "Fri Sep 12 10:19:39 2025: 6 Final nb-AE loss: 4.25454375893969"
[1] "Fri Sep 12 10:19:41 2025: Initial PCA loss: 6.02198671707807"
[1] "Fri Sep 12 10:19:43 2025: Iteration: 1 loss: 4.35594779072543"
[1] "Fri Sep 12 10:19:44 2025: Iteration: 2 loss: 4.28577049644644"
[1] "Fri Sep 12 10:19:44 2025: Iteration: 3 loss: 4.26816326810787"
[1] "Fri Sep 12 10:19:45 2025: Iteration: 4 loss: 4.26128703133725"
[1] "Fri Sep 12 10:19:46 2025: Iteration: 5 loss: 4.25751015569151"
[1] "Fri Sep 12 10:19:47 2025: Iteration: 6 loss: 4.25454375893969"
Time difference of 5.66898 secs
[1] "Fri Sep 12 10:19:47 2025: 6 Final nb-AE loss: 4.25454375893969"
class: OutriderDataSet
class: RangedSummarizedExperiment 
dim: 100 50 
metadata(1): version
assays(1): counts
rownames(100): ENSG00000223972.4 ENSG00000227232.4 ...
  ENSG00000107404.13 ENSG00000162576.12
rowData names(0):
colnames(50): GTEX.UPK5.0426.SM.3GAEK GTEX.WFG7.2026.SM.3GIL7 ...
  GTEX.11UD2.2526.SM.5CVNU GTEX.13O61.1426.SM.5KM3D
colData names(1): sampleID
[1] "Fri Sep 12 10:19:57 2025: Initial PCA loss: 4.52343539290159"
[1] "Fri Sep 12 10:19:59 2025: Iteration: 1 loss: 4.21736873299796"
[1] "Fri Sep 12 10:20:00 2025: Iteration: 2 loss: 4.19879456272413"
Time difference of 2.145809 secs
[1] "Fri Sep 12 10:20:00 2025: 2 Final nb-AE loss: 4.19879456272413"
[1] "Evaluation loss: 0.481130171173405 for q=3"
[1] "Fri Sep 12 10:20:02 2025: Initial PCA loss: 4.46841044116657"
[1] "Fri Sep 12 10:20:04 2025: Iteration: 1 loss: 4.05400043791354"
[1] "Fri Sep 12 10:20:05 2025: Iteration: 2 loss: 4.04704009143373"
Time difference of 2.073386 secs
[1] "Fri Sep 12 10:20:05 2025: 2 Final nb-AE loss: 4.04704009143373"
[1] "Evaluation loss: 0.465167207597193 for q=4"
[1] "Fri Sep 12 10:20:06 2025: Initial PCA loss: 4.44298409768445"
[1] "Fri Sep 12 10:20:07 2025: Iteration: 1 loss: 3.98073407144776"
[1] "Fri Sep 12 10:20:08 2025: Iteration: 2 loss: 3.97143178097336"
Time difference of 1.804368 secs
[1] "Fri Sep 12 10:20:08 2025: 2 Final nb-AE loss: 3.97143178097336"
[1] "Evaluation loss: 0.457307381312658 for q=5"
Optimal encoding dimension: 4 
Optimal encoding dimension: 50 
Optimal encoding dimension: 20 
Optimal encoding dimension: 2 
Optimal encoding dimension: 4 
[1] "Fri Sep 12 10:20:39 2025: Initial PCA loss: 7.16457134714849"
[1] "Fri Sep 12 10:20:42 2025: Iteration: 1 loss: 6.82914904822917"
[1] "Fri Sep 12 10:20:43 2025: Iteration: 2 loss: 6.82749374530494"
Time difference of 2.441706 secs
[1] "Fri Sep 12 10:20:43 2025: 2 Final nb-AE loss: 6.82749374530494"
[ FAIL 1 | WARN 12 | SKIP 0 | PASS 128 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_plotting.R:87:5'): plotting ────────────────────────────────────
<lifecycle_error_deprecated/defunctError/rlang_error/error/condition>
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. ├─testthat::expect_is(...) at test_plotting.R:87:5
  2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
  3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
  4. ├─OUTRIDER::plotManhattan(ods, "sample_1", featureRanges = gr)
  5. └─OUTRIDER::plotManhattan(ods, "sample_1", featureRanges = gr)
  6.   └─OUTRIDER (local) .local(object, ...)
  7.     └─OUTRIDER:::plotGrandLinear.adapted(...)
  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