##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:OUTRIDER.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings OUTRIDER_1.29.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/OUTRIDER.Rcheck’
* using R Under development (unstable) (2025-10-20 r88955)
* 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 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘OUTRIDER/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OUTRIDER’ version ‘1.29.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 23 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: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* 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 ... INFO
Note: information on .o files is not available
* checking sizes of PDF files under ‘inst/doc’ ...* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                          user system elapsed
plotFunctions           23.628  0.612  24.689
estimateBestQ           15.288  0.692  16.335
OUTRIDER                11.507  3.608  13.411
getter_setter_functions  5.435  0.074   5.750
* 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:
  ── Error ('test_methods.R:35:5'): result method ────────────────────────────────
  Error in `expect(nrow(results(ods, round = TRUE)), 3)`: `ok` must be `TRUE` or `FALSE`, not the number 1.
  Backtrace:
      ▆
   1. └─testthat::expect(ok = nrow(results(ods, round = TRUE))) at test_methods.R:35:5
   2.   └─testthat:::check_bool(ok)
   3.     └─testthat:::stop_input_type(...)
   4.       └─rlang::abort(message, ..., call = call, arg = arg)
  
  [ FAIL 1 | WARN 12 | SKIP 2 | PASS 130 ]
  Error:
  ! Test failures.
  Warning message:
  call dbDisconnect() when finished working with a connection 
  Execution halted
* 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 ERROR, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.23-bioc/meat/OUTRIDER.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL OUTRIDER
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’
* installing *source* package ‘OUTRIDER’ ...
** this is package ‘OUTRIDER’ version ‘1.29.0’
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/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
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/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
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.23-bioc/R/lib -L/usr/local/lib -o OUTRIDER.so RcppExports.o loss_n_gradient_functions.o -fopenmp -llapack -L/home/biocbuild/bbs-3.23-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.23-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.23-bioc/R/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 Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences"
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(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

> 
> register(SerialParam())
> 
> test_check("OUTRIDER")
[1] "Fri Nov 21 02:30:06 2025: Initial PCA loss: 6.30204813791489"
[1] "Fri Nov 21 02:30:09 2025: Iteration: 1 loss: 4.8579080191925"
[1] "Fri Nov 21 02:30:09 2025: Iteration: 2 loss: 4.80275898698546"
[1] "Fri Nov 21 02:30:10 2025: Iteration: 3 loss: 4.76360706003829"
[1] "Fri Nov 21 02:30:11 2025: Iteration: 4 loss: 4.72640307588715"
[1] "Fri Nov 21 02:30:12 2025: Iteration: 5 loss: 4.71591135002586"
[1] "Fri Nov 21 02:30:14 2025: Iteration: 6 loss: 4.71306663204402"
Time difference of 6.101418 secs
[1] "Fri Nov 21 02:30:14 2025: 6 Final nb-AE loss: 4.71306663204402"
[1] "Fri Nov 21 02:30:16 2025: Initial PCA loss: 6.30204813791489"
[1] "Fri Nov 21 02:30:20 2025: Iteration: 1 loss: 4.8579080191925"
[1] "Fri Nov 21 02:30:21 2025: Iteration: 2 loss: 4.80275898698546"
[1] "Fri Nov 21 02:30:22 2025: Iteration: 3 loss: 4.76360706003829"
[1] "Fri Nov 21 02:30:23 2025: Iteration: 4 loss: 4.72640307588715"
[1] "Fri Nov 21 02:30:23 2025: Iteration: 5 loss: 4.71591135002586"
[1] "Fri Nov 21 02:30:24 2025: Iteration: 6 loss: 4.71306663204402"
Time difference of 6.326845 secs
[1] "Fri Nov 21 02:30:24 2025: 6 Final nb-AE loss: 4.71306663204402"
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 Nov 21 02:30:30 2025: Initial PCA loss: 4.4534284820349"
[1] "Fri Nov 21 02:30:31 2025: Iteration: 1 loss: 4.11062042454717"
[1] "Fri Nov 21 02:30:31 2025: Iteration: 2 loss: 4.09927243066737"
Time difference of 1.326654 secs
[1] "Fri Nov 21 02:30:31 2025: 2 Final nb-AE loss: 4.09927243066737"
[1] "Evaluation loss: 0.549225950780723 for q=3"
[1] "Fri Nov 21 02:30:32 2025: Initial PCA loss: 4.43167939042909"
[1] "Fri Nov 21 02:30:33 2025: Iteration: 1 loss: 4.04019733129089"
[1] "Fri Nov 21 02:30:34 2025: Iteration: 2 loss: 4.01911450661202"
Time difference of 1.227988 secs
[1] "Fri Nov 21 02:30:34 2025: 2 Final nb-AE loss: 4.01911450661202"
[1] "Evaluation loss: 0.548066350728669 for q=4"
[1] "Fri Nov 21 02:30:35 2025: Initial PCA loss: 4.41058436374299"
[1] "Fri Nov 21 02:30:36 2025: Iteration: 1 loss: 3.9506443984451"
[1] "Fri Nov 21 02:30:36 2025: Iteration: 2 loss: 3.92843554691283"
Time difference of 1.241321 secs
[1] "Fri Nov 21 02:30:36 2025: 2 Final nb-AE loss: 3.92843554691283"
[1] "Evaluation loss: 0.635516006341069 for q=5"
Optimal encoding dimension: 4 
Optimal encoding dimension: 50 
Optimal encoding dimension: 20 
Optimal encoding dimension: 2 
Optimal encoding dimension: 4 
Error in x$.self$finalize() : attempt to apply non-function
[1] "Fri Nov 21 02:31:04 2025: Initial PCA loss: 7.16457134714849"
[1] "Fri Nov 21 02:31:05 2025: Iteration: 1 loss: 6.82914112812595"
[1] "Fri Nov 21 02:31:06 2025: Iteration: 2 loss: 6.82749097859465"
Time difference of 1.569486 secs
[1] "Fri Nov 21 02:31:06 2025: 2 Final nb-AE loss: 6.82749097859465"
Saving _problems/test_methods-35.R
[ FAIL 1 | WARN 12 | SKIP 2 | PASS 130 ]

══ Skipped tests (2) ═══════════════════════════════════════════════════════════
• empty test (2): ,

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_methods.R:35:5'): result method ────────────────────────────────
Error in `expect(nrow(results(ods, round = TRUE)), 3)`: `ok` must be `TRUE` or `FALSE`, not the number 1.
Backtrace:
    ▆
 1. └─testthat::expect(ok = nrow(results(ods, round = TRUE))) at test_methods.R:35:5
 2.   └─testthat:::check_bool(ok)
 3.     └─testthat:::stop_input_type(...)
 4.       └─rlang::abort(message, ..., call = call, arg = arg)

[ FAIL 1 | WARN 12 | SKIP 2 | PASS 130 ]
Error:
! Test failures.
Warning message:
call dbDisconnect() when finished working with a connection 
Execution halted