##############################################################################
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###
### Running command:
###
###   /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_1.29.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/OUTRIDER.Rcheck’
* using R Under development (unstable) (2025-10-21 r88958)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.8
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘OUTRIDER/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OUTRIDER’ version ‘1.29.0’
* 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: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’
* 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 ... INFO
Note: information on .o files is not available
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
plotFunctions  18.427  0.804  19.396
OUTRIDER       13.322  2.940  14.854
estimateBestQ  13.868  0.269  14.219
computePvalues  3.037  2.075   3.152
* 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:
  
  ══ 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.
  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: 1 ERROR, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.23-bioc/meat/OUTRIDER.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL OUTRIDER
###
##############################################################################
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library’
* installing *source* package ‘OUTRIDER’ ...
** this is package ‘OUTRIDER’ version ‘1.29.0’
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’
using SDK: ‘MacOSX11.3.1.sdk’
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/RcppArmadillo/include' -I/opt/R/x86_64/include    -DARMA_DONT_USE_OPENMP -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppExports.cpp -o RcppExports.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/RcppArmadillo/include' -I/opt/R/x86_64/include    -DARMA_DONT_USE_OPENMP -fPIC  -falign-functions=64 -Wall -g -O2   -c loss_n_gradient_functions.cpp -o loss_n_gradient_functions.o
clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o OUTRIDER.so RcppExports.o loss_n_gradient_functions.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/14.2.0 -L/opt/gfortran/lib -lemutls_w -lheapt_w -lgfortran -lquadmath -F/Library/Frameworks/R.framework/.. -framework R
installing to /Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/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) (2025-10-21 r88958) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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] "Thu Nov 20 23:09:46 2025: Initial PCA loss: 6.09691626331258"
[1] "Thu Nov 20 23:09:48 2025: Iteration: 1 loss: 4.26146461808151"
[1] "Thu Nov 20 23:09:48 2025: Iteration: 2 loss: 4.17137617748764"
[1] "Thu Nov 20 23:09:49 2025: Iteration: 3 loss: 4.12825069391239"
[1] "Thu Nov 20 23:09:50 2025: Iteration: 4 loss: 4.10960169166869"
[1] "Thu Nov 20 23:09:51 2025: Iteration: 5 loss: 4.09741354518853"
[1] "Thu Nov 20 23:09:52 2025: Iteration: 6 loss: 4.09592881574802"
Time difference of 4.80364 secs
[1] "Thu Nov 20 23:09:52 2025: 6 Final nb-AE loss: 4.09592881574802"
[1] "Thu Nov 20 23:09:53 2025: Initial PCA loss: 6.09691626331258"
[1] "Thu Nov 20 23:09:55 2025: Iteration: 1 loss: 4.26146461808151"
[1] "Thu Nov 20 23:09:55 2025: Iteration: 2 loss: 4.17137617748764"
[1] "Thu Nov 20 23:09:56 2025: Iteration: 3 loss: 4.12825069391239"
[1] "Thu Nov 20 23:09:57 2025: Iteration: 4 loss: 4.10960169166869"
[1] "Thu Nov 20 23:09:58 2025: Iteration: 5 loss: 4.09741354518853"
[1] "Thu Nov 20 23:09:58 2025: Iteration: 6 loss: 4.09592881574802"
Time difference of 4.730925 secs
[1] "Thu Nov 20 23:09:58 2025: 6 Final nb-AE loss: 4.09592881574802"
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] "Thu Nov 20 23:10:05 2025: Initial PCA loss: 4.44712693158218"
[1] "Thu Nov 20 23:10:07 2025: Iteration: 1 loss: 4.07197775206475"
[1] "Thu Nov 20 23:10:07 2025: Iteration: 2 loss: 4.05928379006795"
Time difference of 1.463157 secs
[1] "Thu Nov 20 23:10:07 2025: 2 Final nb-AE loss: 4.05928379006795"
[1] "Evaluation loss: 0.352491604052732 for q=3"
[1] "Thu Nov 20 23:10:08 2025: Initial PCA loss: 4.42364222132766"
[1] "Thu Nov 20 23:10:09 2025: Iteration: 1 loss: 3.99640141035262"
[1] "Thu Nov 20 23:10:10 2025: Iteration: 2 loss: 3.98015581248527"
Time difference of 1.361653 secs
[1] "Thu Nov 20 23:10:10 2025: 2 Final nb-AE loss: 3.98015581248527"
[1] "Evaluation loss: 0.354167153038047 for q=4"
[1] "Thu Nov 20 23:10:11 2025: Initial PCA loss: 4.40441866180684"
[1] "Thu Nov 20 23:10:12 2025: Iteration: 1 loss: 3.91902855813004"
[1] "Thu Nov 20 23:10:13 2025: Iteration: 2 loss: 3.90050491834609"
Time difference of 1.504368 secs
[1] "Thu Nov 20 23:10:13 2025: 2 Final nb-AE loss: 3.90050491834609"
[1] "Evaluation loss: 0.469221068720506 for q=5"
Optimal encoding dimension: 4 
Optimal encoding dimension: 50 
Optimal encoding dimension: 20 
Optimal encoding dimension: 2 
Optimal encoding dimension: 4 
[1] "Thu Nov 20 23:10:47 2025: Initial PCA loss: 7.16457134714849"
[1] "Thu Nov 20 23:10:49 2025: Iteration: 1 loss: 6.829134836161"
[1] "Thu Nov 20 23:10:50 2025: Iteration: 2 loss: 6.82748717238399"
Time difference of 1.979297 secs
[1] "Thu Nov 20 23:10:50 2025: 2 Final nb-AE loss: 6.82748717238399"
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.
Execution halted