##############################################################################
##############################################################################
###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:OUTRIDER.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings OUTRIDER_1.26.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/OUTRIDER.Rcheck'
* using R version 4.5.1 (2025-06-13 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'OUTRIDER/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'OUTRIDER' version '1.26.3'
* 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 whether package 'OUTRIDER' can be installed ... OK
* used C++ compiler: 'G__~1.EXE (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 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 for x64 is not available
File 'E:/biocbuild/bbs-3.21-bioc/R/library/OUTRIDER/libs/x64/OUTRIDER.dll':
  Found '_exit', possibly from '_exit' (C)
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* 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  16.94   0.93   17.94
OUTRIDER       13.76   0.38  114.14
estimateBestQ  13.44   0.14   13.59
computePvalues  8.28   0.06  127.16
results         5.89   0.18    6.23
aberrant        3.34   0.05   48.32
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 4 NOTEs
See
  'E:/biocbuild/bbs-3.21-bioc/meat/OUTRIDER.Rcheck/00check.log'
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL OUTRIDER
###
##############################################################################
##############################################################################


* installing to library 'E:/biocbuild/bbs-3.21-bioc/R/library'
* installing *source* package 'OUTRIDER' ...
** this is package 'OUTRIDER' version '1.26.3'
** using staged installation
** libs
using C++ compiler: 'G__~1.EXE (GCC) 14.2.0'
g++ -std=gnu++17  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/RcppArmadillo/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"   -fopenmp -DARMA_DONT_USE_OPENMP   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/RcppArmadillo/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"   -fopenmp -DARMA_DONT_USE_OPENMP   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c loss_n_gradient_functions.cpp -o loss_n_gradient_functions.o
g++ -std=gnu++17 -shared -s -static-libgcc -o OUTRIDER.dll tmp.def RcppExports.o loss_n_gradient_functions.o -fopenmp -LE:/biocbuild/bbs-3.21-bioc/R/bin/x64 -lRlapack -LE:/biocbuild/bbs-3.21-bioc/R/bin/x64 -lRblas -lgfortran -lquadmath -LC:/rtools45/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools45/x86_64-w64-mingw32.static.posix/lib -LE:/biocbuild/bbs-3.21-bioc/R/bin/x64 -lR
installing to E:/biocbuild/bbs-3.21-bioc/R/library/00LOCK-OUTRIDER/00new/OUTRIDER/libs/x64
** 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
** 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 4.5.1 (2025-06-13 ucrt) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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

Attaching package: 'IRanges'

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

    windows

Loading required package: GenomeInfoDb
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 Aug  8 04:59:01 2025: Initial PCA loss: 6.11428600067583"
[1] "Fri Aug  8 04:59:02 2025: Iteration: 1 loss: 4.50083395270077"
[1] "Fri Aug  8 04:59:03 2025: Iteration: 2 loss: 4.42944708919735"
[1] "Fri Aug  8 04:59:03 2025: Iteration: 3 loss: 4.39877300165897"
[1] "Fri Aug  8 04:59:04 2025: Iteration: 4 loss: 4.38899864482785"
[1] "Fri Aug  8 04:59:05 2025: Iteration: 5 loss: 4.38754054968329"
[1] "Fri Aug  8 04:59:06 2025: Iteration: 6 loss: 4.38752302362231"
Time difference of 4.490258 secs
[1] "Fri Aug  8 04:59:06 2025: 6 Final nb-AE loss: 4.38752302362231"
[1] "Fri Aug  8 04:59:07 2025: Initial PCA loss: 6.11428600067583"
[1] "Fri Aug  8 04:59:09 2025: Iteration: 1 loss: 4.50083395270077"
[1] "Fri Aug  8 04:59:10 2025: Iteration: 2 loss: 4.42944708919735"
[1] "Fri Aug  8 04:59:11 2025: Iteration: 3 loss: 4.39877300165897"
[1] "Fri Aug  8 04:59:12 2025: Iteration: 4 loss: 4.38899864482785"
[1] "Fri Aug  8 04:59:12 2025: Iteration: 5 loss: 4.38754054968329"
[1] "Fri Aug  8 04:59:13 2025: Iteration: 6 loss: 4.38752302362231"
Time difference of 5.360768 secs
[1] "Fri Aug  8 04:59:13 2025: 6 Final nb-AE loss: 4.38752302362231"
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 Aug  8 04:59:24 2025: Initial PCA loss: 4.6201288638567"
[1] "Fri Aug  8 04:59:25 2025: Iteration: 1 loss: 4.24743002425873"
[1] "Fri Aug  8 04:59:26 2025: Iteration: 2 loss: 4.24130986518939"
Time difference of 1.350851 secs
[1] "Fri Aug  8 04:59:26 2025: 2 Final nb-AE loss: 4.24130986518939"
[1] "Evaluation loss: 0.609481362161986 for q=3"
[1] "Fri Aug  8 04:59:27 2025: Initial PCA loss: 4.51478859161423"
[1] "Fri Aug  8 04:59:28 2025: Iteration: 1 loss: 4.15196414609752"
[1] "Fri Aug  8 04:59:28 2025: Iteration: 2 loss: 4.13138923095893"
Time difference of 1.351979 secs
[1] "Fri Aug  8 04:59:28 2025: 2 Final nb-AE loss: 4.13138923095893"
[1] "Evaluation loss: 0.55669195510584 for q=4"
[1] "Fri Aug  8 04:59:29 2025: Initial PCA loss: 4.47496591059798"
[1] "Fri Aug  8 04:59:31 2025: Iteration: 1 loss: 4.08239850317234"
[1] "Fri Aug  8 04:59:31 2025: Iteration: 2 loss: 4.0564375282959"
Time difference of 1.392019 secs
[1] "Fri Aug  8 04:59:31 2025: 2 Final nb-AE loss: 4.0564375282959"
[1] "Evaluation loss: 0.47774778700465 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 Aug  8 04:59:58 2025: Initial PCA loss: 7.16457134714849"
[1] "Fri Aug  8 05:00:00 2025: Iteration: 1 loss: 6.82914738092401"
[1] "Fri Aug  8 05:00:01 2025: Iteration: 2 loss: 6.82748931657223"
Time difference of 1.902207 secs
[1] "Fri Aug  8 05:00:01 2025: 2 Final nb-AE loss: 6.82748931657223"
[ FAIL 0 | WARN 5 | SKIP 0 | PASS 131 ]

[ FAIL 0 | WARN 5 | SKIP 0 | PASS 131 ]
> 
> proc.time()
   user  system elapsed 
  99.01    3.01  109.75