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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:OUTRIDER.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings OUTRIDER_1.23.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/OUTRIDER.Rcheck’
* using R version 4.4.0 RC (2024-04-16 r86468)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘OUTRIDER/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OUTRIDER’ version ‘1.23.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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 11.4.0-1ubuntu1~22.04) 11.4.0’
* checking C++ specification ... NOTE
  Specified C++11: please drop specification unless essential
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub is invalid DCF.
* 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.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... NOTE
checkRd: (-1) results.Rd:48-50: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) results.Rd:51-52: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) results.Rd:53-54: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) results.Rd:55: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) results.Rd:56-57: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) results.Rd:58-60: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) results.Rd:61-62: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) results.Rd:63-64: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) results.Rd:65-66: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) results.Rd:67: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) results.Rd:68-71: Lost braces in \itemize; \value handles \item{}{} directly
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
OUTRIDER              11.472  3.340  14.144
findEncodingDim       13.864  0.485  14.524
plotFunctions         13.716  0.252  13.986
computePvalues         3.158  3.292   4.565
aberrant               3.963  2.023   5.030
computeGeneLength      3.765  0.454   6.561
filterExpression       3.031  0.068   5.535
controlForConfounders  2.452  0.173   7.308
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 5 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/OUTRIDER.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL OUTRIDER
###
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* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘OUTRIDER’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
using C++11
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/RcppArmadillo/include' -I/usr/local/include   -fopenmp -DARMA_DONT_USE_OPENMP -fpic  -g -O2  -Wall  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/RcppArmadillo/include' -I/usr/local/include   -fopenmp -DARMA_DONT_USE_OPENMP -fpic  -g -O2  -Wall  -c loss_n_gradient_functions.cpp -o loss_n_gradient_functions.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.20-bioc/R/lib -L/usr/local/lib -o OUTRIDER.so RcppExports.o loss_n_gradient_functions.o -fopenmp -llapack -L/home/biocbuild/bbs-3.20-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.20-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.20-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 version 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup"
Copyright (C) 2024 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

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, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply,
    union, 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: 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] "Thu Jun 27 01:56:55 2024: Initial PCA loss: 6.20320336341779"
[1] "Thu Jun 27 01:56:56 2024: Iteration: 1 loss: 4.55971445444721"
[1] "Thu Jun 27 01:56:57 2024: Iteration: 2 loss: 4.4032778281008"
[1] "Thu Jun 27 01:56:57 2024: Iteration: 3 loss: 4.34675992279274"
[1] "Thu Jun 27 01:56:58 2024: Iteration: 4 loss: 4.33085709786114"
[1] "Thu Jun 27 01:56:58 2024: Iteration: 5 loss: 4.32321755847952"
[1] "Thu Jun 27 01:56:59 2024: Iteration: 6 loss: 4.32240723309635"
Time difference of 3.431858 secs
[1] "Thu Jun 27 01:56:59 2024: 6 Final nb-AE loss: 4.32240723309635"
[1] "Thu Jun 27 01:57:00 2024: Initial PCA loss: 6.20320336341779"
[1] "Thu Jun 27 01:57:01 2024: Iteration: 1 loss: 4.55971445444721"
[1] "Thu Jun 27 01:57:02 2024: Iteration: 2 loss: 4.4032778281008"
[1] "Thu Jun 27 01:57:02 2024: Iteration: 3 loss: 4.34675992279274"
[1] "Thu Jun 27 01:57:03 2024: Iteration: 4 loss: 4.33085709786114"
[1] "Thu Jun 27 01:57:03 2024: Iteration: 5 loss: 4.32321755847952"
[1] "Thu Jun 27 01:57:04 2024: Iteration: 6 loss: 4.32240723309635"
Time difference of 3.637845 secs
[1] "Thu Jun 27 01:57:04 2024: 6 Final nb-AE loss: 4.32240723309635"
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 Jun 27 01:57:18 2024: Initial PCA loss: 4.47019016765934"
[1] "Thu Jun 27 01:57:21 2024: Iteration: 1 loss: 4.07573404327167"
[1] "Thu Jun 27 01:57:23 2024: Iteration: 2 loss: 4.05788995111528"
Time difference of 4.083982 secs
[1] "Thu Jun 27 01:57:23 2024: 2 Final nb-AE loss: 4.05788995111528"
[1] "Evaluation loss: 0.296200356135637 for q=3"
[1] "Thu Jun 27 01:57:25 2024: Initial PCA loss: 4.43717075084769"
[1] "Thu Jun 27 01:57:26 2024: Iteration: 1 loss: 4.01084843539471"
[1] "Thu Jun 27 01:57:27 2024: Iteration: 2 loss: 3.97860238335687"
Time difference of 1.420087 secs
[1] "Thu Jun 27 01:57:27 2024: 2 Final nb-AE loss: 3.97860238335687"
[1] "Evaluation loss: 0.149781397060088 for q=4"
[1] "Thu Jun 27 01:57:28 2024: Initial PCA loss: 4.4158868665861"
[1] "Thu Jun 27 01:57:30 2024: Iteration: 1 loss: 3.93805749469994"
[1] "Thu Jun 27 01:57:32 2024: Iteration: 2 loss: 3.90201167447811"
Time difference of 4.047435 secs
[1] "Thu Jun 27 01:57:32 2024: 2 Final nb-AE loss: 3.90201167447811"
[1] "Evaluation loss: 0.213555410902188 for q=5"
[1] "Thu Jun 27 01:57:40 2024: Initial PCA loss: 7.16457134714849"
[1] "Thu Jun 27 01:57:41 2024: Iteration: 1 loss: 6.82915165643358"
[1] "Thu Jun 27 01:57:42 2024: Iteration: 2 loss: 6.82749554346071"
Time difference of 1.679273 secs
[1] "Thu Jun 27 01:57:42 2024: 2 Final nb-AE loss: 6.82749554346071"
[ FAIL 0 | WARN 10 | SKIP 0 | PASS 115 ]

[ FAIL 0 | WARN 10 | SKIP 0 | PASS 115 ]
> 
> proc.time()
   user  system elapsed 
 90.849   2.068  96.825