##############################################################################
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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_1.22.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/OUTRIDER.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.4
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘OUTRIDER/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OUTRIDER’ version ‘1.22.0’
* 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: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* 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 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 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           33.969  1.394  40.421
findEncodingDim         27.627  0.544  33.268
OUTRIDER                21.244  4.549  27.962
results                  8.617  0.100   9.624
computePvalues           5.761  2.696   7.433
getter_setter_functions  7.638  0.057   8.944
aberrant                 4.653  1.212   5.307
* 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: 5 NOTEs
See
  ‘/Users/biocbuild/bbs-3.19-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/4.4-x86_64/Resources/library’
* installing *source* package ‘OUTRIDER’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using C++11
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-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++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-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++11 -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-darwin20.0/12.2.0 -L/opt/gfortran/lib -lgfortran -lquadmath -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.4-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 version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 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

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 20 09:04:39 2024: Initial PCA loss: 6.25745626087683"
[1] "Thu Jun 20 09:04:43 2024: Iteration: 1 loss: 4.51792490423293"
[1] "Thu Jun 20 09:04:44 2024: Iteration: 2 loss: 4.41531182479163"
[1] "Thu Jun 20 09:04:46 2024: Iteration: 3 loss: 4.36449503359656"
[1] "Thu Jun 20 09:04:48 2024: Iteration: 4 loss: 4.34140760414209"
[1] "Thu Jun 20 09:04:50 2024: Iteration: 5 loss: 4.33088026422663"
[1] "Thu Jun 20 09:04:52 2024: Iteration: 6 loss: 4.32356110545234"
Time difference of 11.17475 secs
[1] "Thu Jun 20 09:04:52 2024: 6 Final nb-AE loss: 4.32356110545234"
[1] "Thu Jun 20 09:04:55 2024: Initial PCA loss: 6.25745626087683"
[1] "Thu Jun 20 09:04:58 2024: Iteration: 1 loss: 4.51792490423293"
[1] "Thu Jun 20 09:05:00 2024: Iteration: 2 loss: 4.41531182479163"
[1] "Thu Jun 20 09:05:02 2024: Iteration: 3 loss: 4.36449503359656"
[1] "Thu Jun 20 09:05:04 2024: Iteration: 4 loss: 4.34140760414209"
[1] "Thu Jun 20 09:05:05 2024: Iteration: 5 loss: 4.33088026422663"
[1] "Thu Jun 20 09:05:07 2024: Iteration: 6 loss: 4.32356110545234"
Time difference of 10.94568 secs
[1] "Thu Jun 20 09:05:07 2024: 6 Final nb-AE loss: 4.32356110545234"
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 20 09:05:42 2024: Initial PCA loss: 4.45967360232336"
[1] "Thu Jun 20 09:05:45 2024: Iteration: 1 loss: 4.09458522832007"
[1] "Thu Jun 20 09:05:47 2024: Iteration: 2 loss: 4.08599890683862"
Time difference of 3.877436 secs
[1] "Thu Jun 20 09:05:47 2024: 2 Final nb-AE loss: 4.08599890683862"
[1] "Evaluation loss: 0.212570991466252 for q=3"
[1] "Thu Jun 20 09:05:49 2024: Initial PCA loss: 4.43482078931978"
[1] "Thu Jun 20 09:05:53 2024: Iteration: 1 loss: 4.02457943783766"
[1] "Thu Jun 20 09:05:54 2024: Iteration: 2 loss: 4.00901056935011"
Time difference of 3.749026 secs
[1] "Thu Jun 20 09:05:54 2024: 2 Final nb-AE loss: 4.00901056935011"
[1] "Evaluation loss: 0.217873075104226 for q=4"
[1] "Thu Jun 20 09:05:57 2024: Initial PCA loss: 4.41088796963224"
[1] "Thu Jun 20 09:06:00 2024: Iteration: 1 loss: 3.93463130225256"
[1] "Thu Jun 20 09:06:02 2024: Iteration: 2 loss: 3.91354581205529"
Time difference of 3.915898 secs
[1] "Thu Jun 20 09:06:02 2024: 2 Final nb-AE loss: 3.91354581205529"
[1] "Evaluation loss: 0.22455833309189 for q=5"
[1] "Thu Jun 20 09:06:26 2024: Initial PCA loss: 7.16457134714849"
[1] "Thu Jun 20 09:06:31 2024: Iteration: 1 loss: 6.82914691619536"
[1] "Thu Jun 20 09:06:33 2024: Iteration: 2 loss: 6.82749524418065"
Time difference of 4.398842 secs
[1] "Thu Jun 20 09:06:33 2024: 2 Final nb-AE loss: 6.82749524418065"
[ FAIL 0 | WARN 10 | SKIP 0 | PASS 115 ]

[ FAIL 0 | WARN 10 | SKIP 0 | PASS 115 ]
> 
> proc.time()
   user  system elapsed 
173.830   4.174 203.174