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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_1.16.3.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/OUTRIDER.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘OUTRIDER/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OUTRIDER’ version ‘1.16.3’
* 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
* 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 R 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 ... OK
* 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 ... OK
* 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
computePvalues   6.607  8.477   5.477
OUTRIDER        10.618  3.899  12.149
findEncodingDim  8.588  0.034   8.639
aberrant         5.554  2.543   3.046
plotFunctions    7.075  0.320   7.421
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.16-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/4.2/Resources/library’
* installing *source* package ‘OUTRIDER’ ...
** using staged installation
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include' -I/usr/local/include   -DARMA_DONT_USE_OPENMP -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include' -I/usr/local/include   -DARMA_DONT_USE_OPENMP -fPIC  -Wall -g -O2  -c loss_n_gradient_functions.cpp -o loss_n_gradient_functions.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/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/usr/local/gfortran/lib/gcc/x86_64-apple-darwin18/8.2.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: warning: dylib (/usr/local/gfortran/lib/libgfortran.dylib) was built for newer macOS version (10.14) than being linked (10.13)
ld: warning: dylib (/usr/local/gfortran/lib/libquadmath.dylib) was built for newer macOS version (10.14) than being linked (10.13)
installing to /Library/Frameworks/R.framework/Versions/4.2/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 4.2.3 (2023-03-15) -- "Shortstop Beagle"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)

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, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

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] "Mon Apr 10 21:48:01 2023: Initial PCA loss: 6.2591227654409"
[1] "Mon Apr 10 21:48:02 2023: Iteration: 1 loss: 4.81321670782819"
[1] "Mon Apr 10 21:48:03 2023: Iteration: 2 loss: 4.72834754412541"
[1] "Mon Apr 10 21:48:04 2023: Iteration: 3 loss: 4.68601905425694"
[1] "Mon Apr 10 21:48:04 2023: Iteration: 4 loss: 4.67269407234438"
[1] "Mon Apr 10 21:48:05 2023: Iteration: 5 loss: 4.66502965123478"
[1] "Mon Apr 10 21:48:05 2023: Iteration: 6 loss: 4.66109502024113"
Time difference of 3.434031 secs
[1] "Mon Apr 10 21:48:05 2023: 6 Final nb-AE loss: 4.66109502024113"
[1] "Mon Apr 10 21:48:06 2023: Initial PCA loss: 6.2591227654409"
[1] "Mon Apr 10 21:48:07 2023: Iteration: 1 loss: 4.81321670782819"
[1] "Mon Apr 10 21:48:08 2023: Iteration: 2 loss: 4.72834754412541"
[1] "Mon Apr 10 21:48:09 2023: Iteration: 3 loss: 4.68601905425694"
[1] "Mon Apr 10 21:48:09 2023: Iteration: 4 loss: 4.67269407234438"
[1] "Mon Apr 10 21:48:10 2023: Iteration: 5 loss: 4.66502965123478"
[1] "Mon Apr 10 21:48:10 2023: Iteration: 6 loss: 4.66109502024113"
Time difference of 3.491937 secs
[1] "Mon Apr 10 21:48:10 2023: 6 Final nb-AE loss: 4.66109502024113"
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] "Mon Apr 10 21:48:23 2023: Initial PCA loss: 4.46377550449446"
[1] "Mon Apr 10 21:48:24 2023: Iteration: 1 loss: 4.11301495832941"
[1] "Mon Apr 10 21:48:25 2023: Iteration: 2 loss: 4.10413540413027"
Time difference of 1.057522 secs
[1] "Mon Apr 10 21:48:25 2023: 2 Final nb-AE loss: 4.10413540413027"
[1] "Evaluation loss: 0.398582317283891 for q=3"
[1] "Mon Apr 10 21:48:25 2023: Initial PCA loss: 4.43997373105908"
[1] "Mon Apr 10 21:48:26 2023: Iteration: 1 loss: 4.04185576748175"
[1] "Mon Apr 10 21:48:27 2023: Iteration: 2 loss: 4.02904111226015"
Time difference of 1.043682 secs
[1] "Mon Apr 10 21:48:27 2023: 2 Final nb-AE loss: 4.02904111226015"
[1] "Evaluation loss: 0.26015990099979 for q=4"
[1] "Mon Apr 10 21:48:28 2023: Initial PCA loss: 4.4166095991099"
[1] "Mon Apr 10 21:48:29 2023: Iteration: 1 loss: 3.95332748903477"
[1] "Mon Apr 10 21:48:29 2023: Iteration: 2 loss: 3.94071337131332"
Time difference of 1.086584 secs
[1] "Mon Apr 10 21:48:29 2023: 2 Final nb-AE loss: 3.94071337131332"
[1] "Evaluation loss: 0.329666442290344 for q=5"
[1] "Mon Apr 10 21:48:36 2023: Initial PCA loss: 6.46616282459584"
[1] "Mon Apr 10 21:48:37 2023: Iteration: 1 loss: 4.81532982163844"
[1] "Mon Apr 10 21:48:38 2023: Iteration: 2 loss: 4.78946214931152"
Time difference of 1.391298 secs
[1] "Mon Apr 10 21:48:38 2023: 2 Final nb-AE loss: 4.78946214931152"
[ FAIL 0 | WARN 32 | SKIP 0 | PASS 103 ]

[ FAIL 0 | WARN 32 | SKIP 0 | PASS 103 ]
> 
> proc.time()
   user  system elapsed 
 58.343   1.282  59.748