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This page was generated on 2022-01-21 13:06:48 -0500 (Fri, 21 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4329
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4079
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4140
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for OUTRIDER on tokay2


To the developers/maintainers of the OUTRIDER package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/OUTRIDER.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1356/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
OUTRIDER 1.12.0  (landing page)
Christian Mertes
Snapshot Date: 2022-01-20 01:55:04 -0500 (Thu, 20 Jan 2022)
git_url: https://git.bioconductor.org/packages/OUTRIDER
git_branch: RELEASE_3_14
git_last_commit: 2aa8599
git_last_commit_date: 2021-10-26 12:45:42 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: OUTRIDER
Version: 1.12.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:OUTRIDER.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings OUTRIDER_1.12.0.tar.gz
StartedAt: 2022-01-21 00:11:24 -0500 (Fri, 21 Jan 2022)
EndedAt: 2022-01-21 00:29:53 -0500 (Fri, 21 Jan 2022)
EllapsedTime: 1108.4 seconds
RetCode: 0
Status:   OK  
CheckDir: OUTRIDER.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:OUTRIDER.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings OUTRIDER_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/OUTRIDER.Rcheck'
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'OUTRIDER/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'OUTRIDER' version '1.12.0'
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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
Namespace in Imports field not imported from: 'Rcpp'
  All declared Imports should be used.
* 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 for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.14-bioc/R/library/OUTRIDER/libs/i386/OUTRIDER.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)
File 'C:/Users/biocbuild/bbs-3.14-bioc/R/library/OUTRIDER/libs/x64/OUTRIDER.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)

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. 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                         user system elapsed
findEncodingDim         31.84   0.04   34.12
plotFunctions           11.91   0.35   12.55
getter_setter_functions  9.80   0.00   12.14
OUTRIDER                 7.92   0.61   47.58
aberrant                 5.52   0.00   46.60
results                  5.29   0.01    5.31
computePvalues           3.50   0.03   38.33
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                         user system elapsed
findEncodingDim         25.36   0.03   25.45
plotFunctions           11.39   0.17   11.56
OUTRIDER                 8.00   0.17   38.90
getter_setter_functions  6.92   0.00    6.92
results                  6.69   0.05    6.73
computePvalues           4.95   0.00   35.83
aberrant                 4.82   0.01   43.51
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/OUTRIDER.Rcheck/00check.log'
for details.



Installation output

OUTRIDER.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/OUTRIDER_1.12.0.tar.gz && rm -rf OUTRIDER.buildbin-libdir && mkdir OUTRIDER.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=OUTRIDER.buildbin-libdir OUTRIDER_1.12.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL OUTRIDER_1.12.0.zip && rm OUTRIDER_1.12.0.tar.gz OUTRIDER_1.12.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  711k  100  711k    0     0  2114k      0 --:--:-- --:--:-- --:--:-- 2122k

install for i386

* installing *source* package 'OUTRIDER' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include'   -I"C:/extsoft/include"  -fopenmp -DARMA_DONT_USE_OPENMP   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include'   -I"C:/extsoft/include"  -fopenmp -DARMA_DONT_USE_OPENMP   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c loss_n_gradient_functions.cpp -o loss_n_gradient_functions.o
C:/rtools40/mingw32/bin/g++ -shared -s -static-libgcc -o OUTRIDER.dll tmp.def RcppExports.o loss_n_gradient_functions.o -fopenmp -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/i386 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/i386 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/OUTRIDER.buildbin-libdir/00LOCK-OUTRIDER/00new/OUTRIDER/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'OUTRIDER'
    finding HTML links ... done
    OUTRIDER                                html  
    OutriderDataSet-class                   html  
    aberrant                                html  
    computeGeneLength                       html  
    computeLatentSpace                      html  
    computePvalues                          html  
    computeZscores                          html  
    controlForConfounders                   html  
    counts                                  html  
    estimateBestQ                           html  
    filterExpression                        html  
    findEncodingDim                         html  
    fit                                     html  
    fpkm                                    html  
    getter_setter_functions                 html  
    makeExampleOutriderDataSet              html  
    normalizationFactors                    html  
    plotFunctions                           html  
    results                                 html  
    sampleExclusionMask                     html  
    sizeFactors                             html  
** 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

install for x64

* installing *source* package 'OUTRIDER' ...
** libs
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include'   -I"C:/extsoft/include"  -fopenmp -DARMA_DONT_USE_OPENMP   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include'   -I"C:/extsoft/include"  -fopenmp -DARMA_DONT_USE_OPENMP   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c loss_n_gradient_functions.cpp -o loss_n_gradient_functions.o
C:/rtools40/mingw64/bin/g++ -shared -s -static-libgcc -o OUTRIDER.dll tmp.def RcppExports.o loss_n_gradient_functions.o -fopenmp -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/x64 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/OUTRIDER.buildbin-libdir/OUTRIDER/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'OUTRIDER' as OUTRIDER_1.12.0.zip
* DONE (OUTRIDER)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'OUTRIDER' successfully unpacked and MD5 sums checked

Tests output

OUTRIDER.Rcheck/tests_i386/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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, 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

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 Jan 21 00:26:26 2022: Initial PCA loss: 6.18687872799884"
[1] "Fri Jan 21 00:26:28 2022: Iteration: 1 loss: 4.59467714012092"
[1] "Fri Jan 21 00:26:29 2022: Iteration: 2 loss: 4.54266016243574"
[1] "Fri Jan 21 00:26:31 2022: Iteration: 3 loss: 4.51787635087694"
[1] "Fri Jan 21 00:26:32 2022: Iteration: 4 loss: 4.50014817638679"
[1] "Fri Jan 21 00:26:33 2022: Iteration: 5 loss: 4.48437859102388"
[1] "Fri Jan 21 00:26:35 2022: Iteration: 6 loss: 4.47148346329339"
Time difference of 8.000006 secs
[1] "Fri Jan 21 00:26:35 2022: 6 Final nb-AE loss: 4.47148346329339"
[1] "Fri Jan 21 00:26:37 2022: Initial PCA loss: 6.18687872799884"
[1] "Fri Jan 21 00:26:39 2022: Iteration: 1 loss: 4.59467714012092"
[1] "Fri Jan 21 00:26:41 2022: Iteration: 2 loss: 4.54266016243574"
[1] "Fri Jan 21 00:26:42 2022: Iteration: 3 loss: 4.51787635087694"
[1] "Fri Jan 21 00:26:43 2022: Iteration: 4 loss: 4.50014817638679"
[1] "Fri Jan 21 00:26:44 2022: Iteration: 5 loss: 4.48437859102388"
[1] "Fri Jan 21 00:26:46 2022: Iteration: 6 loss: 4.47148346329339"
Time difference of 8.140664 secs
[1] "Fri Jan 21 00:26:46 2022: 6 Final nb-AE loss: 4.47148346329339"
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 Jan 21 00:27:07 2022: Initial PCA loss: 4.49720195740342"
[1] "Fri Jan 21 00:27:10 2022: Iteration: 1 loss: 4.14568573854352"
[1] "Fri Jan 21 00:27:11 2022: Iteration: 2 loss: 4.11743344427288"
Time difference of 2.828137 secs
[1] "Fri Jan 21 00:27:11 2022: 2 Final nb-AE loss: 4.11743344427288"
[1] "Evaluation loss: 0.248399368914935 for q=3"
[1] "Fri Jan 21 00:27:13 2022: Initial PCA loss: 4.45552822528247"
[1] "Fri Jan 21 00:27:16 2022: Iteration: 1 loss: 4.08042971594717"
[1] "Fri Jan 21 00:27:18 2022: Iteration: 2 loss: 4.05698783647946"
Time difference of 3.984398 secs
[1] "Fri Jan 21 00:27:18 2022: 2 Final nb-AE loss: 4.05698783647946"
[1] "Evaluation loss: 0.281031114361757 for q=4"
[1] "Fri Jan 21 00:27:20 2022: Initial PCA loss: 4.43207736074168"
[1] "Fri Jan 21 00:27:24 2022: Iteration: 1 loss: 4.01774906416564"
[1] "Fri Jan 21 00:27:26 2022: Iteration: 2 loss: 3.98836079589511"
Time difference of 3.906268 secs
[1] "Fri Jan 21 00:27:26 2022: 2 Final nb-AE loss: 3.98836079589511"
[1] "Evaluation loss: 0.213750430743907 for q=5"
[1] "Fri Jan 21 00:27:42 2022: Initial PCA loss: 6.46616282459584"
[1] "Fri Jan 21 00:27:45 2022: Iteration: 1 loss: 4.81544153905003"
[1] "Fri Jan 21 00:27:46 2022: Iteration: 2 loss: 4.78966886254391"
Time difference of 3.796896 secs
[1] "Fri Jan 21 00:27:46 2022: 2 Final nb-AE loss: 4.78966886254391"
Error in x$.self$finalize() : attempt to apply non-function
[ FAIL 0 | WARN 2 | SKIP 0 | PASS 103 ]
> 
> proc.time()
   user  system elapsed 
 110.73    2.09  112.82 

OUTRIDER.Rcheck/tests_x64/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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, 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

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 Jan 21 00:28:18 2022: Initial PCA loss: 6.29620974216952"
[1] "Fri Jan 21 00:28:21 2022: Iteration: 1 loss: 4.65394157436641"
[1] "Fri Jan 21 00:28:22 2022: Iteration: 2 loss: 4.53524423705431"
[1] "Fri Jan 21 00:28:24 2022: Iteration: 3 loss: 4.48372136283611"
[1] "Fri Jan 21 00:28:25 2022: Iteration: 4 loss: 4.45811947553087"
[1] "Fri Jan 21 00:28:26 2022: Iteration: 5 loss: 4.44638999804708"
[1] "Fri Jan 21 00:28:27 2022: Iteration: 6 loss: 4.44167570499838"
Time difference of 7.796908 secs
[1] "Fri Jan 21 00:28:27 2022: 6 Final nb-AE loss: 4.44167570499838"
[1] "Fri Jan 21 00:28:29 2022: Initial PCA loss: 6.29620974216952"
[1] "Fri Jan 21 00:28:32 2022: Iteration: 1 loss: 4.65394157436641"
[1] "Fri Jan 21 00:28:33 2022: Iteration: 2 loss: 4.53524423705431"
[1] "Fri Jan 21 00:28:34 2022: Iteration: 3 loss: 4.48372136283611"
[1] "Fri Jan 21 00:28:35 2022: Iteration: 4 loss: 4.45811947553087"
[1] "Fri Jan 21 00:28:37 2022: Iteration: 5 loss: 4.44638999804708"
[1] "Fri Jan 21 00:28:38 2022: Iteration: 6 loss: 4.44167570499838"
Time difference of 7.515659 secs
[1] "Fri Jan 21 00:28:38 2022: 6 Final nb-AE loss: 4.44167570499838"
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 Jan 21 00:28:57 2022: Initial PCA loss: 4.49556982204972"
[1] "Fri Jan 21 00:29:00 2022: Iteration: 1 loss: 4.16033804598975"
[1] "Fri Jan 21 00:29:01 2022: Iteration: 2 loss: 4.15624145847388"
Time difference of 2.640665 secs
[1] "Fri Jan 21 00:29:01 2022: 2 Final nb-AE loss: 4.15624145847388"
[1] "Evaluation loss: 0.552982281892009 for q=3"
[1] "Fri Jan 21 00:29:02 2022: Initial PCA loss: 4.47038948997318"
[1] "Fri Jan 21 00:29:05 2022: Iteration: 1 loss: 4.08463968395636"
[1] "Fri Jan 21 00:29:06 2022: Iteration: 2 loss: 4.07618477047587"
Time difference of 2.578175 secs
[1] "Fri Jan 21 00:29:06 2022: 2 Final nb-AE loss: 4.07618477047587"
[1] "Evaluation loss: 0.480501435791035 for q=4"
[1] "Fri Jan 21 00:29:07 2022: Initial PCA loss: 4.44521312183557"
[1] "Fri Jan 21 00:29:10 2022: Iteration: 1 loss: 4.00210815963701"
[1] "Fri Jan 21 00:29:11 2022: Iteration: 2 loss: 3.98781728323097"
Time difference of 2.765669 secs
[1] "Fri Jan 21 00:29:11 2022: 2 Final nb-AE loss: 3.98781728323097"
[1] "Evaluation loss: 0.478098975093027 for q=5"
[1] "Fri Jan 21 00:29:25 2022: Initial PCA loss: 6.46616282459584"
[1] "Fri Jan 21 00:29:28 2022: Iteration: 1 loss: 4.81544153905003"
[1] "Fri Jan 21 00:29:29 2022: Iteration: 2 loss: 4.78966886254391"
Time difference of 3.125015 secs
[1] "Fri Jan 21 00:29:29 2022: 2 Final nb-AE loss: 4.78966886254391"
[ FAIL 0 | WARN 2 | SKIP 0 | PASS 103 ]
> 
> proc.time()
   user  system elapsed 
 100.50    0.89  101.45 

Example timings

OUTRIDER.Rcheck/examples_i386/OUTRIDER-Ex.timings

nameusersystemelapsed
OUTRIDER 7.92 0.6147.58
OutriderDataSet-class1.720.101.86
aberrant 5.52 0.0046.60
computeGeneLength1.730.081.81
computeLatentSpace1.350.001.34
computePvalues 3.50 0.0338.33
computeZscores2.860.012.92
controlForConfounders3.310.023.35
counts1.30.01.3
estimateBestQ1.280.001.28
filterExpression3.960.003.96
findEncodingDim31.84 0.0434.12
fit2.610.023.44
fpkm1.310.031.34
getter_setter_functions 9.80 0.0012.14
makeExampleOutriderDataSet202
normalizationFactors1.280.001.28
plotFunctions11.91 0.3512.55
results5.290.015.31
sampleExclusionMask0.770.000.77
sizeFactors1.110.001.11

OUTRIDER.Rcheck/examples_x64/OUTRIDER-Ex.timings

nameusersystemelapsed
OUTRIDER 8.00 0.1738.90
OutriderDataSet-class1.890.001.89
aberrant 4.82 0.0143.51
computeGeneLength2.020.022.04
computeLatentSpace1.530.001.53
computePvalues 4.95 0.0035.83
computeZscores2.150.002.14
controlForConfounders2.150.002.15
counts1.130.001.13
estimateBestQ0.860.000.86
filterExpression2.920.002.92
findEncodingDim25.36 0.0325.45
fit1.560.021.58
fpkm1.690.001.69
getter_setter_functions6.920.006.92
makeExampleOutriderDataSet2.20.02.2
normalizationFactors1.380.001.38
plotFunctions11.39 0.1711.56
results6.690.056.73
sampleExclusionMask0.870.000.88
sizeFactors1.310.011.33