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CHECK report for OUTRIDER on tokay1

This page was generated on 2021-05-06 12:32:40 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the OUTRIDER package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1285/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
OUTRIDER 1.8.0  (landing page)
Christian Mertes
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/OUTRIDER
Branch: RELEASE_3_12
Last Commit: ab85565
Last Changed Date: 2020-10-27 11:37:07 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: OUTRIDER
Version: 1.8.0
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:OUTRIDER.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings OUTRIDER_1.8.0.tar.gz
StartedAt: 2021-05-06 05:18:10 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 05:38:29 -0400 (Thu, 06 May 2021)
EllapsedTime: 1218.6 seconds
RetCode: 0
Status:   OK   
CheckDir: OUTRIDER.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:OUTRIDER.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings OUTRIDER_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/OUTRIDER.Rcheck'
* using R version 4.0.5 (2021-03-31)
* 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 '1.8.0'
* 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-3.12-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-3.12-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 21.15   0.00   21.15
plotFunctions   18.48   0.32   18.80
OUTRIDER         6.23   0.34   61.02
results          5.04   0.00    5.03
aberrant         3.29   0.02   48.97
computePvalues   2.53   0.01   40.37
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                         user system elapsed
findEncodingDim         28.80   0.03   28.83
plotFunctions           25.73   0.30   26.01
getter_setter_functions  7.52   0.00    7.51
OUTRIDER                 6.52   0.12   50.62
results                  6.13   0.02    6.14
fit                      5.20   0.00    5.20
computePvalues           4.29   0.02   49.92
aberrant                 4.23   0.05   53.63
* 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-3.12-bioc/meat/OUTRIDER.Rcheck/00check.log'
for details.

Installation output

OUTRIDER.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/OUTRIDER_1.8.0.tar.gz && rm -rf OUTRIDER.buildbin-libdir && mkdir OUTRIDER.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=OUTRIDER.buildbin-libdir OUTRIDER_1.8.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL OUTRIDER_1.8.0.zip && rm OUTRIDER_1.8.0.tar.gz OUTRIDER_1.8.0.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  712k  100  712k    0     0  15.7M      0 --:--:-- --:--:-- --:--:-- 16.1M

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-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-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-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-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-3~1.12-/R/bin/i386 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/i386 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.12-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-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-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-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-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-3~1.12-/R/bin/x64 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.12-bioc/meat/OUTRIDER.buildbin-libdir/OUTRIDER/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'OUTRIDER' as OUTRIDER_1.8.0.zip
* DONE (OUTRIDER)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'OUTRIDER' successfully unpacked and MD5 sums checked

Tests output

OUTRIDER.Rcheck/tests_i386/testthat.Rout


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
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
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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 object is masked from 'package:base':

    expand.grid

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] "Thu May 06 05:33:50 2021: Initial PCA loss: 6.13617788302031"
[1] "Thu May 06 05:33:55 2021: Iteration: 1 loss: 4.41505390848352"
[1] "Thu May 06 05:33:57 2021: Iteration: 2 loss: 4.3447263589289"
[1] "Thu May 06 05:33:59 2021: Iteration: 3 loss: 4.31128534248763"
[1] "Thu May 06 05:34:01 2021: Iteration: 4 loss: 4.28820938514157"
[1] "Thu May 06 05:34:03 2021: Iteration: 5 loss: 4.27684051528838"
[1] "Thu May 06 05:34:05 2021: Iteration: 6 loss: 4.27065307214277"
Time difference of 13.46384 secs
[1] "Thu May 06 05:34:05 2021: 6 Final nb-AE loss: 4.27065307214277"
[1] "Thu May 06 05:34:08 2021: Initial PCA loss: 6.13617788302031"
[1] "Thu May 06 05:34:11 2021: Iteration: 1 loss: 4.41505390848352"
[1] "Thu May 06 05:34:13 2021: Iteration: 2 loss: 4.3447263589289"
[1] "Thu May 06 05:34:14 2021: Iteration: 3 loss: 4.31128534248763"
[1] "Thu May 06 05:34:16 2021: Iteration: 4 loss: 4.28820938514157"
[1] "Thu May 06 05:34:18 2021: Iteration: 5 loss: 4.27684051528838"
[1] "Thu May 06 05:34:20 2021: Iteration: 6 loss: 4.27065307214277"
Time difference of 9.789906 secs
[1] "Thu May 06 05:34:20 2021: 6 Final nb-AE loss: 4.27065307214277"
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 May 06 05:34:45 2021: Initial PCA loss: 4.56552186523373"
[1] "Thu May 06 05:34:50 2021: Iteration: 1 loss: 4.1378791028164"
[1] "Thu May 06 05:34:53 2021: Iteration: 2 loss: 4.12399758495306"
Time difference of 5.421905 secs
[1] "Thu May 06 05:34:53 2021: 2 Final nb-AE loss: 4.12399758495306"
[1] "Evaluation loss: 0.481529892058462 for q=3"
[1] "Thu May 06 05:34:54 2021: Initial PCA loss: 4.47375470449318"
[1] "Thu May 06 05:34:59 2021: Iteration: 1 loss: 4.06549719606376"
[1] "Thu May 06 05:35:01 2021: Iteration: 2 loss: 4.05447422948826"
Time difference of 4.328149 secs
[1] "Thu May 06 05:35:01 2021: 2 Final nb-AE loss: 4.05447422948826"
[1] "Evaluation loss: 0.328028157904621 for q=4"
[1] "Thu May 06 05:35:03 2021: Initial PCA loss: 4.44270751600819"
[1] "Thu May 06 05:35:06 2021: Iteration: 1 loss: 3.97719516157074"
[1] "Thu May 06 05:35:08 2021: Iteration: 2 loss: 3.94876930927105"
Time difference of 3.62789 secs
[1] "Thu May 06 05:35:08 2021: 2 Final nb-AE loss: 3.94876930927105"
[1] "Evaluation loss: 0.256262110011134 for q=5"
[1] "Thu May 06 05:35:21 2021: Initial PCA loss: 6.46616282459584"
[1] "Thu May 06 05:35:33 2021: Iteration: 1 loss: 4.81542744661623"
[1] "Thu May 06 05:35:39 2021: Iteration: 2 loss: 4.79019053974505"
Time difference of 13.58628 secs
[1] "Thu May 06 05:35:39 2021: 2 Final nb-AE loss: 4.79019053974505"
[ FAIL 0 | WARN 2 | SKIP 0 | PASS 103 ]
> 
> proc.time()
   user  system elapsed 
 145.04    2.71  149.34

OUTRIDER.Rcheck/tests_x64/testthat.Rout


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
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
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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 object is masked from 'package:base':

    expand.grid

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] "Thu May 06 05:36:19 2021: Initial PCA loss: 6.00350526172662"
[1] "Thu May 06 05:36:23 2021: Iteration: 1 loss: 4.23281372158205"
[1] "Thu May 06 05:36:25 2021: Iteration: 2 loss: 4.17655333109502"
[1] "Thu May 06 05:36:28 2021: Iteration: 3 loss: 4.1635391796389"
[1] "Thu May 06 05:36:30 2021: Iteration: 4 loss: 4.15377239949135"
[1] "Thu May 06 05:36:32 2021: Iteration: 5 loss: 4.14716159408274"
[1] "Thu May 06 05:36:33 2021: Iteration: 6 loss: 4.14568868748284"
Time difference of 13.09397 secs
[1] "Thu May 06 05:36:33 2021: 6 Final nb-AE loss: 4.14568868748284"
[1] "Thu May 06 05:36:36 2021: Initial PCA loss: 6.00350526172662"
[1] "Thu May 06 05:36:39 2021: Iteration: 1 loss: 4.23281372158205"
[1] "Thu May 06 05:36:41 2021: Iteration: 2 loss: 4.17655333109502"
[1] "Thu May 06 05:36:42 2021: Iteration: 3 loss: 4.1635391796389"
[1] "Thu May 06 05:36:46 2021: Iteration: 4 loss: 4.15377239949135"
[1] "Thu May 06 05:36:48 2021: Iteration: 5 loss: 4.14716159408274"
[1] "Thu May 06 05:36:51 2021: Iteration: 6 loss: 4.14568868748284"
Time difference of 13.73244 secs
[1] "Thu May 06 05:36:51 2021: 6 Final nb-AE loss: 4.14568868748284"
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 May 06 05:37:13 2021: Initial PCA loss: 4.46567897127942"
[1] "Thu May 06 05:37:18 2021: Iteration: 1 loss: 4.1174221062789"
[1] "Thu May 06 05:37:19 2021: Iteration: 2 loss: 4.10036537396839"
Time difference of 4.343775 secs
[1] "Thu May 06 05:37:19 2021: 2 Final nb-AE loss: 4.10036537396839"
[1] "Evaluation loss: 0.443487088955431 for q=3"
[1] "Thu May 06 05:37:21 2021: Initial PCA loss: 4.44513117590504"
[1] "Thu May 06 05:37:24 2021: Iteration: 1 loss: 4.05722965227466"
[1] "Thu May 06 05:37:27 2021: Iteration: 2 loss: 4.04328941248115"
Time difference of 4.015647 secs
[1] "Thu May 06 05:37:27 2021: 2 Final nb-AE loss: 4.04328941248115"
[1] "Evaluation loss: 0.40709440191265 for q=4"
[1] "Thu May 06 05:37:28 2021: Initial PCA loss: 4.42199005515031"
[1] "Thu May 06 05:37:32 2021: Iteration: 1 loss: 3.97650502626864"
[1] "Thu May 06 05:37:34 2021: Iteration: 2 loss: 3.9581389284888"
Time difference of 3.296893 secs
[1] "Thu May 06 05:37:34 2021: 2 Final nb-AE loss: 3.9581389284888"
[1] "Evaluation loss: 0.434243172395617 for q=5"
[1] "Thu May 06 05:37:45 2021: Initial PCA loss: 6.46616282459584"
[1] "Thu May 06 05:37:56 2021: Iteration: 1 loss: 4.81542744661623"
[1] "Thu May 06 05:38:01 2021: Iteration: 2 loss: 4.79019053974505"
Time difference of 11.03131 secs
[1] "Thu May 06 05:38:01 2021: 2 Final nb-AE loss: 4.79019053974505"
[ FAIL 0 | WARN 2 | SKIP 0 | PASS 103 ]
> 
> proc.time()
   user  system elapsed 
 138.56    1.17  141.31

Example timings

OUTRIDER.Rcheck/examples_i386/OUTRIDER-Ex.timings

nameusersystemelapsed
OUTRIDER 6.23 0.3461.02
OutriderDataSet-class0.940.311.35
aberrant 3.29 0.0248.97
computeGeneLength1.490.031.51
computeLatentSpace0.870.000.88
computePvalues 2.53 0.0140.37
computeZscores101
controlForConfounders1.380.001.38
counts0.670.000.67
estimateBestQ0.440.000.44
filterExpression1.610.001.61
findEncodingDim21.15 0.0021.15
fit3.990.003.99
fpkm0.920.000.92
getter_setter_functions4.310.004.31
makeExampleOutriderDataSet1.220.001.22
normalizationFactors0.860.000.86
plotFunctions18.48 0.3218.80
results5.040.005.03
sampleExclusionMask0.560.000.56
sizeFactors0.760.000.77

OUTRIDER.Rcheck/examples_x64/OUTRIDER-Ex.timings

nameusersystemelapsed
OUTRIDER 6.52 0.1250.62
OutriderDataSet-class0.970.000.97
aberrant 4.23 0.0553.63
computeGeneLength2.520.032.54
computeLatentSpace1.330.001.33
computePvalues 4.29 0.0249.92
computeZscores1.80.01.8
controlForConfounders2.540.002.54
counts1.390.001.39
estimateBestQ0.920.000.92
filterExpression3.190.003.19
findEncodingDim28.80 0.0328.83
fit5.20.05.2
fpkm1.010.001.02
getter_setter_functions7.520.007.51
makeExampleOutriderDataSet2.330.012.34
normalizationFactors1.150.001.16
plotFunctions25.73 0.3026.01
results6.130.026.14
sampleExclusionMask0.590.000.60
sizeFactors1.210.001.20