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This page was generated on 2021-10-15 15:06:46 -0400 (Fri, 15 Oct 2021).

CHECK results for OUTRIDER on machv2

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 1330/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
OUTRIDER 1.10.0  (landing page)
Christian Mertes
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/OUTRIDER
git_branch: RELEASE_3_13
git_last_commit: c9c57ae
git_last_commit_date: 2021-05-19 12:36:45 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 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: 1.10.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:OUTRIDER.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings OUTRIDER_1.10.0.tar.gz
StartedAt: 2021-10-14 22:01:58 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 22:14:42 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 763.4 seconds
RetCode: 0
Status:   OK  
CheckDir: OUTRIDER.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:OUTRIDER.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings OUTRIDER_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/OUTRIDER.Rcheck’
* using R version 4.1.1 (2021-08-10)
* 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 ‘1.10.0’
* 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
* 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 ... 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 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
findEncodingDim         45.792  0.264  46.106
plotFunctions           25.280  0.422  25.744
aberrant                 9.698  2.282   6.260
getter_setter_functions 11.571  0.035  11.632
OUTRIDER                 8.735  1.119   9.025
results                  9.427  0.069   9.505
fit                      6.078  0.106   6.188
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.13-bioc/meat/OUTRIDER.Rcheck/00check.log’
for details.



Installation output

OUTRIDER.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL OUTRIDER
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/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/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/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/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/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
installing to /Library/Frameworks/R.framework/Versions/4.1/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)

Tests output

OUTRIDER.Rcheck/tests/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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
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 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 Oct 14 22:11:31 2021: Initial PCA loss: 6.52820461605301"
[1] "Thu Oct 14 22:11:36 2021: Iteration: 1 loss: 4.63297178626901"
[1] "Thu Oct 14 22:11:39 2021: Iteration: 2 loss: 4.55234173455206"
[1] "Thu Oct 14 22:11:42 2021: Iteration: 3 loss: 4.51899616672322"
[1] "Thu Oct 14 22:11:45 2021: Iteration: 4 loss: 4.49726795737891"
[1] "Thu Oct 14 22:11:48 2021: Iteration: 5 loss: 4.48712179628123"
[1] "Thu Oct 14 22:11:51 2021: Iteration: 6 loss: 4.4855176435821"
Time difference of 17.62503 secs
[1] "Thu Oct 14 22:11:51 2021: 6 Final nb-AE loss: 4.4855176435821"
[1] "Thu Oct 14 22:11:54 2021: Initial PCA loss: 6.52820461605301"
[1] "Thu Oct 14 22:12:00 2021: Iteration: 1 loss: 4.63297178626901"
[1] "Thu Oct 14 22:12:03 2021: Iteration: 2 loss: 4.55234173455206"
[1] "Thu Oct 14 22:12:06 2021: Iteration: 3 loss: 4.51899616672322"
[1] "Thu Oct 14 22:12:09 2021: Iteration: 4 loss: 4.49726795737891"
[1] "Thu Oct 14 22:12:12 2021: Iteration: 5 loss: 4.48712179628123"
[1] "Thu Oct 14 22:12:15 2021: Iteration: 6 loss: 4.4855176435821"
Time difference of 17.77195 secs
[1] "Thu Oct 14 22:12:15 2021: 6 Final nb-AE loss: 4.4855176435821"
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 Oct 14 22:12:45 2021: Initial PCA loss: 4.44901974982455"
[1] "Thu Oct 14 22:12:52 2021: Iteration: 1 loss: 4.13588958470146"
[1] "Thu Oct 14 22:12:55 2021: Iteration: 2 loss: 4.12842508846871"
Time difference of 6.781232 secs
[1] "Thu Oct 14 22:12:55 2021: 2 Final nb-AE loss: 4.12842508846871"
[1] "Evaluation loss: 0.349664859208444 for q=3"
[1] "Thu Oct 14 22:12:58 2021: Initial PCA loss: 4.42436019015585"
[1] "Thu Oct 14 22:13:05 2021: Iteration: 1 loss: 4.05226640142655"
[1] "Thu Oct 14 22:13:08 2021: Iteration: 2 loss: 4.0402760863617"
Time difference of 7.203056 secs
[1] "Thu Oct 14 22:13:08 2021: 2 Final nb-AE loss: 4.0402760863617"
[1] "Evaluation loss: 0.334758330229599 for q=4"
[1] "Thu Oct 14 22:13:11 2021: Initial PCA loss: 4.40145640895893"
[1] "Thu Oct 14 22:13:17 2021: Iteration: 1 loss: 3.9744594315801"
[1] "Thu Oct 14 22:13:21 2021: Iteration: 2 loss: 3.96167869389219"
Time difference of 6.591168 secs
[1] "Thu Oct 14 22:13:21 2021: 2 Final nb-AE loss: 3.96167869389219"
[1] "Evaluation loss: 0.382425131359587 for q=5"
[1] "Thu Oct 14 22:13:44 2021: Initial PCA loss: 6.46616282459588"
[1] "Thu Oct 14 22:13:57 2021: Iteration: 1 loss: 4.81534335542007"
[1] "Thu Oct 14 22:14:04 2021: Iteration: 2 loss: 4.78989160274581"
Time difference of 13.39809 secs
[1] "Thu Oct 14 22:14:04 2021: 2 Final nb-AE loss: 4.78989160274581"
[ FAIL 0 | WARN 36 | SKIP 0 | PASS 103 ]
> 
> proc.time()
   user  system elapsed 
202.097   1.728 204.030 

Example timings

OUTRIDER.Rcheck/OUTRIDER-Ex.timings

nameusersystemelapsed
OUTRIDER8.7351.1199.025
OutriderDataSet-class2.4710.0232.496
aberrant9.6982.2826.260
computeGeneLength2.9840.0743.083
computeLatentSpace2.1480.0072.155
computePvalues3.0220.9062.923
computeZscores2.2340.0822.320
controlForConfounders2.9820.0263.011
counts1.6240.0101.638
estimateBestQ0.9310.0030.937
filterExpression3.5140.0233.541
findEncodingDim45.792 0.26446.106
fit6.0780.1066.188
fpkm2.2210.0332.256
getter_setter_functions11.571 0.03511.632
makeExampleOutriderDataSet3.3830.0403.431
normalizationFactors2.0480.0052.055
plotFunctions25.280 0.42225.744
results9.4270.0699.505
sampleExclusionMask1.2960.0181.317
sizeFactors1.7550.0171.776