Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2021-10-23 14:06:46 -0400 (Sat, 23 Oct 2021).

CHECK results for singleCellTK on riesling1

To the developers/maintainers of the singleCellTK package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/singleCellTK.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 1807/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
singleCellTK 2.3.1  (landing page)
Yichen Wang
Snapshot Date: 2021-10-22 14:50:11 -0400 (Fri, 22 Oct 2021)
git_url: https://git.bioconductor.org/packages/singleCellTK
git_branch: master
git_last_commit: fd2ca2e
git_last_commit_date: 2021-10-17 15:51:44 -0400 (Sun, 17 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  YES

Summary

Package: singleCellTK
Version: 2.3.1
Command: set _R_CHECK_FORCE_SUGGESTS_=0&& D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:singleCellTK.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings singleCellTK_2.3.1.tar.gz
StartedAt: 2021-10-23 08:32:24 -0400 (Sat, 23 Oct 2021)
EndedAt: 2021-10-23 08:50:11 -0400 (Sat, 23 Oct 2021)
EllapsedTime: 1067.5 seconds
RetCode: 0
Status:   OK  
CheckDir: singleCellTK.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   set _R_CHECK_FORCE_SUGGESTS_=0&& D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:singleCellTK.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings singleCellTK_2.3.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.14-bioc/meat/singleCellTK.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'singleCellTK/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'singleCellTK' version '2.3.1'
* 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 'singleCellTK' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  7.7Mb
  sub-directories of 1Mb or more:
    extdata   1.5Mb
    html      1.2Mb
    shiny     2.7Mb
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
expTaggedData: no visible binding for global variable 'assayTag'
Undefined global functions or variables:
  assayTag
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* 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
runSeurat                34.51   0.28   35.03
plotScDblFinderResults   19.69   0.72   20.40
plotDoubletFinderResults 15.01   0.07   15.11
importExampleData        11.04   1.02   13.22
runDoubletFinder         10.59   0.00   10.61
runScDblFinder            9.53   0.40    9.94
plotEmptyDropsResults     9.88   0.00    9.88
plotEmptyDropsScatter     9.87   0.00    9.87
runEmptyDrops             9.85   0.00    9.85
plotScdsHybridResults     6.41   0.22    6.11
plotBcdsResults           5.91   0.19    5.58
plotDecontXResults        5.12   0.01    5.14
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                          user system elapsed
runSeurat                31.59   0.44   32.05
plotScDblFinderResults   18.16   0.40   18.53
plotDoubletFinderResults 17.81   0.06   17.89
importExampleData        11.67   0.68   13.64
runDoubletFinder         12.19   0.03   12.25
plotEmptyDropsResults    10.19   0.00   10.18
plotEmptyDropsScatter     9.87   0.00    9.88
runEmptyDrops             9.61   0.00    9.61
runScDblFinder            8.61   0.35    8.97
plotScdsHybridResults     6.40   0.14    6.05
plotBcdsResults           6.36   0.11    6.03
plotDecontXResults        5.81   0.02    5.83
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'spelling.R'
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  Running 'spelling.R'
  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
  'D:/biocbuild/bbs-3.14-bioc/meat/singleCellTK.Rcheck/00check.log'
for details.



Installation output

singleCellTK.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/singleCellTK_2.3.1.tar.gz && rm -rf singleCellTK.buildbin-libdir && mkdir singleCellTK.buildbin-libdir && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=singleCellTK.buildbin-libdir singleCellTK_2.3.1.tar.gz && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL singleCellTK_2.3.1.zip && rm singleCellTK_2.3.1.tar.gz singleCellTK_2.3.1.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
  2 41.5M    2  983k    0     0  2636k      0  0:00:16 --:--:--  0:00:16 2629k
 16 41.5M   16 6860k    0     0  4993k      0  0:00:08  0:00:01  0:00:07 4993k
 31 41.5M   31 13.2M    0     0  5730k      0  0:00:07  0:00:02  0:00:05 5727k
 50 41.5M   50 20.8M    0     0  6312k      0  0:00:06  0:00:03  0:00:03 6310k
 70 41.5M   70 29.2M    0     0  6844k      0  0:00:06  0:00:04  0:00:02 6843k
 80 41.5M   80 33.3M    0     0  6326k      0  0:00:06  0:00:05  0:00:01 6600k
100 41.5M  100 41.5M    0     0  6816k      0  0:00:06  0:00:06 --:--:-- 7330k

install for i386

* installing *source* package 'singleCellTK' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** exec
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'singleCellTK'
    finding HTML links ... done
    MitoGenes                               html  
    SEG                                     html  
    calcEffectSizes                         html  
    combineSCE                              html  
    computeHeatmap                          html  
    computeZScore                           html  
    constructSCE                            html  
    convertGeneIDs                          html  
    finding level-2 HTML links ... done

    convertSCEToSeurat                      html  
    convertSeuratToSCE                      html  
    dataAnnotationColor                     html  
    dedupRowNames                           html  
    detectCellOutlier                       html  
    diffAbundanceFET                        html  
    discreteColorPalette                    html  
    distinctColors                          html  
    dot-addSeuratToMetaDataSCE              html  
    dot-checkDiffExpResultExists            html  
    dot-computeSignificantPC                html  
    dot-extractSCEAnnotation                html  
    dot-formatDEAList                       html  
    dot-getComponentNames                   html  
    dot-ggBar                               html  
    dot-ggDensity                           html  
    dot-ggScatter                           html  
    dot-ggViolin                            html  
    dot-sce2adata                           html  
    dot-seuratGetVariableFeatures           html  
    dot-seuratInvalidate                    html  
    dot-updateAssaySCE                      html  
    downSampleCells                         html  
    downSampleDepth                         html  
    enrichRSCE                              html  
    expData-ANY-character-method            html  
    expData-set-ANY-character-CharacterOrNullOrMissing-logical-method
                                            html  
    expData-set                             html  
    expData                                 html  
    expDataNames-ANY-method                 html  
    expDataNames                            html  
    expDeleteDataTag                        html  
    expSetDataTag                           html  
    expTaggedData                           html  
    exportSCE                               html  
    exportSCEToSeurat                       html  
    exportSCEtoAnnData                      html  
    exportSCEtoFlatFile                     html  
    featureIndex                            html  
    findMarkerDiffExp                       html  
    findMarkerTopTable                      html  
    generateHTANMeta                        html  
    generateMeta                            html  
    generateSimulatedData                   html  
    getBiomarker                            html  
    getMSigDBTable                          html  
    getSceParams                            html  
    getTSNE                                 html  
    getTopHVG                               html  
    getUMAP                                 html  
    importAlevin                            html  
    importAnnData                           html  
    importBUStools                          html  
    importCellRanger                        html  
    importCellRangerV2Sample                html  
    importCellRangerV3Sample                html  
    importDropEst                           html  
    importExampleData                       html  
    importFromFiles                         html  
    importGeneSetsFromCollection            html  
    importGeneSetsFromGMT                   html  
    importGeneSetsFromList                  html  
    importGeneSetsFromMSigDB                html  
    importMitoGeneSet                       html  
    importMultipleSources                   html  
    importOptimus                           html  
    importSEQC                              html  
    importSTARsolo                          html  
    iterateSimulations                      html  
    mergeSCEColData                         html  
    mouseBrainSubsetSCE                     html  
    msigdb_table                            html  
    plotBarcodeRankDropsResults             html  
    plotBarcodeRankScatter                  html  
    plotBatchVariance                       html  
    plotBcdsResults                         html  
    plotBiomarker                           html  
    plotClusterAbundance                    html  
    plotCxdsResults                         html  
    plotDEGHeatmap                          html  
    plotDEGRegression                       html  
    plotDEGViolin                           html  
    plotDecontXResults                      html  
    plotDimRed                              html  
    plotDoubletFinderResults                html  
    plotEmptyDropsResults                   html  
    plotEmptyDropsScatter                   html  
    plotMASTThresholdGenes                  html  
    plotMarkerDiffExp                       html  
    plotPCA                                 html  
    plotRunPerCellQCResults                 html  
    plotSCEBarAssayData                     html  
    plotSCEBarColData                       html  
    plotSCEBatchFeatureMean                 html  
    plotSCEDensity                          html  
    plotSCEDensityAssayData                 html  
    plotSCEDensityColData                   html  
    plotSCEDimReduceColData                 html  
    plotSCEDimReduceFeatures                html  
    plotSCEHeatmap                          html  
    plotSCEScatter                          html  
    plotSCEViolin                           html  
    plotSCEViolinAssayData                  html  
    plotSCEViolinColData                    html  
    plotScDblFinderResults                  html  
    plotScdsHybridResults                   html  
    plotScrubletResults                     html  
    plotTSNE                                html  
    plotTopHVG                              html  
    plotUMAP                                html  
    qcInputProcess                          html  
    readSingleCellMatrix                    html  
    reportCellQC                            html  
    reportDiffExp                           html  
    reportDropletQC                         html  
    reportFindMarker                        html  
    reportQCTool                            html  
    retrieveSCEIndex                        html  
    runANOVA                                html  
    runBBKNN                                html  
    runBarcodeRankDrops                     html  
    runBcds                                 html  
    runCellQC                               html  
    runComBatSeq                            html  
    runCxds                                 html  
    runCxdsBcdsHybrid                       html  
    runDEAnalysis                           html  
    runDESeq2                               html  
    runDecontX                              html  
    runDimReduce                            html  
    runDoubletFinder                        html  
    runDropletQC                            html  
    runEmptyDrops                           html  
    runFastMNN                              html  
    runFeatureSelection                     html  
    runGSVA                                 html  
    runKMeans                               html  
    runLimmaBC                              html  
    runLimmaDE                              html  
    runMAST                                 html  
    runMNNCorrect                           html  
    runNormalization                        html  
    runPerCellQC                            html  
    runSCANORAMA                            html  
    runSCMerge                              html  
    runScDblFinder                          html  
    runScranSNN                             html  
    runScrublet                             html  
    runSeurat                               html  
    runSingleR                              html  
    runVAM                                  html  
    runWilcox                               html  
    runZINBWaVE                             html  
    sampleSummaryStats                      html  
    scaterCPM                               html  
    scaterPCA                               html  
    scaterlogNormCounts                     html  
    sce                                     html  
    sceBatches                              html  
    scranModelGeneVar                       html  
    sctkListGeneSetCollections              html  
    sctkPythonInstallConda                  html  
    sctkPythonInstallVirtualEnv             html  
    selectSCTKConda                         html  
    selectSCTKVirtualEnvironment            html  
    setSCTKDisplayRow                       html  
    seuratComputeHeatmap                    html  
    seuratComputeJackStraw                  html  
    seuratElbowPlot                         html  
    seuratFindClusters                      html  
    seuratFindHVG                           html  
    seuratFindMarkers                       html  
    seuratGenePlot                          html  
    seuratHeatmapPlot                       html  
    seuratICA                               html  
    seuratIntegration                       html  
    seuratJackStrawPlot                     html  
    seuratNormalizeData                     html  
    seuratPCA                               html  
    seuratPlotHVG                           html  
    seuratReductionPlot                     html  
    seuratReport                            html  
    seuratRunTSNE                           html  
    seuratRunUMAP                           html  
    seuratSCTransform                       html  
    seuratScaleData                         html  
    seuratVariableFeatures                  html  
    simpleLog                               html  
    singleCellTK                            html  
    subDiffEx                               html  
    subsetSCECols                           html  
    subsetSCERows                           html  
    summarizeSCE                            html  
    trimCounts                              html  
    visPlot                                 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 'singleCellTK' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'singleCellTK' as singleCellTK_2.3.1.zip
* DONE (singleCellTK)
* installing to library 'D:/biocbuild/bbs-3.14-bioc/R/library'
package 'singleCellTK' successfully unpacked and MD5 sums checked

Tests output

singleCellTK.Rcheck/tests_i386/spelling.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
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.

> if (requireNamespace('spelling', quietly = TRUE))
+   spelling::spell_check_test(vignettes = TRUE, error = FALSE, skip_on_cran = TRUE)
NULL
> 
> proc.time()
   user  system elapsed 
   0.18    0.03    0.18 

singleCellTK.Rcheck/tests_x64/spelling.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
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.

> if (requireNamespace('spelling', quietly = TRUE))
+   spelling::spell_check_test(vignettes = TRUE, error = FALSE, skip_on_cran = TRUE)
NULL
> 
> proc.time()
   user  system elapsed 
   0.09    0.04    0.14 

singleCellTK.Rcheck/tests_i386/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
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(singleCellTK)
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

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

Loading required package: GenomicRanges
Loading required package: stats4
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

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: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'Biobase'

The following object is masked from 'package:MatrixGenerics':

    rowMedians

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

    anyMissing, rowMedians

Loading required package: SingleCellExperiment
Loading required package: DelayedArray
Loading required package: Matrix

Attaching package: 'Matrix'

The following object is masked from 'package:S4Vectors':

    expand


Attaching package: 'DelayedArray'

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

    aperm, apply, rowsum, scale, sweep


Attaching package: 'singleCellTK'

The following object is masked from 'package:BiocGenerics':

    plotPCA

> 
> test_check("singleCellTK")
Estimating GSVA scores for 34 gene sets.
Estimating ECDFs with Gaussian kernels
Performing log-normalization
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating gene variances
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |======================================================================| 100%
[08:45:07] WARNING: amalgamation/../src/learner.cc:1095: Starting in XGBoost 1.3.0, the default evaluation metric used with the objective 'binary:logistic' was changed from 'error' to 'logloss'. Explicitly set eval_metric if you'd like to restore the old behavior.
[08:45:08] WARNING: amalgamation/../src/learner.cc:1095: Starting in XGBoost 1.3.0, the default evaluation metric used with the objective 'binary:logistic' was changed from 'error' to 'logloss'. Explicitly set eval_metric if you'd like to restore the old behavior.
[08:45:32] WARNING: amalgamation/../src/learner.cc:1095: Starting in XGBoost 1.3.0, the default evaluation metric used with the objective 'binary:logistic' was changed from 'error' to 'logloss'. Explicitly set eval_metric if you'd like to restore the old behavior.
[ FAIL 0 | WARN 12 | SKIP 0 | PASS 46 ]
> 
> proc.time()
   user  system elapsed 
 100.00    2.92  102.96 

singleCellTK.Rcheck/tests_x64/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
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(singleCellTK)
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

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

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

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    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

Attaching package: 'S4Vectors'

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    I, expand.grid, unname

Loading required package: IRanges

Attaching package: 'IRanges'

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    windows

Loading required package: GenomeInfoDb
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")'.


Attaching package: 'Biobase'

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    rowMedians

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    anyMissing, rowMedians

Loading required package: SingleCellExperiment
Loading required package: DelayedArray
Loading required package: Matrix

Attaching package: 'Matrix'

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Attaching package: 'DelayedArray'

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Attaching package: 'singleCellTK'

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> 
> test_check("singleCellTK")
Estimating GSVA scores for 34 gene sets.
Estimating ECDFs with Gaussian kernels
Performing log-normalization
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating gene variances
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |======================================================================| 100%
[08:46:50] WARNING: amalgamation/../src/learner.cc:1095: Starting in XGBoost 1.3.0, the default evaluation metric used with the objective 'binary:logistic' was changed from 'error' to 'logloss'. Explicitly set eval_metric if you'd like to restore the old behavior.
[08:46:51] WARNING: amalgamation/../src/learner.cc:1095: Starting in XGBoost 1.3.0, the default evaluation metric used with the objective 'binary:logistic' was changed from 'error' to 'logloss'. Explicitly set eval_metric if you'd like to restore the old behavior.
[08:47:09] WARNING: amalgamation/../src/learner.cc:1095: Starting in XGBoost 1.3.0, the default evaluation metric used with the objective 'binary:logistic' was changed from 'error' to 'logloss'. Explicitly set eval_metric if you'd like to restore the old behavior.
[ FAIL 0 | WARN 12 | SKIP 0 | PASS 46 ]
> 
> proc.time()
   user  system elapsed 
  92.76    2.59   95.78 

Example timings

singleCellTK.Rcheck/examples_i386/singleCellTK-Ex.timings

nameusersystemelapsed
MitoGenes0.020.000.02
SEG000
calcEffectSizes0.110.000.11
combineSCE1.420.001.42
computeZScore0.630.030.66
convertGeneIDs2.950.663.61
convertSCEToSeurat1.470.281.75
convertSeuratToSCE0.390.000.39
dedupRowNames0.050.000.05
detectCellOutlier3.800.153.95
diffAbundanceFET0.030.000.03
discreteColorPalette000
distinctColors0.010.000.02
downSampleCells0.580.100.67
downSampleDepth0.470.010.48
enrichRSCE0.310.021.28
exportSCE000
exportSCEtoAnnData0.130.000.13
exportSCEtoFlatFile0.090.050.14
featureIndex0.020.000.01
findMarkerDiffExp3.810.143.96
findMarkerTopTable3.500.063.57
generateSimulatedData0.040.020.04
getBiomarker0.010.000.02
getMSigDBTable0.000.010.01
getTSNE0.270.000.27
getTopHVG0.230.020.25
getUMAP2.830.032.84
importAnnData000
importBUStools0.230.000.24
importCellRanger1.210.974.72
importCellRangerV2Sample0.230.000.23
importCellRangerV3Sample0.450.482.16
importDropEst0.320.000.31
importExampleData11.04 1.0213.22
importGeneSetsFromCollection0.570.040.61
importGeneSetsFromGMT0.040.000.04
importGeneSetsFromList0.110.020.13
importGeneSetsFromMSigDB2.770.393.16
importMitoGeneSet0.030.000.03
importOptimus000
importSEQC0.200.000.21
importSTARsolo0.210.010.21
iterateSimulations0.340.020.36
mergeSCEColData0.610.472.29
mouseBrainSubsetSCE000
msigdb_table000
plotBarcodeRankDropsResults0.750.030.78
plotBarcodeRankScatter0.560.000.61
plotBatchVariance0.170.010.18
plotBcdsResults5.910.195.58
plotBiomarker0.50.00.5
plotClusterAbundance0.440.020.45
plotCxdsResults4.030.044.05
plotDEGHeatmap3.520.033.54
plotDEGRegression2.440.032.47
plotDEGViolin2.780.102.88
plotDecontXResults5.120.015.14
plotDimRed0.210.000.20
plotDoubletFinderResults15.01 0.0715.11
plotEmptyDropsResults9.880.009.88
plotEmptyDropsScatter9.870.009.87
plotMASTThresholdGenes1.220.011.24
plotMarkerDiffExp4.190.014.20
plotPCA0.450.000.46
plotRunPerCellQCResults000
plotSCEBarAssayData0.080.000.08
plotSCEBarColData0.060.000.06
plotSCEBatchFeatureMean0.130.000.12
plotSCEDensity0.120.000.13
plotSCEDensityAssayData0.130.000.12
plotSCEDensityColData0.120.000.13
plotSCEDimReduceColData0.610.000.61
plotSCEDimReduceFeatures0.300.000.29
plotSCEHeatmap0.610.000.61
plotSCEScatter0.260.000.27
plotSCEViolin0.130.000.12
plotSCEViolinAssayData0.120.000.13
plotSCEViolinColData0.140.020.16
plotScDblFinderResults19.69 0.7220.40
plotScdsHybridResults6.410.226.11
plotScrubletResults000
plotTSNE0.420.010.44
plotTopHVG0.410.000.40
plotUMAP3.570.003.58
readSingleCellMatrix0.020.000.02
reportCellQC0.140.000.14
reportDropletQC000
reportQCTool0.160.000.16
retrieveSCEIndex0.010.000.01
runANOVA0.850.000.84
runBBKNN000
runBarcodeRankDrops0.450.000.46
runBcds2.190.111.75
runCellQC0.180.020.20
runComBatSeq0.50.00.5
runCxds0.460.000.45
runCxdsBcdsHybrid2.310.091.84
runDEAnalysis0.740.020.75
runDESeq23.700.003.71
runDecontX3.600.003.59
runDimReduce0.810.000.81
runDoubletFinder10.59 0.0010.61
runDropletQC000
runEmptyDrops9.850.009.85
runFastMNN1.430.011.45
runFeatureSelection0.210.000.20
runGSVA0.760.000.77
runKMeans0.440.000.44
runLimmaBC0.080.000.07
runLimmaDE0.650.000.66
runMAST2.580.002.58
runMNNCorrect0.50.00.5
runNormalization1.130.021.14
runPerCellQC0.280.000.28
runSCANORAMA000
runSCMerge000
runScDblFinder9.530.409.94
runScranSNN0.440.040.47
runScrublet000
runSeurat34.51 0.2835.03
runSingleR0.030.000.03
runVAM0.540.010.56
runWilcox0.70.00.7
runZINBWaVE000
sampleSummaryStats0.320.000.31
scaterCPM0.150.000.16
scaterPCA0.50.00.5
scaterlogNormCounts0.590.020.61
sce000
scranModelGeneVar0.190.010.21
sctkListGeneSetCollections0.160.050.20
sctkPythonInstallConda000
sctkPythonInstallVirtualEnv000
selectSCTKConda000
selectSCTKVirtualEnvironment000
setSCTKDisplayRow0.300.000.29
seuratComputeHeatmap000
seuratComputeJackStraw000
seuratElbowPlot000
seuratFindClusters000
seuratFindHVG000
seuratICA0.010.000.02
seuratJackStrawPlot000
seuratNormalizeData000
seuratPCA000
seuratPlotHVG000
seuratReductionPlot000
seuratRunUMAP000
seuratSCTransform2.440.002.44
seuratScaleData000
singleCellTK000
subDiffEx0.410.030.44
subsetSCECols0.150.010.17
subsetSCERows0.430.000.42
summarizeSCE0.040.020.06
trimCounts0.30.00.3
visPlot0.500.010.52

singleCellTK.Rcheck/examples_x64/singleCellTK-Ex.timings

nameusersystemelapsed
MitoGenes0.000.020.02
SEG000
calcEffectSizes0.110.020.13
combineSCE1.980.062.05
computeZScore0.220.010.23
convertGeneIDs3.240.974.20
convertSCEToSeurat1.810.111.99
convertSeuratToSCE0.40.00.4
dedupRowNames0.050.000.05
detectCellOutlier3.950.114.06
diffAbundanceFET0.040.000.04
discreteColorPalette000
distinctColors000
downSampleCells0.560.050.61
downSampleDepth0.440.010.45
enrichRSCE0.240.051.19
exportSCE000
exportSCEtoAnnData0.120.000.13
exportSCEtoFlatFile0.090.020.11
featureIndex0.040.000.03
findMarkerDiffExp4.200.064.26
findMarkerTopTable4.420.054.47
generateSimulatedData0.030.000.03
getBiomarker0.030.000.03
getMSigDBTable000
getTSNE0.330.000.33
getTopHVG0.300.010.31
getUMAP3.510.063.58
importAnnData000
importBUStools0.30.00.3
importCellRanger1.420.934.87
importCellRangerV2Sample0.250.000.25
importCellRangerV3Sample0.500.572.33
importDropEst0.350.000.35
importExampleData11.67 0.6813.64
importGeneSetsFromCollection0.600.070.67
importGeneSetsFromGMT0.040.000.05
importGeneSetsFromList0.160.000.16
importGeneSetsFromMSigDB2.990.243.22
importMitoGeneSet0.040.010.06
importOptimus000
importSEQC0.350.000.35
importSTARsolo0.320.000.33
iterateSimulations0.360.000.36
mergeSCEColData0.660.582.48
mouseBrainSubsetSCE0.050.000.05
msigdb_table0.010.000.01
plotBarcodeRankDropsResults0.770.030.80
plotBarcodeRankScatter0.710.000.71
plotBatchVariance0.180.000.19
plotBcdsResults6.360.116.03
plotBiomarker0.580.000.57
plotClusterAbundance0.450.000.46
plotCxdsResults4.600.054.64
plotDEGHeatmap3.640.033.67
plotDEGRegression2.610.012.63
plotDEGViolin3.200.083.28
plotDecontXResults5.810.025.83
plotDimRed1.140.001.14
plotDoubletFinderResults17.81 0.0617.89
plotEmptyDropsResults10.19 0.0010.18
plotEmptyDropsScatter9.870.009.88
plotMASTThresholdGenes1.30.01.3
plotMarkerDiffExp4.590.034.62
plotPCA0.440.020.45
plotRunPerCellQCResults000
plotSCEBarAssayData0.080.000.08
plotSCEBarColData0.110.000.11
plotSCEBatchFeatureMean0.120.000.13
plotSCEDensity0.130.000.12
plotSCEDensityAssayData0.090.000.10
plotSCEDensityColData0.130.000.12
plotSCEDimReduceColData0.620.000.63
plotSCEDimReduceFeatures0.330.000.32
plotSCEHeatmap0.610.000.61
plotSCEScatter0.290.000.30
plotSCEViolin0.180.000.17
plotSCEViolinAssayData0.120.010.14
plotSCEViolinColData0.110.020.13
plotScDblFinderResults18.16 0.4018.53
plotScdsHybridResults6.400.146.05
plotScrubletResults000
plotTSNE0.490.030.51
plotTopHVG0.360.020.38
plotUMAP4.330.034.36
readSingleCellMatrix000
reportCellQC0.170.000.17
reportDropletQC000
reportQCTool0.170.000.18
retrieveSCEIndex000
runANOVA0.990.000.98
runBBKNN000
runBarcodeRankDrops0.580.000.58
runBcds1.780.081.50
runCellQC0.190.030.22
runComBatSeq0.500.020.51
runCxds0.50.00.5
runCxdsBcdsHybrid1.900.151.69
runDEAnalysis0.740.000.73
runDESeq23.730.033.77
runDecontX4.270.024.28
runDimReduce0.820.000.83
runDoubletFinder12.19 0.0312.25
runDropletQC000
runEmptyDrops9.610.009.61
runFastMNN1.270.001.26
runFeatureSelection0.200.020.22
runGSVA0.700.010.72
runKMeans0.490.000.49
runLimmaBC0.080.000.07
runLimmaDE0.790.000.80
runMAST2.710.002.70
runMNNCorrect0.530.020.55
runNormalization1.180.041.24
runPerCellQC0.320.000.31
runSCANORAMA000
runSCMerge000
runScDblFinder8.610.358.97
runScranSNN0.420.010.43
runScrublet000
runSeurat31.59 0.4432.05
runSingleR0.030.020.05
runVAM0.570.010.58
runWilcox0.750.000.75
runZINBWaVE000
sampleSummaryStats0.310.000.31
scaterCPM0.140.000.14
scaterPCA0.560.020.58
scaterlogNormCounts0.610.030.64
sce000
scranModelGeneVar0.190.000.19
sctkListGeneSetCollections0.140.010.16
sctkPythonInstallConda000
sctkPythonInstallVirtualEnv000
selectSCTKConda000
selectSCTKVirtualEnvironment000
setSCTKDisplayRow0.370.020.39
seuratComputeHeatmap000
seuratComputeJackStraw0.000.010.01
seuratElbowPlot000
seuratFindClusters000
seuratFindHVG000
seuratICA000
seuratJackStrawPlot000
seuratNormalizeData000
seuratPCA0.020.000.02
seuratPlotHVG000
seuratReductionPlot000
seuratRunUMAP000
seuratSCTransform2.530.022.55
seuratScaleData000
singleCellTK000
subDiffEx0.530.000.53
subsetSCECols0.160.010.17
subsetSCERows0.450.020.47
summarizeSCE0.050.010.06
trimCounts0.280.040.31
visPlot0.520.000.52