Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-01-14 13:07:11 -0500 (Fri, 14 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4327
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4076
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4137
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 singleCellTK on tokay2


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 2.4.0  (landing page)
Yichen Wang
Snapshot Date: 2022-01-13 01:55:04 -0500 (Thu, 13 Jan 2022)
git_url: https://git.bioconductor.org/packages/singleCellTK
git_branch: RELEASE_3_14
git_last_commit: 91f98fc
git_last_commit_date: 2021-10-27 11:24:49 -0500 (Wed, 27 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    ERROR    OK  
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: singleCellTK
Version: 2.4.0
Command: set _R_CHECK_FORCE_SUGGESTS_=0&& C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:singleCellTK.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings singleCellTK_2.4.0.tar.gz
StartedAt: 2022-01-14 02:27:11 -0500 (Fri, 14 Jan 2022)
EndedAt: 2022-01-14 02:41:05 -0500 (Fri, 14 Jan 2022)
EllapsedTime: 834.0 seconds
RetCode: 1
Status:   ERROR  
CheckDir: singleCellTK.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   set _R_CHECK_FORCE_SUGGESTS_=0&& C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:singleCellTK.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings singleCellTK_2.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/singleCellTK.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 'singleCellTK/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'singleCellTK' version '2.4.0'
* 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 'singleCellTK' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  7.8Mb
  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 ... NOTE
Namespaces in Imports field not imported from:
  'AnnotationDbi' 'RColorBrewer'
  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 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' ... ERROR
Running examples in 'singleCellTK-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: enrichRSCE
> ### Title: enrichR Given a list of genes this function runs the enrichR()
> ###   to perform Gene enrichment
> ### Aliases: enrichRSCE
> 
> ### ** Examples
> 
> enrichRSCE(mouseBrainSubsetSCE, "Cmtm5", "GO_Cellular_Component_2017")
EnrichR website not responding
Error in enrichRSCE(mouseBrainSubsetSCE, "Cmtm5", "GO_Cellular_Component_2017") : 
  database 'GO_Cellular_Component_2017' does not exist.
Execution halted
** running examples for arch 'x64' ... ERROR
Running examples in 'singleCellTK-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: enrichRSCE
> ### Title: enrichR Given a list of genes this function runs the enrichR()
> ###   to perform Gene enrichment
> ### Aliases: enrichRSCE
> 
> ### ** Examples
> 
> enrichRSCE(mouseBrainSubsetSCE, "Cmtm5", "GO_Cellular_Component_2017")
EnrichR website not responding
Error in enrichRSCE(mouseBrainSubsetSCE, "Cmtm5", "GO_Cellular_Component_2017") : 
  database 'GO_Cellular_Component_2017' does not exist.
Execution halted
* 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 ERRORs, 2 NOTEs
See
  'C:/Users/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_2.4.0.tar.gz && rm -rf singleCellTK.buildbin-libdir && mkdir singleCellTK.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=singleCellTK.buildbin-libdir singleCellTK_2.4.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL singleCellTK_2.4.0.zip && rm singleCellTK_2.4.0.tar.gz singleCellTK_2.4.0.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
  4 42.2M    4 1841k    0     0  3764k      0  0:00:11 --:--:--  0:00:11 3765k
 19 42.2M   19 8265k    0     0  5549k      0  0:00:07  0:00:01  0:00:06 5547k
 37 42.2M   37 15.6M    0     0  6437k      0  0:00:06  0:00:02  0:00:04 6437k
 59 42.2M   59 25.0M    0     0  7342k      0  0:00:05  0:00:03  0:00:02 7343k
 85 42.2M   85 36.2M    0     0  8268k      0  0:00:05  0:00:04  0:00:01 8269k
100 42.2M  100 42.2M    0     0  8646k      0  0:00:05  0:00:05 --:--:-- 9176k

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  
    convertSCEToSeurat                      html  
    convertSeuratToSCE                      html  
    dataAnnotationColor                     html  
    finding level-2 HTML links ... done

    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  
    getDEGTopTable                          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  
    plotBatchCorrCompare                    html  
    plotBatchVariance                       html  
    plotBcdsResults                         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  
    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  
** 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_2.4.0.zip
* DONE (singleCellTK)
* installing to library 'C:/Users/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 4.1.2 (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.

> if (requireNamespace('spelling', quietly = TRUE))
+   spelling::spell_check_test(vignettes = TRUE, error = FALSE, skip_on_cran = TRUE)
NULL
> 
> proc.time()
   user  system elapsed 
   0.29    0.04    0.31 

singleCellTK.Rcheck/tests_x64/spelling.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.

> if (requireNamespace('spelling', quietly = TRUE))
+   spelling::spell_check_test(vignettes = TRUE, error = FALSE, skip_on_cran = TRUE)
NULL
> 
> proc.time()
   user  system elapsed 
   0.28    0.03    0.29 

singleCellTK.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(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")
Found 2 batches
Using null model in ComBat-seq.
Adjusting for 0 covariate(s) or covariate level(s)
Estimating dispersions
Fitting the GLM model
Shrinkage off - using GLM estimates for parameters
Adjusting the data
Found 2 batches
Using null model in ComBat-seq.
Adjusting for 1 covariate(s) or covariate level(s)
Estimating dispersions
Fitting the GLM model
Shrinkage off - using GLM estimates for parameters
Adjusting the data
Performing log-normalization
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |======================================================================| 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%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Estimating GSVA scores for 34 gene sets.
Estimating ECDFs with Gaussian kernels

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Performing log-normalization
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[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating gene variances
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[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
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[----|----|----|----|----|----|----|----|----|----|
**************************************************|

  |                                                                            
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  |======================================================================| 100%
[02:34:58] WARNING: amalgamation/../src/learner.cc:1115: 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.
[02:35:00] WARNING: amalgamation/../src/learner.cc:1115: 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.
[02:35:23] WARNING: amalgamation/../src/learner.cc:1115: 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.
Performing log-normalization
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Performing log-normalization
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[----|----|----|----|----|----|----|----|----|----|
**************************************************|

  |                                                                            
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  |                                                                            
  |======================================================================| 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%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck

Number of nodes: 390
Number of edges: 9849

Running Louvain algorithm...
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Maximum modularity in 10 random starts: 0.8351
Number of communities: 7
Elapsed time: 0 seconds
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[----|----|----|----|----|----|----|----|----|----|
**************************************************|

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[----|----|----|----|----|----|----|----|----|----|
**************************************************|
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[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Error in x$.self$finalize() : attempt to apply non-function
[ FAIL 0 | WARN 15 | SKIP 0 | PASS 126 ]
> 
> proc.time()
   user  system elapsed 
 234.93    7.68  243.35 

singleCellTK.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(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")
Found 2 batches
Using null model in ComBat-seq.
Adjusting for 0 covariate(s) or covariate level(s)
Estimating dispersions
Fitting the GLM model
Shrinkage off - using GLM estimates for parameters
Adjusting the data
Found 2 batches
Using null model in ComBat-seq.
Adjusting for 1 covariate(s) or covariate level(s)
Estimating dispersions
Fitting the GLM model
Shrinkage off - using GLM estimates for parameters
Adjusting the data
Performing log-normalization
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|

  |                                                                            
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  |======================================================================| 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%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Estimating GSVA scores for 34 gene sets.
Estimating ECDFs with Gaussian kernels

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Performing log-normalization
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[----|----|----|----|----|----|----|----|----|----|
**************************************************|
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%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|

  |                                                                            
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  |                                                                            
  |======================================================================| 100%
[02:39:04] WARNING: amalgamation/../src/learner.cc:1115: 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.
[02:39:07] WARNING: amalgamation/../src/learner.cc:1115: 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.
[02:39:28] WARNING: amalgamation/../src/learner.cc:1115: 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.
Performing log-normalization
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Performing log-normalization
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |======================================================================| 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%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck

Number of nodes: 390
Number of edges: 9849

Running Louvain algorithm...
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Maximum modularity in 10 random starts: 0.8351
Number of communities: 7
Elapsed time: 0 seconds
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|

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[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
[ FAIL 0 | WARN 15 | SKIP 0 | PASS 126 ]
> 
> proc.time()
   user  system elapsed 
 237.03    4.68  244.43 

Example timings

singleCellTK.Rcheck/examples_i386/singleCellTK-Ex.timings

nameusersystemelapsed
MitoGenes000
SEG0.000.010.02
calcEffectSizes0.150.000.15
combineSCE2.110.002.11
computeZScore0.910.020.94
convertSCEToSeurat2.200.252.45
convertSeuratToSCE0.610.000.61
dedupRowNames0.060.000.06
detectCellOutlier4.950.125.67
diffAbundanceFET0.050.000.05
discreteColorPalette0.010.000.02
distinctColors000
downSampleCells0.850.351.18
downSampleDepth0.670.030.71

singleCellTK.Rcheck/examples_x64/singleCellTK-Ex.timings

nameusersystemelapsed
MitoGenes0.020.000.02
SEG0.000.010.01
calcEffectSizes0.20.00.2
combineSCE2.750.092.85
computeZScore0.300.030.33
convertSCEToSeurat2.340.112.45
convertSeuratToSCE0.690.000.69
dedupRowNames0.060.000.06
detectCellOutlier6.020.136.19
diffAbundanceFET0.030.000.03
discreteColorPalette0.010.000.01
distinctColors000
downSampleCells0.800.010.82
downSampleDepth0.620.020.64