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This page was generated on 2021-10-23 14:07:18 -0400 (Sat, 23 Oct 2021).

CHECK results for singleCellTK on merida1

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: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:singleCellTK.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings singleCellTK_2.3.1.tar.gz
StartedAt: 2021-10-23 09:21:45 -0400 (Sat, 23 Oct 2021)
EndedAt: 2021-10-23 09:37:13 -0400 (Sat, 23 Oct 2021)
EllapsedTime: 928.1 seconds
RetCode: 0
Status:   OK  
CheckDir: singleCellTK.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:singleCellTK.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings singleCellTK_2.3.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/singleCellTK.Rcheck’
* using R version 4.1.1 Patched (2021-08-22 r80813)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘singleCellTK’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  6.3Mb
  sub-directories of 1Mb or more:
    extdata   1.5Mb
    shiny     2.8Mb
* 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 ... 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                           user system elapsed
runSeurat                53.015  0.560  53.673
importExampleData        26.624  1.670  29.404
plotDoubletFinderResults 25.944  0.334  26.366
runScDblFinder           25.052  0.382  25.516
plotScDblFinderResults   21.138  0.547  21.790
runDoubletFinder         18.760  0.140  18.972
plotMarkerDiffExp        10.631  0.083  10.771
plotScdsHybridResults     9.845  0.126   9.993
plotBcdsResults           9.702  0.146   9.857
findMarkerDiffExp         9.093  0.109   9.211
runDESeq2                 9.156  0.045   9.216
plotEmptyDropsResults     8.850  0.064   8.941
findMarkerTopTable        8.863  0.048   8.923
plotEmptyDropsScatter     8.752  0.090   8.902
plotDecontXResults        8.594  0.066   8.673
runEmptyDrops             8.465  0.034   8.519
plotDEGHeatmap            8.404  0.068   8.483
plotCxdsResults           6.633  0.048   6.686
detectCellOutlier         6.449  0.099   6.556
runMAST                   6.491  0.049   6.554
runDecontX                6.376  0.068   6.475
plotDEGViolin             6.206  0.124   6.365
importGeneSetsFromMSigDB  5.743  0.310   6.061
plotUMAP                  5.912  0.106   6.049
convertGeneIDs            5.253  0.563   5.825
plotDEGRegression         5.671  0.037   5.715
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  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
  ‘/Users/biocbuild/bbs-3.14-bioc/meat/singleCellTK.Rcheck/00check.log’
for details.



Installation output

singleCellTK.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL singleCellTK
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* 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
** 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
* DONE (singleCellTK)

Tests output

singleCellTK.Rcheck/tests/spelling.Rout


R version 4.1.1 Patched (2021-08-22 r80813) -- "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.

> if (requireNamespace('spelling', quietly = TRUE))
+   spelling::spell_check_test(vignettes = TRUE, error = FALSE, skip_on_cran = TRUE)
NULL
> 
> proc.time()
   user  system elapsed 
  0.460   0.142   0.546 

singleCellTK.Rcheck/tests/testthat.Rout


R version 4.1.1 Patched (2021-08-22 r80813) -- "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(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
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%
[09:35:41] 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.
[09:35:44] 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.
[09:36:18] 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 
153.445   2.614 156.202 

Example timings

singleCellTK.Rcheck/singleCellTK-Ex.timings

nameusersystemelapsed
MitoGenes0.0040.0020.006
SEG0.0030.0020.005
calcEffectSizes0.3020.0090.311
combineSCE3.1180.0173.138
computeZScore0.5080.0200.528
convertGeneIDs5.2530.5635.825
convertSCEToSeurat3.4600.2463.709
convertSeuratToSCE1.1100.0051.117
dedupRowNames0.1010.0010.101
detectCellOutlier6.4490.0996.556
diffAbundanceFET0.0510.0000.052
discreteColorPalette0.0080.0000.008
distinctColors0.0030.0000.003
downSampleCells1.1500.0791.233
downSampleDepth1.0470.0351.084
enrichRSCE0.5410.0231.273
exportSCE0.0010.0010.003
exportSCEtoAnnData0.1760.0040.180
exportSCEtoFlatFile0.1980.0050.204
featureIndex0.0470.0020.048
findMarkerDiffExp9.0930.1099.211
findMarkerTopTable8.8630.0488.923
generateSimulatedData0.0580.0030.060
getBiomarker0.0580.0000.058
getMSigDBTable0.0040.0020.007
getTSNE0.6010.0070.609
getTopHVG0.4830.0090.493
getUMAP4.1270.0524.176
importAnnData0.0010.0010.002
importBUStools0.4950.0030.498
importCellRanger1.8970.0901.993
importCellRangerV2Sample0.5670.0020.572
importCellRangerV3Sample0.6860.0120.701
importDropEst0.6370.0040.643
importExampleData26.624 1.67029.404
importGeneSetsFromCollection1.2360.0841.321
importGeneSetsFromGMT0.1020.0020.105
importGeneSetsFromList0.2490.0090.258
importGeneSetsFromMSigDB5.7430.3106.061
importMitoGeneSet0.0920.0040.097
importOptimus0.0020.0000.002
importSEQC0.4970.0030.502
importSTARsolo0.6620.0050.668
iterateSimulations0.8450.0050.852
mergeSCEColData0.9540.0521.009
mouseBrainSubsetSCE0.0010.0020.003
msigdb_table0.0010.0010.003
plotBarcodeRankDropsResults2.6730.0242.700
plotBarcodeRankScatter1.1900.0091.200
plotBatchVariance0.4140.0080.423
plotBcdsResults9.7020.1469.857
plotBiomarker1.2260.0081.235
plotClusterAbundance1.0330.0061.042
plotCxdsResults6.6330.0486.686
plotDEGHeatmap8.4040.0688.483
plotDEGRegression5.6710.0375.715
plotDEGViolin6.2060.1246.365
plotDecontXResults8.5940.0668.673
plotDimRed0.6040.0510.659
plotDoubletFinderResults25.944 0.33426.366
plotEmptyDropsResults8.8500.0648.941
plotEmptyDropsScatter8.7520.0908.902
plotMASTThresholdGenes2.9840.0203.007
plotMarkerDiffExp10.631 0.08310.771
plotPCA1.1660.0081.177
plotRunPerCellQCResults0.0020.0000.002
plotSCEBarAssayData0.1890.0030.193
plotSCEBarColData0.1360.0010.138
plotSCEBatchFeatureMean0.2710.0110.283
plotSCEDensity0.2670.0020.269
plotSCEDensityAssayData0.2580.0040.263
plotSCEDensityColData0.2500.0030.255
plotSCEDimReduceColData1.5290.0331.581
plotSCEDimReduceFeatures0.7310.0160.755
plotSCEHeatmap1.5620.0281.604
plotSCEScatter0.7070.0030.711
plotSCEViolin0.2870.0010.290
plotSCEViolinAssayData0.2970.0010.300
plotSCEViolinColData0.2830.0020.286
plotScDblFinderResults21.138 0.54721.790
plotScdsHybridResults9.8450.1269.993
plotScrubletResults0.0020.0010.002
plotTSNE1.2180.0351.255
plotTopHVG0.8270.0070.837
plotUMAP5.9120.1066.049
readSingleCellMatrix0.0040.0000.004
reportCellQC0.4130.0030.417
reportDropletQC0.0020.0010.002
reportQCTool0.4170.0050.421
retrieveSCEIndex0.0190.0010.020
runANOVA2.3970.0232.423
runBBKNN000
runBarcodeRankDrops1.1070.0071.115
runBcds3.6230.0273.655
runCellQC0.4340.0030.437
runComBatSeq0.8330.0130.846
runCxds1.0880.0311.124
runCxdsBcdsHybrid3.8170.0563.902
runDEAnalysis2.0190.0292.051
runDESeq29.1560.0459.216
runDecontX6.3760.0686.475
runDimReduce1.8520.0151.870
runDoubletFinder18.760 0.14018.972
runDropletQC0.0020.0010.003
runEmptyDrops8.4650.0348.519
runFastMNN2.7370.0342.781
runFeatureSelection0.3240.0100.340
runGSVA1.5160.0311.563
runKMeans0.9270.0080.938
runLimmaBC0.2150.0040.218
runLimmaDE1.4820.0061.490
runMAST6.4910.0496.554
runMNNCorrect1.2290.0201.262
runNormalization2.8100.0542.887
runPerCellQC0.7170.0030.721
runSCANORAMA0.0010.0000.001
runSCMerge0.0030.0000.003
runScDblFinder25.052 0.38225.516
runScranSNN0.9870.0080.996
runScrublet0.0010.0000.002
runSeurat53.015 0.56053.673
runSingleR0.0770.0010.079
runVAM1.3770.0081.387
runWilcox1.7590.0081.770
runZINBWaVE0.0020.0010.003
sampleSummaryStats0.7560.0060.762
scaterCPM0.3020.0080.310
scaterPCA1.1140.0061.121
scaterlogNormCounts1.5370.0151.556
sce0.0010.0020.004
scranModelGeneVar0.4020.0090.412
sctkListGeneSetCollections0.3820.0180.401
sctkPythonInstallConda000
sctkPythonInstallVirtualEnv000
selectSCTKConda0.0000.0000.001
selectSCTKVirtualEnvironment000
setSCTKDisplayRow0.6330.0050.638
seuratComputeHeatmap0.0020.0010.002
seuratComputeJackStraw0.0030.0010.002
seuratElbowPlot0.0030.0010.002
seuratFindClusters0.0020.0000.002
seuratFindHVG0.0020.0000.003
seuratICA0.0030.0000.003
seuratJackStrawPlot0.0020.0000.002
seuratNormalizeData0.0010.0000.001
seuratPCA0.0020.0010.002
seuratPlotHVG0.0010.0000.002
seuratReductionPlot0.0020.0000.002
seuratRunUMAP0.0020.0000.002
seuratSCTransform4.5120.0904.617
seuratScaleData0.0020.0000.002
singleCellTK0.0000.0010.000
subDiffEx0.9070.0080.916
subsetSCECols0.3900.0040.395
subsetSCERows0.8860.0060.893
summarizeSCE0.0940.0020.095
trimCounts0.4500.0110.463
visPlot1.1380.0341.175