Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-01-14 13:08:37 -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 machv2


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: /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_2.4.0.tar.gz
StartedAt: 2022-01-13 18:11:17 -0500 (Thu, 13 Jan 2022)
EndedAt: 2022-01-13 18:29:59 -0500 (Thu, 13 Jan 2022)
EllapsedTime: 1122.0 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_2.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/singleCellTK.Rcheck’
* using R version 4.1.2 (2021-11-01)
* 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 ‘2.4.0’
* 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 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 ... 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                           user system elapsed
plotScDblFinderResults   31.744  0.541  32.334
importExampleData        25.577  2.082  28.995
plotDoubletFinderResults 27.015  0.145  27.179
runScDblFinder           26.229  0.400  26.652
runDoubletFinder         19.911  0.073  20.016
plotBatchCorrCompare     12.339  0.068  12.400
plotMarkerDiffExp        11.664  0.042  11.718
findMarkerDiffExp        11.336  0.090  11.432
plotScdsHybridResults    11.207  0.110  11.321
plotBcdsResults          10.795  0.237  11.038
runDESeq2                10.615  0.033  10.658
findMarkerTopTable       10.159  0.043  10.208
plotDEGHeatmap            9.787  0.121   9.922
plotEmptyDropsScatter     9.721  0.018   9.745
plotEmptyDropsResults     9.603  0.020   9.634
plotDecontXResults        9.270  0.072   9.351
runEmptyDrops             9.230  0.028   9.275
plotCxdsResults           7.763  0.053   7.815
plotDEGViolin             7.326  0.126   7.460
runMAST                   7.172  0.039   7.215
runDecontX                7.019  0.017   7.042
detectCellOutlier         6.633  0.252   6.893
plotUMAP                  6.504  0.046   6.550
plotDEGRegression         6.497  0.045   6.551
importGeneSetsFromMSigDB  6.164  0.274   6.443
* 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 4.1.2 (2021-11-01) -- "Bird Hippie"
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 
  0.291   0.072   0.338 

singleCellTK.Rcheck/tests/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
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")
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
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%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|

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  |======================================================================| 100%
[18:27:12] 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.
[18:27:14] 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.
[18:27:52] 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%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|

  |                                                                            
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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
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%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Error in x$.self$finalize() : attempt to apply non-function
[ FAIL 0 | WARN 15 | SKIP 0 | PASS 126 ]
> 
> proc.time()
   user  system elapsed 
327.578   4.486 333.475 

Example timings

singleCellTK.Rcheck/singleCellTK-Ex.timings

nameusersystemelapsed
MitoGenes0.0030.0010.005
SEG0.0020.0020.004
calcEffectSizes0.3690.0100.379
combineSCE3.5370.0153.552
computeZScore0.5290.0250.554
convertSCEToSeurat4.2630.1494.414
convertSeuratToSCE1.0090.0941.103
dedupRowNames0.1330.0130.147
detectCellOutlier6.6330.2526.893
diffAbundanceFET0.0730.0020.076
discreteColorPalette0.0100.0010.011
distinctColors0.0040.0000.004
downSampleCells1.4700.0821.554
downSampleDepth0.9490.0290.979
enrichRSCE0.7160.0362.302
exportSCE0.0020.0030.005
exportSCEtoAnnData0.2290.0080.238
exportSCEtoFlatFile0.2370.0140.251
featureIndex0.0560.0040.060
findMarkerDiffExp11.336 0.09011.432
findMarkerTopTable10.159 0.04310.208
generateSimulatedData0.0590.0030.061
getBiomarker0.0640.0010.066
getDEGTopTable1.5730.0091.582
getMSigDBTable0.0060.0030.009
getTSNE0.7170.0080.725
getTopHVG0.5450.0110.557
getUMAP4.3670.0474.412
importAnnData0.0010.0000.001
importBUStools0.6050.0020.609
importCellRanger2.2250.0602.290
importCellRangerV2Sample0.5220.0020.524
importCellRangerV3Sample0.9010.0140.917
importDropEst0.7300.0030.733
importExampleData25.577 2.08228.995
importGeneSetsFromCollection1.2150.0851.300
importGeneSetsFromGMT0.0990.0030.101
importGeneSetsFromList0.2430.0040.247
importGeneSetsFromMSigDB6.1640.2746.443
importMitoGeneSet0.0970.0050.102
importOptimus0.0020.0000.002
importSEQC0.6320.0060.643
importSTARsolo0.6420.0030.646
iterateSimulations1.0300.0071.038
mergeSCEColData1.1020.0171.121
mouseBrainSubsetSCE0.0010.0030.005
msigdb_table0.0010.0030.004
plotBarcodeRankDropsResults1.9670.0191.991
plotBarcodeRankScatter1.7100.0081.720
plotBatchCorrCompare12.339 0.06812.400
plotBatchVariance0.5110.0350.546
plotBcdsResults10.795 0.23711.038
plotClusterAbundance1.2600.0281.290
plotCxdsResults7.7630.0537.815
plotDEGHeatmap9.7870.1219.922
plotDEGRegression6.4970.0456.551
plotDEGViolin7.3260.1267.460
plotDecontXResults9.2700.0729.351
plotDimRed0.6270.0040.632
plotDoubletFinderResults27.015 0.14527.179
plotEmptyDropsResults9.6030.0209.634
plotEmptyDropsScatter9.7210.0189.745
plotMASTThresholdGenes3.2660.0183.287
plotMarkerDiffExp11.664 0.04211.718
plotPCA1.2960.0081.305
plotRunPerCellQCResults0.0020.0010.003
plotSCEBarAssayData0.1780.0010.179
plotSCEBarColData0.1440.0020.146
plotSCEBatchFeatureMean0.3520.0030.354
plotSCEDensity0.3030.0020.306
plotSCEDensityAssayData0.2290.0020.231
plotSCEDensityColData0.2860.0020.288
plotSCEDimReduceColData1.4350.0061.441
plotSCEDimReduceFeatures0.8770.0030.882
plotSCEHeatmap1.5810.0081.590
plotSCEScatter0.6110.0030.615
plotSCEViolin0.3530.0020.359
plotSCEViolinAssayData0.3100.0010.313
plotSCEViolinColData0.2490.0010.250
plotScDblFinderResults31.744 0.54132.334
plotScdsHybridResults11.207 0.11011.321
plotScrubletResults0.0010.0010.002
plotTSNE1.0450.0091.055
plotTopHVG0.9240.0090.933
plotUMAP6.5040.0466.550
readSingleCellMatrix0.0070.0010.007
reportCellQC0.3210.0020.323
reportDropletQC0.0020.0010.002
reportQCTool0.4580.0020.461
retrieveSCEIndex0.0250.0010.025
runANOVA2.3220.0082.332
runBBKNN0.0000.0000.001
runBarcodeRankDrops1.1930.0051.199
runBcds4.1330.0294.166
runCellQC0.4810.0040.488
runComBatSeq0.9940.0131.036
runCxds1.4520.0231.476
runCxdsBcdsHybrid4.3830.0284.415
runDEAnalysis2.0310.0282.061
runDESeq210.615 0.03310.658
runDecontX7.0190.0177.042
runDimReduce2.2340.0092.244
runDoubletFinder19.911 0.07320.016
runDropletQC0.0020.0010.003
runEmptyDrops9.2300.0289.275
runFastMNN3.3630.0243.401
runFeatureSelection0.4020.0020.405
runGSVA1.5550.0191.580
runKMeans1.2380.0071.246
runLimmaBC0.2150.0010.216
runLimmaDE1.7750.0061.782
runMAST7.1720.0397.215
runMNNCorrect1.2200.0051.227
runNormalization2.9300.0242.956
runPerCellQC0.8970.0070.905
runSCANORAMA000
runSCMerge0.0020.0010.004
runScDblFinder26.229 0.40026.652
runScranSNN1.2480.0091.259
runScrublet0.0020.0010.003
runSingleR0.1080.0040.111
runVAM1.6490.0291.681
runWilcox1.8310.0061.838
runZINBWaVE0.0030.0010.003
sampleSummaryStats0.7280.0030.733
scaterCPM0.2800.0090.290
scaterPCA1.4320.0081.441
scaterlogNormCounts1.6730.0131.686
sce0.0020.0030.004
scranModelGeneVar0.4670.0090.476
sctkListGeneSetCollections0.3670.0110.377
sctkPythonInstallConda0.0000.0010.000
sctkPythonInstallVirtualEnv0.0010.0000.001
selectSCTKConda0.0000.0000.001
selectSCTKVirtualEnvironment000
setSCTKDisplayRow0.7980.0110.810
seuratComputeHeatmap0.0020.0010.003
seuratComputeJackStraw0.0030.0010.004
seuratElbowPlot0.0020.0010.003
seuratFindClusters0.0030.0010.003
seuratFindHVG0.0020.0010.003
seuratICA0.0030.0010.004
seuratJackStrawPlot0.0020.0020.004
seuratNormalizeData0.0020.0010.004
seuratPCA0.0020.0010.003
seuratPlotHVG0.0030.0010.003
seuratReductionPlot0.0020.0010.004
seuratRunUMAP0.0030.0010.004
seuratSCTransform4.9000.0614.993
seuratScaleData0.0020.0010.004
singleCellTK0.0010.0010.001
subDiffEx1.1340.0141.150
subsetSCECols0.4420.0060.448
subsetSCERows0.9020.0080.910
summarizeSCE0.0990.0020.101
trimCounts0.5360.0150.553