Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-01-26 13:05:59 -0500 (Wed, 26 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4329
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4080
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4141
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 nebbiolo2


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: 2022-01-25 01:55:07 -0500 (Tue, 25 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: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:singleCellTK.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings singleCellTK_2.4.0.tar.gz
StartedAt: 2022-01-25 09:38:49 -0500 (Tue, 25 Jan 2022)
EndedAt: 2022-01-25 09:50:40 -0500 (Tue, 25 Jan 2022)
EllapsedTime: 710.8 seconds
RetCode: 0
Status:   OK  
CheckDir: singleCellTK.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:singleCellTK.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings singleCellTK_2.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/singleCellTK.Rcheck’
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-pc-linux-gnu (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  6.5Mb
  sub-directories of 1Mb or more:
    extdata   1.6Mb
    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
plotDoubletFinderResults 24.541  0.148  24.679
importExampleData        20.943  1.492  23.302
plotScDblFinderResults   21.926  0.248  22.118
runDoubletFinder         16.700  0.020  16.719
plotBatchCorrCompare     12.561  0.056  12.602
runScDblFinder           11.624  0.212  11.792
plotBcdsResults           9.347  0.175   8.521
plotScdsHybridResults     9.169  0.132   8.351
plotDecontXResults        7.900  0.036   7.936
findMarkerDiffExp         6.908  0.800   7.708
plotEmptyDropsResults     6.894  0.008   6.902
plotEmptyDropsScatter     6.722  0.004   6.727
runEmptyDrops             6.487  0.000   6.486
plotCxdsResults           6.390  0.053   6.435
plotUMAP                  6.240  0.064   6.296
runDecontX                6.053  0.012   6.065
plotMarkerDiffExp         5.918  0.000   5.918
findMarkerTopTable        5.871  0.028   5.900
getUMAP                   5.143  0.424   5.559
runDESeq2                 5.076  0.068   5.143
enrichRSCE                0.470  0.004   8.831
* 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
  ‘/home/biocbuild/bbs-3.14-bioc/meat/singleCellTK.Rcheck/00check.log’
for details.



Installation output

singleCellTK.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL singleCellTK
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/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-pc-linux-gnu (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 
  0.188   0.056   0.228 

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-pc-linux-gnu (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%
[09:49:10] 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.
[09:49:11] 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.
[09:49:31] 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%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
[ FAIL 0 | WARN 15 | SKIP 0 | PASS 126 ]

[ FAIL 0 | WARN 15 | SKIP 0 | PASS 126 ]
> 
> proc.time()
   user  system elapsed 
200.872   5.421 205.205 

Example timings

singleCellTK.Rcheck/singleCellTK-Ex.timings

nameusersystemelapsed
MitoGenes0.0020.0000.002
SEG0.0020.0000.002
calcEffectSizes0.1300.0120.142
combineSCE1.8380.0091.845
computeZScore0.2870.0240.311
convertSCEToSeurat2.6630.0512.715
convertSeuratToSCE0.5250.0650.589
dedupRowNames0.0640.0000.065
detectCellOutlier4.4810.1234.606
diffAbundanceFET0.0360.0030.040
discreteColorPalette0.0050.0000.005
distinctColors0.0010.0000.001
downSampleCells0.6730.0160.689
downSampleDepth0.5580.0010.558
enrichRSCE0.4700.0048.831
exportSCE0.0010.0000.001
exportSCEtoAnnData0.1240.0120.136
exportSCEtoFlatFile0.1180.0320.150
featureIndex0.0440.0100.054
findMarkerDiffExp6.9080.8007.708
findMarkerTopTable5.8710.0285.900
generateSimulatedData0.0510.0000.052
getBiomarker0.0400.0000.041
getDEGTopTable0.8970.0040.901
getMSigDBTable0.0000.0030.003
getTSNE0.3890.0280.416
getTopHVG0.3250.0280.353
getUMAP5.1430.4245.559
importAnnData0.0010.0000.001
importBUStools0.3730.0000.374
importCellRanger1.4770.0081.486
importCellRangerV2Sample0.3690.0000.368
importCellRangerV3Sample0.5080.0040.513
importDropEst0.4770.0080.485
importExampleData20.943 1.49223.302
importGeneSetsFromCollection0.8020.0040.807
importGeneSetsFromGMT0.0680.0000.068
importGeneSetsFromList0.1920.0000.192
importGeneSetsFromMSigDB4.2190.2364.455
importMitoGeneSet0.0540.0000.054
importOptimus0.0010.0000.001
importSEQC0.3370.0000.337
importSTARsolo0.350.000.35
iterateSimulations0.5940.0000.594
mergeSCEColData0.5590.0000.559
mouseBrainSubsetSCE0.0010.0000.001
msigdb_table0.0010.0000.001
plotBarcodeRankDropsResults1.1110.0241.135
plotBarcodeRankScatter0.9210.0000.922
plotBatchCorrCompare12.561 0.05612.602
plotBatchVariance0.2640.0360.300
plotBcdsResults9.3470.1758.521
plotClusterAbundance0.6880.0080.696
plotCxdsResults6.3900.0536.435
plotDEGHeatmap4.8950.0044.900
plotDEGRegression3.2730.0153.280
plotDEGViolin3.8800.0883.953
plotDecontXResults7.9000.0367.936
plotDimRed0.3160.0120.329
plotDoubletFinderResults24.541 0.14824.679
plotEmptyDropsResults6.8940.0086.902
plotEmptyDropsScatter6.7220.0046.727
plotMASTThresholdGenes2.8440.0002.844
plotMarkerDiffExp5.9180.0005.918
plotPCA0.6820.0040.686
plotRunPerCellQCResults0.0020.0000.002
plotSCEBarAssayData0.1160.0000.116
plotSCEBarColData0.0930.0000.093
plotSCEBatchFeatureMean0.1740.0000.174
plotSCEDensity0.1530.0040.157
plotSCEDensityAssayData0.1260.0000.126
plotSCEDensityColData0.1620.0000.162
plotSCEDimReduceColData0.8640.0000.864
plotSCEDimReduceFeatures0.4160.0000.416
plotSCEHeatmap0.8970.0000.897
plotSCEScatter0.3820.0000.382
plotSCEViolin0.170.000.17
plotSCEViolinAssayData0.1860.0080.194
plotSCEViolinColData0.1830.0000.183
plotScDblFinderResults21.926 0.24822.118
plotScdsHybridResults9.1690.1328.351
plotScrubletResults0.0010.0000.001
plotTSNE0.6070.0000.607
plotTopHVG0.5050.0080.513
plotUMAP6.2400.0646.296
readSingleCellMatrix0.0040.0000.003
reportCellQC0.2310.0000.231
reportDropletQC0.0010.0000.002
reportQCTool0.2270.0000.227
retrieveSCEIndex0.0160.0000.016
runANOVA1.2630.0001.264
runBBKNN000
runBarcodeRankDrops0.6900.0280.719
runBcds2.6350.0241.738
runCellQC0.2300.0040.234
runComBatSeq0.4610.0040.465
runCxds0.6970.0000.698
runCxdsBcdsHybrid2.5760.0041.699
runDEAnalysis1.0420.0001.042
runDESeq25.0760.0685.143
runDecontX6.0530.0126.065
runDimReduce1.1320.0161.148
runDoubletFinder16.700 0.02016.719
runDropletQC0.0020.0000.001
runEmptyDrops6.4870.0006.486
runFastMNN1.6360.0041.639
runFeatureSelection0.2030.0000.204
runGSVA0.9530.0120.965
runKMeans0.6140.0000.613
runLimmaBC0.1020.0000.102
runLimmaDE0.9150.0040.920
runMAST3.5810.0083.549
runMNNCorrect0.6680.0000.668
runNormalization1.5760.0081.584
runPerCellQC0.5230.0350.558
runSCANORAMA000
runSCMerge0.0010.0000.001
runScDblFinder11.624 0.21211.792
runScranSNN0.6340.0080.642
runScrublet0.0010.0000.001
runSingleR0.0480.0000.048
runVAM0.8550.0000.856
runWilcox1.1010.0001.101
runZINBWaVE0.0010.0000.001
sampleSummaryStats0.4420.0000.442
scaterCPM0.1840.0000.184
scaterPCA0.7810.0000.782
scaterlogNormCounts0.8220.0000.822
sce0.0010.0000.001
scranModelGeneVar0.2530.0040.257
sctkListGeneSetCollections0.1960.0160.212
sctkPythonInstallConda000
sctkPythonInstallVirtualEnv000
selectSCTKConda000
selectSCTKVirtualEnvironment000
setSCTKDisplayRow0.4580.0320.490
seuratComputeHeatmap0.0020.0000.002
seuratComputeJackStraw0.0020.0000.001
seuratElbowPlot0.0010.0000.001
seuratFindClusters0.0010.0000.001
seuratFindHVG0.0010.0000.001
seuratICA0.0010.0000.001
seuratJackStrawPlot0.0010.0000.001
seuratNormalizeData0.0010.0000.001
seuratPCA0.0010.0000.001
seuratPlotHVG0.0010.0000.001
seuratReductionPlot0.0010.0000.001
seuratRunUMAP0.0010.0000.001
seuratSCTransform3.0560.0603.118
seuratScaleData0.0010.0000.001
singleCellTK000
subDiffEx0.6080.0000.608
subsetSCECols0.2280.0000.227
subsetSCERows0.6240.0000.623
summarizeSCE0.0550.0040.060
trimCounts0.3300.0000.331