Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-05-16 11:05:35 -0400 (Mon, 16 May 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4379
palomino3Windows Server 2022 Datacenterx644.2.0 (2022-04-22 ucrt) -- "Vigorous Calisthenics" 4153
merida1macOS 10.14.6 Mojavex86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4220
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 nebbiolo1


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? 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 1856/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
singleCellTK 2.6.0  (landing page)
Yichen Wang
Snapshot Date: 2022-05-15 13:55:12 -0400 (Sun, 15 May 2022)
git_url: https://git.bioconductor.org/packages/singleCellTK
git_branch: RELEASE_3_15
git_last_commit: b6fc536
git_last_commit_date: 2022-04-26 11:48:48 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    NA  

Summary

Package: singleCellTK
Version: 2.6.0
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:singleCellTK.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings singleCellTK_2.6.0.tar.gz
StartedAt: 2022-05-15 21:38:03 -0400 (Sun, 15 May 2022)
EndedAt: 2022-05-15 21:50:34 -0400 (Sun, 15 May 2022)
EllapsedTime: 751.3 seconds
RetCode: 0
Status:   OK  
CheckDir: singleCellTK.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:singleCellTK.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings singleCellTK_2.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/singleCellTK.Rcheck’
* using R version 4.2.0 (2022-04-22)
* 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 ‘2.6.0’
* 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  5.3Mb
  sub-directories of 1Mb or more:
    shiny   2.3Mb
* 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 ... 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 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     25.442  0.456  25.616
plotDoubletFinderResults   23.595  0.327  23.913
importExampleData          15.732  2.880  19.208
runDoubletFinder           18.331  0.116  18.448
runScDblFinder             17.012  1.008  17.734
plotBatchCorrCompare       11.532  0.493  12.004
plotScdsHybridResults       9.918  0.184   9.155
plotTSCANPseudotimeHeatmap 10.085  0.012  10.097
plotBcdsResults             8.769  0.248   8.064
plotDecontXResults          7.451  0.203   7.656
runDecontX                  6.783  0.076   6.860
plotEmptyDropsScatter       6.533  0.040   6.573
plotEmptyDropsResults       6.477  0.003   6.480
plotCxdsResults             6.250  0.228   6.468
plotMarkerDiffExp           6.396  0.080   6.476
plotUMAP                    6.387  0.088   6.467
detectCellOutlier           6.066  0.196   6.264
runEmptyDrops               6.243  0.004   6.247
* 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.15-bioc/meat/singleCellTK.Rcheck/00check.log’
for details.



Installation output

singleCellTK.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL singleCellTK
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/library’
* installing *source* package ‘singleCellTK’ ...
** using staged installation
** R
** data
** 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 4.2.0 (2022-04-22) -- "Vigorous Calisthenics"
Copyright (C) 2022 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 
  0.172   0.018   0.173 

singleCellTK.Rcheck/tests/testthat.Rout


R version 4.2.0 (2022-04-22) -- "Vigorous Calisthenics"
Copyright (C) 2022 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%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Uploading data to Enrichr... Done.
  Querying HDSigDB_Human_2021... Done.
Parsing results... Done.
Estimating GSVA scores for 34 gene sets.
Estimating ECDFs with Gaussian kernels

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Estimating GSVA scores for 2 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%
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 17 | SKIP 0 | PASS 162 ]

[ FAIL 0 | WARN 17 | SKIP 0 | PASS 162 ]
> 
> proc.time()
   user  system elapsed 
203.130   7.878 210.480 

Example timings

singleCellTK.Rcheck/singleCellTK-Ex.timings

nameusersystemelapsed
MitoGenes0.0040.0000.003
SEG0.0000.0030.003
calcEffectSizes0.1820.0120.194
combineSCE1.4660.0521.518
computeZScore0.2620.0240.287
convertSCEToSeurat3.5160.1963.712
convertSeuratToSCE0.5340.0120.546
dedupRowNames0.0560.0040.060
detectCellOutlier6.0660.1966.264
diffAbundanceFET0.1120.0040.115
discreteColorPalette0.0070.0000.008
distinctColors0.0000.0020.002
downSampleCells0.6590.0160.675
downSampleDepth0.5130.0120.525
expData-ANY-character-method0.3210.0160.337
expData-set-ANY-character-CharacterOrNullOrMissing-logical-method0.4020.0240.425
expData-set0.3660.0080.375
expData0.3140.0040.318
expDataNames-ANY-method0.320.000.32
expDataNames0.2990.0040.303
expDeleteDataTag0.0410.0000.041
expSetDataTag0.0250.0000.026
expTaggedData0.0270.0000.027
exportSCE0.0250.0000.024
exportSCEtoAnnData0.0930.0040.097
exportSCEtoFlatFile0.0880.0080.095
featureIndex0.0380.0000.038
findMarkerDiffExp3.8060.0683.875
findMarkerTopTable3.3760.0403.416
generateSimulatedData0.0430.0000.043
getBiomarker0.0420.0070.049
getDEGTopTable0.5510.0040.555
getDiffAbundanceResults0.040.000.04
getEnrichRResult0.3120.0681.362
getMSigDBTable0.0010.0040.004
getSampleSummaryStatsTable0.3390.0120.351
getSoupX0.3870.0560.443
getTSNE0.2780.0240.302
getTopHVG0.2420.0280.270
getUMAP4.1870.4934.670
importAnnData0.0010.0000.001
importBUStools0.2480.0080.257
importCellRanger1.0960.0801.178
importCellRangerV2Sample0.3280.0360.364
importCellRangerV3Sample0.3730.0240.397
importDropEst0.3470.0160.364
importExampleData15.732 2.88019.208
importGeneSetsFromCollection0.7210.0600.781
importGeneSetsFromGMT0.0640.0000.064
importGeneSetsFromList0.1090.0120.121
importGeneSetsFromMSigDB3.5710.4554.027
importMitoGeneSet0.0510.0040.055
importOptimus0.0010.0000.001
importSEQC0.2860.0120.298
importSTARsolo0.2540.0080.263
iterateSimulations0.3100.0040.313
listSampleSummaryStatsTables0.4520.0360.487
mergeSCEColData0.4290.0280.457
mouseBrainSubsetSCE0.0270.0000.028
msigdb_table0.0020.0000.001
plotBarcodeRankDropsResults0.8850.0760.961
plotBarcodeRankScatter0.7090.0120.720
plotBatchCorrCompare11.532 0.49312.004
plotBatchVariance0.2620.0240.286
plotBcdsResults8.7690.2488.064
plotClusterAbundance0.9250.0040.929
plotClusterPseudo3.2390.0683.307
plotCxdsResults6.2500.2286.468
plotDEGHeatmap2.7060.1402.847
plotDEGRegression3.2690.0133.268
plotDEGViolin4.0500.0924.130
plotDEGVolcano0.9780.0000.979
plotDecontXResults7.4510.2037.656
plotDimRed0.2790.0000.278
plotDoubletFinderResults23.595 0.32723.913
plotEmptyDropsResults6.4770.0036.480
plotEmptyDropsScatter6.5330.0406.573
plotMASTThresholdGenes1.4510.0201.471
plotMarkerDiffExp6.3960.0806.476
plotPCA0.4590.0030.462
plotPathway0.8590.0120.871
plotRunPerCellQCResults0.0260.0000.026
plotSCEBarAssayData0.1260.0040.129
plotSCEBarColData0.1130.0000.113
plotSCEBatchFeatureMean0.2090.0000.210
plotSCEDensity0.2180.0000.217
plotSCEDensityAssayData0.2020.0040.206
plotSCEDensityColData0.1880.0000.187
plotSCEDimReduceColData0.7380.0000.739
plotSCEDimReduceFeatures0.4020.0360.438
plotSCEHeatmap0.6810.0120.694
plotSCEScatter0.3250.0080.332
plotSCEViolin0.2060.0000.206
plotSCEViolinAssayData0.2690.0070.277
plotSCEViolinColData0.1920.0000.193
plotScDblFinderResults25.442 0.45625.616
plotScdsHybridResults9.9180.1849.155
plotScrubletResults0.0240.0000.025
plotSeuratElbow0.0240.0000.023
plotSeuratHVG0.0240.0000.024
plotSeuratJackStraw0.0230.0000.024
plotSeuratReduction0.0240.0000.024
plotSoupXResults0.1690.0120.180
plotTSCANDEgenes4.1550.0964.250
plotTSCANPseudotimeGenes2.5950.0042.600
plotTSCANPseudotimeHeatmap10.085 0.01210.097
plotTSCANResults2.0850.0082.093
plotTSNE0.4760.0040.480
plotTopHVG0.4310.0040.434
plotUMAP6.3870.0886.467
readSingleCellMatrix0.0040.0000.004
reportCellQC0.1650.0040.169
reportDropletQC0.0230.0000.024
reportQCTool0.1770.0000.177
retrieveSCEIndex0.0290.0000.029
runBBKNN000
runBarcodeRankDrops0.4970.0200.517
runBcds2.3100.0281.436
runCellQC0.1770.0000.177
runComBatSeq0.4960.0080.504
runCxds0.5760.0000.576
runCxdsBcdsHybrid2.3550.0081.502
runDEAnalysis0.6700.0120.681
runDecontX6.7830.0766.860
runDimReduce0.9340.0040.939
runDoubletFinder18.331 0.11618.448
runDropletQC0.0250.0000.025
runEmptyDrops6.2430.0046.247
runEnrichR0.2660.0131.044
runFastMNN1.7480.1361.884
runFeatureSelection0.1910.0200.210
runGSVA0.6900.0960.787
runKMeans0.4620.1040.566
runLimmaBC0.0830.0000.084
runMNNCorrect0.5560.0360.592
runNormalization0.5450.0800.626
runPerCellQC0.4720.0360.509
runSCANORAMA000
runSCMerge0.0040.0000.004
runScDblFinder17.012 1.00817.734
runScranSNN0.4070.0280.435
runScrublet0.0250.0000.025
runSeuratFindClusters0.0210.0040.024
runSeuratFindHVG0.0240.0000.024
runSeuratHeatmap0.0190.0040.023
runSeuratICA0.0190.0040.023
runSeuratJackStraw0.0220.0000.022
runSeuratNormalizeData0.0230.0000.023
runSeuratPCA0.0230.0000.023
runSeuratSCTransform2.9670.2723.239
runSeuratScaleData0.0250.0000.025
runSeuratUMAP0.0240.0000.024
runSingleR0.0300.0040.033
runSoupX0.1750.0000.175
runTSCAN1.9620.0482.010
runTSCANClusterDEAnalysis2.3560.1152.471
runTSCANDEG2.0760.0922.168
runVAM0.5480.0040.552
runZINBWaVE0.0000.0030.004
sampleSummaryStats0.2950.0000.295
scaterCPM0.1320.0120.144
scaterPCA0.4950.0120.506
scaterlogNormCounts0.2420.0120.253
sce0.0230.0000.022
scranModelGeneVar0.1950.0080.203
sctkListGeneSetCollections0.180.020.20
sctkPythonInstallConda0.0000.0000.001
sctkPythonInstallVirtualEnv000
selectSCTKConda000
selectSCTKVirtualEnvironment000
setRowNames0.1100.0040.113
setSCTKDisplayRow0.3480.0040.352
singleCellTK0.0010.0000.000
subDiffEx0.4250.0080.433
subsetSCECols0.1780.0040.181
subsetSCERows0.4010.0120.413
summarizeSCE0.0550.0040.059
trimCounts0.2870.0080.294