Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-01-26 13:08:48 -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 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: 2022-01-25 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: /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: 2022-01-25 18:15:28 -0500 (Tue, 25 Jan 2022)
EndedAt: 2022-01-25 18:33:58 -0500 (Tue, 25 Jan 2022)
EllapsedTime: 1110.3 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   31.938  0.542  32.527
importExampleData        25.970  2.067  29.559
plotDoubletFinderResults 27.638  0.162  27.823
runDoubletFinder         19.335  0.067  19.427
runScDblFinder           16.167  0.317  16.502
plotBatchCorrCompare     12.163  0.094  12.256
plotMarkerDiffExp        11.526  0.034  11.568
plotScdsHybridResults    11.338  0.109  11.451
plotBcdsResults          10.959  0.229  11.196
findMarkerDiffExp        10.467  0.101  10.575
findMarkerTopTable        9.960  0.044  10.013
plotEmptyDropsScatter     9.597  0.015   9.619
plotDecontXResults        9.526  0.071   9.636
plotEmptyDropsResults     9.518  0.023   9.553
runDESeq2                 9.471  0.044   9.528
plotDEGHeatmap            9.254  0.089   9.357
runEmptyDrops             9.028  0.015   9.051
plotCxdsResults           7.571  0.061   7.634
plotDEGViolin             7.272  0.140   7.423
runDecontX                7.312  0.031   7.355
runMAST                   7.055  0.049   7.107
detectCellOutlier         6.626  0.206   6.844
plotUMAP                  6.579  0.038   6.616
plotDEGRegression         6.460  0.040   6.504
importGeneSetsFromMSigDB  5.950  0.337   6.291
* 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   0.071   0.341 

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%
[18:31:18] 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.
[18:31:21] 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.
[18:31:52] 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
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[----|----|----|----|----|----|----|----|----|----|
**************************************************|

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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 ]

[ FAIL 0 | WARN 15 | SKIP 0 | PASS 126 ]
> 
> proc.time()
   user  system elapsed 
327.987   4.604 334.355 

Example timings

singleCellTK.Rcheck/singleCellTK-Ex.timings

nameusersystemelapsed
MitoGenes0.0040.0030.007
SEG0.0030.0040.007
calcEffectSizes0.2510.0050.256
combineSCE3.1860.0153.202
computeZScore0.5600.0270.587
convertSCEToSeurat4.5350.1604.699
convertSeuratToSCE0.9460.0911.040
dedupRowNames0.1470.0140.160
detectCellOutlier6.6260.2066.844
diffAbundanceFET0.0790.0040.083
discreteColorPalette0.0100.0010.012
distinctColors0.0040.0000.004
downSampleCells1.3850.0761.463
downSampleDepth1.2430.0531.296
enrichRSCE0.6870.0402.093
exportSCE0.0010.0030.004
exportSCEtoAnnData0.2020.0040.206
exportSCEtoFlatFile0.2180.0100.229
featureIndex0.0390.0030.042
findMarkerDiffExp10.467 0.10110.575
findMarkerTopTable 9.960 0.04410.013
generateSimulatedData0.0700.0030.073
getBiomarker0.0710.0010.073
getDEGTopTable1.5440.0101.555
getMSigDBTable0.0050.0030.008
getTSNE0.7290.0050.735
getTopHVG0.5750.0030.579
getUMAP4.4300.0514.480
importAnnData0.0020.0000.002
importBUStools0.6310.0030.635
importCellRanger2.2480.0512.302
importCellRangerV2Sample0.6580.0020.661
importCellRangerV3Sample0.8030.0140.818
importDropEst0.8220.0040.827
importExampleData25.970 2.06729.559
importGeneSetsFromCollection1.3910.1011.494
importGeneSetsFromGMT0.1230.0040.127
importGeneSetsFromList0.3730.0070.381
importGeneSetsFromMSigDB5.9500.3376.291
importMitoGeneSet0.1160.0050.121
importOptimus0.0010.0010.003
importSEQC0.6500.0030.654
importSTARsolo0.7070.0030.711
iterateSimulations0.8680.0070.876
mergeSCEColData1.0280.0151.044
mouseBrainSubsetSCE0.0020.0030.004
msigdb_table0.0020.0030.005
plotBarcodeRankDropsResults1.8100.0181.831
plotBarcodeRankScatter1.6610.0081.672
plotBatchCorrCompare12.163 0.09412.256
plotBatchVariance0.4550.0280.484
plotBcdsResults10.959 0.22911.196
plotClusterAbundance1.2040.0251.231
plotCxdsResults7.5710.0617.634
plotDEGHeatmap9.2540.0899.357
plotDEGRegression6.4600.0406.504
plotDEGViolin7.2720.1407.423
plotDecontXResults9.5260.0719.636
plotDimRed0.6070.0040.612
plotDoubletFinderResults27.638 0.16227.823
plotEmptyDropsResults9.5180.0239.553
plotEmptyDropsScatter9.5970.0159.619
plotMASTThresholdGenes3.5520.0203.600
plotMarkerDiffExp11.526 0.03411.568
plotPCA1.2180.0091.229
plotRunPerCellQCResults0.0030.0000.003
plotSCEBarAssayData0.1710.0010.173
plotSCEBarColData0.1320.0010.134
plotSCEBatchFeatureMean0.2930.0020.295
plotSCEDensity0.3330.0020.336
plotSCEDensityAssayData0.2010.0010.202
plotSCEDensityColData0.3220.0020.324
plotSCEDimReduceColData1.6300.0071.640
plotSCEDimReduceFeatures0.7900.0060.798
plotSCEHeatmap1.5880.0091.601
plotSCEScatter0.7000.0040.706
plotSCEViolin0.3010.0050.308
plotSCEViolinAssayData0.3540.0020.357
plotSCEViolinColData0.2880.0020.291
plotScDblFinderResults31.938 0.54232.527
plotScdsHybridResults11.338 0.10911.451
plotScrubletResults0.0020.0020.004
plotTSNE1.2990.0081.309
plotTopHVG0.9580.0080.967
plotUMAP6.5790.0386.616
readSingleCellMatrix0.0060.0000.007
reportCellQC0.4440.0050.450
reportDropletQC0.0020.0010.003
reportQCTool0.4240.0040.430
retrieveSCEIndex0.0200.0020.022
runANOVA2.3200.0082.329
runBBKNN0.0010.0000.001
runBarcodeRankDrops1.1160.0051.123
runBcds3.9520.0303.985
runCellQC0.4270.0020.430
runComBatSeq0.9410.0100.952
runCxds1.4010.0201.423
runCxdsBcdsHybrid4.1940.0274.232
runDEAnalysis2.0610.0272.090
runDESeq29.4710.0449.528
runDecontX7.3120.0317.355
runDimReduce2.0020.0172.025
runDoubletFinder19.335 0.06719.427
runDropletQC0.0020.0010.003
runEmptyDrops9.0280.0159.051
runFastMNN3.2770.0243.306
runFeatureSelection0.3400.0020.342
runGSVA1.7480.0121.761
runKMeans1.2960.0071.304
runLimmaBC0.2210.0020.222
runLimmaDE1.7490.0071.757
runMAST7.0550.0497.107
runMNNCorrect1.2450.0051.252
runNormalization2.8010.0242.827
runPerCellQC0.9240.0070.932
runSCANORAMA000
runSCMerge0.0010.0010.002
runScDblFinder16.167 0.31716.502
runScranSNN1.2850.0101.296
runScrublet0.0020.0010.003
runSingleR0.0950.0040.099
runVAM1.4840.0251.511
runWilcox2.0480.0072.056
runZINBWaVE0.0020.0010.003
sampleSummaryStats0.8630.0040.868
scaterCPM0.3280.0080.336
scaterPCA1.5470.0071.555
scaterlogNormCounts1.6300.0131.643
sce0.0020.0030.004
scranModelGeneVar0.4410.0100.451
sctkListGeneSetCollections0.3880.0110.400
sctkPythonInstallConda0.0000.0010.001
sctkPythonInstallVirtualEnv0.0000.0010.000
selectSCTKConda0.0000.0010.001
selectSCTKVirtualEnvironment0.0000.0010.001
setSCTKDisplayRow0.7960.0110.808
seuratComputeHeatmap0.0030.0010.004
seuratComputeJackStraw0.0020.0010.003
seuratElbowPlot0.0020.0010.002
seuratFindClusters0.0010.0000.003
seuratFindHVG0.0020.0010.002
seuratICA0.0020.0010.002
seuratJackStrawPlot0.0020.0020.004
seuratNormalizeData0.0030.0020.003
seuratPCA0.0020.0010.004
seuratPlotHVG0.0030.0010.003
seuratReductionPlot0.0020.0010.002
seuratRunUMAP0.0010.0010.003
seuratSCTransform4.8290.0754.912
seuratScaleData0.0020.0000.004
singleCellTK0.0000.0010.001
subDiffEx1.2630.0131.276
subsetSCECols0.4710.0100.486
subsetSCERows1.2100.0211.234
summarizeSCE0.1040.0020.107
trimCounts0.5060.0260.532