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This page was generated on 2021-10-23 14:06:13 -0400 (Sat, 23 Oct 2021).

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 2.3.1  (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: /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_2.3.1.tar.gz
StartedAt: 2021-10-22 22:00:04 -0400 (Fri, 22 Oct 2021)
EndedAt: 2021-10-22 22:10:35 -0400 (Fri, 22 Oct 2021)
EllapsedTime: 630.8 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_2.3.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/singleCellTK.Rcheck’
* using R version 4.1.1 (2021-08-10)
* 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 ‘2.3.1’
* 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  6.5Mb
  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 ... 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                40.986  0.120  41.106
plotScDblFinderResults   22.810  0.404  23.189
plotDoubletFinderResults 21.733  0.128  21.851
runDoubletFinder         17.197  0.124  17.321
importExampleData        15.122  1.351  17.427
runScDblFinder           15.715  0.395  16.095
plotBcdsResults           8.546  0.100   7.753
plotScdsHybridResults     8.391  0.100   7.631
plotEmptyDropsResults     6.821  0.024   6.845
plotEmptyDropsScatter     6.677  0.024   6.702
plotDecontXResults        6.613  0.060   6.672
detectCellOutlier         6.455  0.020   6.475
runDecontX                6.406  0.068   6.474
runEmptyDrops             6.440  0.003   6.445
plotCxdsResults           6.082  0.057   6.129
plotUMAP                  5.710  0.041   5.740
plotMarkerDiffExp         5.553  0.008   5.560
plotDEGViolin             5.195  0.136   5.319
findMarkerDiffExp         5.122  0.140   5.262
* 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 4.1.1 (2021-08-10) -- "Kick Things"
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 
  0.216   0.021   0.223 

singleCellTK.Rcheck/tests/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
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")
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%
[22:09:41] 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.
[22:09:42] 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.
[22:10:04] 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 
109.258   2.847 110.358 

Example timings

singleCellTK.Rcheck/singleCellTK-Ex.timings

nameusersystemelapsed
MitoGenes0.0020.0000.002
SEG0.0020.0000.002
calcEffectSizes0.1440.0080.152
combineSCE1.9710.0161.987
computeZScore0.3210.0400.362
convertGeneIDs3.4550.1553.612
convertSCEToSeurat1.9320.0992.032
convertSeuratToSCE0.5040.0000.504
dedupRowNames0.0550.0000.055
detectCellOutlier6.4550.0206.475
diffAbundanceFET0.0440.0000.044
discreteColorPalette0.0070.0000.007
distinctColors0.0020.0000.002
downSampleCells0.7470.0160.763
downSampleDepth0.5810.0040.585
enrichRSCE0.3300.0151.750
exportSCE0.0020.0000.002
exportSCEtoAnnData0.1410.0120.153
exportSCEtoFlatFile0.1190.0120.131
featureIndex0.0270.0000.027
findMarkerDiffExp5.1220.1405.262
findMarkerTopTable4.8250.0524.876
generateSimulatedData0.0390.0000.039
getBiomarker0.0360.0190.056
getMSigDBTable0.0000.0030.004
getTSNE0.350.000.35
getTopHVG0.3120.0120.324
getUMAP4.5550.0404.588
importAnnData0.0010.0000.000
importBUStools0.3020.0000.302
importCellRanger1.1700.0011.170
importCellRangerV2Sample0.340.000.34
importCellRangerV3Sample0.4670.0030.471
importDropEst0.390.000.39
importExampleData15.122 1.35117.427
importGeneSetsFromCollection0.6790.0160.695
importGeneSetsFromGMT0.0590.0000.059
importGeneSetsFromList0.1480.0040.152
importGeneSetsFromMSigDB3.9070.2524.160
importMitoGeneSet0.0480.0030.052
importOptimus0.0010.0000.001
importSEQC0.2820.0000.283
importSTARsolo0.3670.0000.368
iterateSimulations0.4870.0000.487
mergeSCEColData0.5620.0200.581
mouseBrainSubsetSCE0.0010.0000.001
msigdb_table0.0010.0000.001
plotBarcodeRankDropsResults1.2310.0081.239
plotBarcodeRankScatter0.7860.0000.786
plotBatchVariance0.3030.0000.302
plotBcdsResults8.5460.1007.753
plotBiomarker0.7390.0040.743
plotClusterAbundance0.6370.0000.638
plotCxdsResults6.0820.0576.129
plotDEGHeatmap4.8080.0124.821
plotDEGRegression3.5270.0283.541
plotDEGViolin5.1950.1365.319
plotDecontXResults6.6130.0606.672
plotDimRed0.2800.0320.312
plotDoubletFinderResults21.733 0.12821.851
plotEmptyDropsResults6.8210.0246.845
plotEmptyDropsScatter6.6770.0246.702
plotMASTThresholdGenes1.6400.0361.677
plotMarkerDiffExp5.5530.0085.560
plotPCA0.5980.0000.599
plotRunPerCellQCResults0.0020.0000.001
plotSCEBarAssayData0.1180.0000.118
plotSCEBarColData0.0930.0000.093
plotSCEBatchFeatureMean0.2280.0000.228
plotSCEDensity0.1650.0080.172
plotSCEDensityAssayData0.1350.0000.135
plotSCEDensityColData0.1650.0000.165
plotSCEDimReduceColData0.8260.0040.829
plotSCEDimReduceFeatures0.4130.0040.417
plotSCEHeatmap0.8570.0360.893
plotSCEScatter0.3790.0080.387
plotSCEViolin0.1750.0040.179
plotSCEViolinAssayData0.1940.0080.201
plotSCEViolinColData0.1710.0040.176
plotScDblFinderResults22.810 0.40423.189
plotScdsHybridResults8.3910.1007.631
plotScrubletResults0.0010.0000.002
plotTSNE0.6680.0040.672
plotTopHVG0.4750.0000.475
plotUMAP5.7100.0415.740
readSingleCellMatrix0.0030.0000.004
reportCellQC0.2190.0000.220
reportDropletQC0.0020.0000.002
reportQCTool0.2110.0000.212
retrieveSCEIndex0.0130.0000.013
runANOVA1.2050.0001.205
runBBKNN000
runBarcodeRankDrops0.6550.0000.655
runBcds2.4040.0631.599
runCellQC0.2230.0010.223
runComBatSeq0.4680.0000.468
runCxds0.6980.0070.706
runCxdsBcdsHybrid2.5660.0201.726
runDEAnalysis1.0860.0071.094
runDESeq24.9980.0004.998
runDecontX6.4060.0686.474
runDimReduce1.1450.0041.149
runDoubletFinder17.197 0.12417.321
runDropletQC0.0020.0000.001
runEmptyDrops6.4400.0036.445
runFastMNN1.5920.0641.656
runFeatureSelection0.1980.0000.197
runGSVA0.8590.0040.863
runKMeans0.6290.0040.633
runLimmaBC0.1040.0000.105
runLimmaDE0.8970.0000.898
runMAST3.8310.0073.799
runMNNCorrect0.6510.0000.651
runNormalization1.5450.0521.597
runPerCellQC0.4010.0200.421
runSCANORAMA000
runSCMerge0.0010.0000.001
runScDblFinder15.715 0.39516.095
runScranSNN0.6130.0040.618
runScrublet0.0010.0000.001
runSeurat40.986 0.12041.106
runSingleR0.0480.0040.053
runVAM0.8870.0150.902
runWilcox1.0160.0081.023
runZINBWaVE0.0020.0000.001
sampleSummaryStats0.4750.0000.475
scaterCPM0.1800.0000.179
scaterPCA0.7200.0000.719
scaterlogNormCounts0.8870.0000.887
sce0.0010.0000.001
scranModelGeneVar0.2920.0080.300
sctkListGeneSetCollections0.2560.0040.260
sctkPythonInstallConda000
sctkPythonInstallVirtualEnv0.0000.0000.001
selectSCTKConda000
selectSCTKVirtualEnvironment000
setSCTKDisplayRow0.4450.0040.449
seuratComputeHeatmap0.0010.0000.001
seuratComputeJackStraw0.0010.0000.001
seuratElbowPlot0.0010.0000.002
seuratFindClusters0.0020.0000.001
seuratFindHVG0.0010.0000.001
seuratICA0.0010.0000.001
seuratJackStrawPlot0.0020.0000.002
seuratNormalizeData0.0010.0000.001
seuratPCA0.0010.0000.001
seuratPlotHVG0.0020.0000.001
seuratReductionPlot0.0010.0000.001
seuratRunUMAP0.0010.0000.001
seuratSCTransform3.4490.1283.577
seuratScaleData0.0010.0000.001
singleCellTK000
subDiffEx0.6060.0000.606
subsetSCECols0.2240.0000.225
subsetSCERows0.5980.0000.598
summarizeSCE0.0640.0000.064
trimCounts0.3060.0120.318
visPlot0.7060.0000.706