Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-01-14 13:05:47 -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 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: 2022-01-13 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: /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: 2022-01-13 09:39:07 -0500 (Thu, 13 Jan 2022)
EndedAt: 2022-01-13 09:50:54 -0500 (Thu, 13 Jan 2022)
EllapsedTime: 707.8 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 22.199  0.255  22.442
plotScDblFinderResults   21.454  0.365  21.758
importExampleData        19.742  1.745  22.318
runDoubletFinder         16.262  0.064  16.325
runScDblFinder           10.867  0.300  11.125
plotBatchCorrCompare     10.945  0.109  11.032
plotBcdsResults           9.393  0.164   8.406
plotScdsHybridResults     8.766  0.104   7.935
plotDecontXResults        7.239  0.048   7.288
plotEmptyDropsResults     6.848  0.012   6.859
plotCxdsResults           6.664  0.120   6.773
plotEmptyDropsScatter     6.715  0.024   6.739
findMarkerTopTable        5.926  0.556   6.481
findMarkerDiffExp         6.236  0.160   6.397
runEmptyDrops             6.347  0.000   6.346
detectCellOutlier         5.931  0.144   6.077
runDecontX                5.856  0.100   5.956
plotUMAP                  5.749  0.032   5.772
plotMarkerDiffExp         5.538  0.024   5.562
getUMAP                   4.615  0.424   5.033
* 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 
  0.196   0.029   0.211 

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%
[09:49:17] 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.
[09:49:19] 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.
[09:49:43] 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%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|

  |                                                                            
  |                                                                      |   0%
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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%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
[ FAIL 0 | WARN 15 | SKIP 0 | PASS 126 ]
> 
> proc.time()
   user  system elapsed 
205.694   5.798 210.480 

Example timings

singleCellTK.Rcheck/singleCellTK-Ex.timings

nameusersystemelapsed
MitoGenes0.0030.0010.002
SEG0.0020.0000.002
calcEffectSizes0.1570.0080.166
combineSCE2.1050.0112.117
computeZScore0.3410.0290.369
convertSCEToSeurat2.9110.0802.991
convertSeuratToSCE0.5920.0790.672
dedupRowNames0.0630.0080.072
detectCellOutlier5.9310.1446.077
diffAbundanceFET0.0500.0000.051
discreteColorPalette0.0070.0000.006
distinctColors0.0030.0000.002
downSampleCells0.8230.0200.842
downSampleDepth0.6750.0040.680
enrichRSCE0.4520.0281.659
exportSCE0.0010.0000.001
exportSCEtoAnnData0.1300.0000.129
exportSCEtoFlatFile0.1250.0070.134
featureIndex0.0270.0000.027
findMarkerDiffExp6.2360.1606.397
findMarkerTopTable5.9260.5566.481
generateSimulatedData0.0400.0120.051
getBiomarker0.0290.0040.034
getDEGTopTable0.7880.0050.792
getMSigDBTable0.0030.0000.003
getTSNE0.3960.0190.415
getTopHVG0.3350.0170.350
getUMAP4.6150.4245.033
importAnnData0.0000.0000.001
importBUStools0.3250.0000.326
importCellRanger1.2180.0081.228
importCellRangerV2Sample0.3390.0000.339
importCellRangerV3Sample0.4330.0000.433
importDropEst0.4300.0000.431
importExampleData19.742 1.74522.318
importGeneSetsFromCollection0.7260.0080.734
importGeneSetsFromGMT0.0650.0000.065
importGeneSetsFromList0.160.000.16
importGeneSetsFromMSigDB3.7450.2233.968
importMitoGeneSet0.0490.0010.049
importOptimus0.0010.0000.001
importSEQC0.3140.0030.318
importSTARsolo0.3320.0000.332
iterateSimulations0.4930.0030.497
mergeSCEColData0.4910.0160.507
mouseBrainSubsetSCE0.0010.0000.001
msigdb_table0.0010.0010.001
plotBarcodeRankDropsResults0.9640.0080.972
plotBarcodeRankScatter0.7840.0000.784
plotBatchCorrCompare10.945 0.10911.032
plotBatchVariance0.2730.0200.293
plotBcdsResults9.3930.1648.406
plotClusterAbundance0.6440.0120.656
plotCxdsResults6.6640.1206.773
plotDEGHeatmap4.8870.0724.960
plotDEGRegression3.4630.0123.470
plotDEGViolin4.0260.1364.155
plotDecontXResults7.2390.0487.288
plotDimRed0.2900.0040.294
plotDoubletFinderResults22.199 0.25522.442
plotEmptyDropsResults6.8480.0126.859
plotEmptyDropsScatter6.7150.0246.739
plotMASTThresholdGenes2.7750.0082.783
plotMarkerDiffExp5.5380.0245.562
plotPCA0.6440.0000.644
plotRunPerCellQCResults0.0010.0000.001
plotSCEBarAssayData0.1090.0000.109
plotSCEBarColData0.0820.0040.085
plotSCEBatchFeatureMean0.1710.0000.171
plotSCEDensity0.1580.0000.159
plotSCEDensityAssayData0.1200.0000.121
plotSCEDensityColData0.1560.0000.155
plotSCEDimReduceColData0.8320.0040.835
plotSCEDimReduceFeatures0.3790.0000.378
plotSCEHeatmap0.8170.0000.817
plotSCEScatter0.3740.0040.379
plotSCEViolin0.1680.0000.168
plotSCEViolinAssayData0.1840.0000.185
plotSCEViolinColData0.1550.0040.159
plotScDblFinderResults21.454 0.36521.758
plotScdsHybridResults8.7660.1047.935
plotScrubletResults0.0010.0000.002
plotTSNE0.6080.0040.613
plotTopHVG0.4890.0000.489
plotUMAP5.7490.0325.772
readSingleCellMatrix0.0040.0000.004
reportCellQC0.2120.0000.211
reportDropletQC0.0010.0000.001
reportQCTool0.2100.0040.213
retrieveSCEIndex0.0140.0000.014
runANOVA1.250.001.25
runBBKNN000
runBarcodeRankDrops0.6280.0040.632
runBcds2.5450.0561.695
runCellQC0.2110.0000.211
runComBatSeq0.4460.0000.445
runCxds0.7180.0080.726
runCxdsBcdsHybrid2.6240.0401.753
runDEAnalysis1.0450.0041.048
runDESeq24.9340.0204.953
runDecontX5.8560.1005.956
runDimReduce1.1230.0001.123
runDoubletFinder16.262 0.06416.325
runDropletQC0.0020.0000.001
runEmptyDrops6.3470.0006.346
runFastMNN1.5690.0521.620
runFeatureSelection0.2040.0000.204
runGSVA0.8780.0040.882
runKMeans0.5750.0000.575
runLimmaBC0.0940.0000.093
runLimmaDE0.8870.0000.887
runMAST3.4630.0083.429
runMNNCorrect0.6510.0000.650
runNormalization1.4950.0361.531
runPerCellQC0.4770.0120.489
runSCANORAMA000
runSCMerge0.0020.0000.001
runScDblFinder10.867 0.30011.125
runScranSNN0.5860.0040.590
runScrublet0.0010.0000.001
runSingleR0.0450.0000.044
runVAM0.8050.0000.806
runWilcox0.9940.0000.995
runZINBWaVE0.0010.0000.002
sampleSummaryStats0.4350.0000.436
scaterCPM0.1740.0040.179
scaterPCA0.7460.0000.747
scaterlogNormCounts0.8620.0000.863
sce0.0000.0010.001
scranModelGeneVar0.2500.0030.252
sctkListGeneSetCollections0.2260.0000.226
sctkPythonInstallConda000
sctkPythonInstallVirtualEnv000
selectSCTKConda0.0000.0000.001
selectSCTKVirtualEnvironment000
setSCTKDisplayRow0.4550.0000.454
seuratComputeHeatmap0.0020.0000.002
seuratComputeJackStraw0.0010.0000.001
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
seuratReductionPlot0.0020.0000.001
seuratRunUMAP0.0010.0000.001
seuratSCTransform3.2450.0003.250
seuratScaleData0.0020.0000.001
singleCellTK000
subDiffEx0.5730.0000.573
subsetSCECols0.2080.0000.208
subsetSCERows0.5920.0000.592
summarizeSCE0.0590.0000.059
trimCounts0.3140.0000.313