Yusuke Koga
| Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021) |
| git_url: https://git.bioconductor.org/packages/singleCellTK |
| git_branch: RELEASE_3_13 |
| git_last_commit: 9fdc1a1 |
| git_last_commit_date: 2021-05-19 12:35:15 -0400 (Wed, 19 May 2021) |
| Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:05:53 -0400 (Fri, 15 Oct 2021).
|
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. |
| Package 1778/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| singleCellTK 2.2.0 (landing page) Yusuke Koga
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | ERROR | OK | |||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: singleCellTK |
| Version: 2.2.0 |
| Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:singleCellTK.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings singleCellTK_2.2.0.tar.gz |
| StartedAt: 2021-10-14 11:39:17 -0400 (Thu, 14 Oct 2021) |
| EndedAt: 2021-10-14 11:48:54 -0400 (Thu, 14 Oct 2021) |
| EllapsedTime: 577.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: singleCellTK.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:singleCellTK.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings singleCellTK_2.2.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.13-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 ‘2.2.0’
* 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 ... OK
* 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 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 24.599 0.129 24.720
importExampleData 16.366 2.817 20.068
runDoubletFinder 18.062 0.016 18.078
plotScDblFinderResults 17.345 0.316 17.640
plotDecontXResults 12.755 0.132 12.878
runScDblFinder 10.385 0.256 10.634
plotScdsHybridResults 9.680 0.105 8.898
plotBcdsResults 8.716 0.097 7.891
runDecontX 6.793 0.039 6.834
plotEmptyDropsResults 6.804 0.020 6.825
plotEmptyDropsScatter 6.728 0.003 6.732
runEmptyDrops 6.643 0.004 6.647
findMarkerDiffExp 6.410 0.164 6.574
plotCxdsResults 6.417 0.080 6.489
plotUMAP 6.071 0.084 6.153
plotMarkerDiffExp 5.143 0.004 5.148
runDESeq2 4.998 0.056 5.053
* 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: OK
singleCellTK.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL singleCellTK ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.13-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)
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
0.207 0.032 0.230
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
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
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")
[1] "Creating 65 artificial doublets..."
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%
[11:48:00] 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.
[11:48:01] 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.
[11:48:21] 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 1 | SKIP 0 | PASS 44 ]
>
> proc.time()
user system elapsed
102.897 1.933 102.904
singleCellTK.Rcheck/singleCellTK-Ex.timings
| name | user | system | elapsed | |
| MitoGenes | 0.003 | 0.000 | 0.002 | |
| SEG | 0.000 | 0.002 | 0.002 | |
| calcEffectSizes | 0.777 | 0.008 | 0.786 | |
| combineSCE | 2.013 | 0.160 | 2.173 | |
| computeZScore | 0.330 | 0.028 | 0.359 | |
| convertGeneIDs | 3.584 | 0.252 | 3.837 | |
| convertSCEToSeurat | 1.961 | 0.063 | 2.025 | |
| convertSeuratToSCE | 0.702 | 0.013 | 0.714 | |
| dedupRowNames | 0.055 | 0.000 | 0.055 | |
| diffAbundanceFET | 0.037 | 0.011 | 0.048 | |
| discreteColorPalette | 0.010 | 0.001 | 0.009 | |
| distinctColors | 0.002 | 0.000 | 0.002 | |
| downSampleCells | 1.563 | 0.015 | 1.580 | |
| downSampleDepth | 0.612 | 0.004 | 0.616 | |
| enrichRSCE | 0.308 | 0.012 | 1.547 | |
| exportSCE | 0.002 | 0.000 | 0.001 | |
| exportSCEtoAnnData | 0.151 | 0.016 | 0.166 | |
| exportSCEtoFlatFile | 0.121 | 0.022 | 0.143 | |
| featureIndex | 0.028 | 0.000 | 0.029 | |
| findMarkerDiffExp | 6.410 | 0.164 | 6.574 | |
| generateMeta | 0.063 | 0.004 | 0.066 | |
| generateSimulatedData | 0.054 | 0.000 | 0.054 | |
| getBiomarker | 0.033 | 0.007 | 0.040 | |
| getMSigDBTable | 0.005 | 0.000 | 0.005 | |
| getTSNE | 0.548 | 0.012 | 0.559 | |
| getTopHVG | 0.286 | 0.012 | 0.297 | |
| getUMAP | 4.798 | 0.068 | 4.858 | |
| importAnnData | 0.001 | 0.000 | 0.001 | |
| importBUStools | 0.335 | 0.004 | 0.338 | |
| importCellRanger | 1.247 | 0.020 | 1.268 | |
| importCellRangerV2Sample | 0.328 | 0.000 | 0.328 | |
| importCellRangerV3Sample | 0.521 | 0.012 | 0.535 | |
| importDropEst | 0.480 | 0.000 | 0.481 | |
| importExampleData | 16.366 | 2.817 | 20.068 | |
| importGeneSetsFromCollection | 0.722 | 0.044 | 0.766 | |
| importGeneSetsFromGMT | 0.061 | 0.004 | 0.065 | |
| importGeneSetsFromList | 0.157 | 0.004 | 0.161 | |
| importGeneSetsFromMSigDB | 3.995 | 0.175 | 4.174 | |
| importMitoGeneSet | 0.053 | 0.000 | 0.053 | |
| importOptimus | 0.000 | 0.001 | 0.002 | |
| importSEQC | 0.264 | 0.002 | 0.267 | |
| importSTARsolo | 0.323 | 0.003 | 0.326 | |
| iterateSimulations | 0.51 | 0.02 | 0.53 | |
| mergeSCEColData | 0.502 | 0.004 | 0.506 | |
| mouseBrainSubsetSCE | 0.001 | 0.000 | 0.001 | |
| msigdb_table | 0.001 | 0.000 | 0.001 | |
| plotBarcodeRankDropsResults | 1.140 | 0.016 | 1.156 | |
| plotBarcodeRankScatter | 0.859 | 0.004 | 0.863 | |
| plotBatchVariance | 0.272 | 0.000 | 0.272 | |
| plotBcdsResults | 8.716 | 0.097 | 7.891 | |
| plotBiomarker | 0.729 | 0.004 | 0.733 | |
| plotClusterAbundance | 0.655 | 0.000 | 0.654 | |
| plotCxdsResults | 6.417 | 0.080 | 6.489 | |
| plotDEGHeatmap | 2.888 | 0.032 | 2.920 | |
| plotDEGRegression | 3.387 | 0.016 | 3.391 | |
| plotDEGViolin | 3.962 | 0.075 | 4.022 | |
| plotDecontXResults | 12.755 | 0.132 | 12.878 | |
| plotDimRed | 0.374 | 0.052 | 0.425 | |
| plotDoubletFinderResults | 24.599 | 0.129 | 24.720 | |
| plotEmptyDropsResults | 6.804 | 0.020 | 6.825 | |
| plotEmptyDropsScatter | 6.728 | 0.003 | 6.732 | |
| plotMASTThresholdGenes | 1.703 | 0.015 | 1.718 | |
| plotMarkerDiffExp | 5.143 | 0.004 | 5.148 | |
| plotPCA | 0.707 | 0.000 | 0.706 | |
| plotRunPerCellQCResults | 0.002 | 0.000 | 0.002 | |
| plotSCEBarAssayData | 0.107 | 0.000 | 0.106 | |
| plotSCEBarColData | 0.086 | 0.000 | 0.087 | |
| plotSCEBatchFeatureMean | 0.179 | 0.000 | 0.178 | |
| plotSCEDensity | 0.169 | 0.000 | 0.168 | |
| plotSCEDensityAssayData | 0.139 | 0.000 | 0.139 | |
| plotSCEDensityColData | 0.168 | 0.000 | 0.169 | |
| plotSCEDimReduceColData | 0.929 | 0.000 | 0.928 | |
| plotSCEDimReduceFeatures | 0.412 | 0.000 | 0.412 | |
| plotSCEHeatmap | 0.732 | 0.000 | 0.732 | |
| plotSCEScatter | 0.452 | 0.000 | 0.452 | |
| plotSCEViolin | 0.173 | 0.000 | 0.173 | |
| plotSCEViolinAssayData | 0.189 | 0.000 | 0.190 | |
| plotSCEViolinColData | 0.173 | 0.000 | 0.173 | |
| plotScDblFinderResults | 17.345 | 0.316 | 17.640 | |
| plotScdsHybridResults | 9.680 | 0.105 | 8.898 | |
| plotScrubletResults | 0.002 | 0.000 | 0.002 | |
| plotTSNE | 0.672 | 0.000 | 0.673 | |
| plotTopHVG | 0.485 | 0.000 | 0.484 | |
| plotUMAP | 6.071 | 0.084 | 6.153 | |
| readSingleCellMatrix | 0.000 | 0.003 | 0.004 | |
| reportCellQC | 0.218 | 0.001 | 0.218 | |
| reportDropletQC | 0.002 | 0.000 | 0.001 | |
| reportQCTool | 0.223 | 0.000 | 0.223 | |
| retrieveSCEIndex | 0.010 | 0.003 | 0.014 | |
| runANOVA | 1.247 | 0.009 | 1.254 | |
| runBBKNN | 0.000 | 0.001 | 0.000 | |
| runBarcodeRankDrops | 0.622 | 0.002 | 0.624 | |
| runBcds | 2.601 | 0.052 | 1.744 | |
| runCellQC | 0.222 | 0.000 | 0.222 | |
| runComBatSeq | 0.472 | 0.008 | 0.479 | |
| runCxds | 0.677 | 0.000 | 0.677 | |
| runCxdsBcdsHybrid | 2.768 | 0.057 | 1.894 | |
| runDEAnalysis | 1.036 | 0.000 | 1.037 | |
| runDESeq2 | 4.998 | 0.056 | 5.053 | |
| runDecontX | 6.793 | 0.039 | 6.834 | |
| runDimensionalityReduction | 0.935 | 0.004 | 0.939 | |
| runDoubletFinder | 18.062 | 0.016 | 18.078 | |
| runDropletQC | 0.002 | 0.000 | 0.002 | |
| runEmptyDrops | 6.643 | 0.004 | 6.647 | |
| runFastMNN | 1.808 | 0.000 | 1.808 | |
| runFeatureSelection | 0.195 | 0.004 | 0.198 | |
| runKMeans | 0.624 | 0.004 | 0.629 | |
| runLimmaBC | 0.119 | 0.000 | 0.118 | |
| runLimmaDE | 1.018 | 0.008 | 1.026 | |
| runMAST | 3.623 | 0.020 | 3.613 | |
| runMNNCorrect | 0.763 | 0.000 | 0.763 | |
| runNormalization | 1.216 | 0.012 | 1.228 | |
| runPerCellQC | 0.403 | 0.000 | 0.404 | |
| runSCANORAMA | 0 | 0 | 0 | |
| runSCMerge | 0.001 | 0.000 | 0.002 | |
| runScDblFinder | 10.385 | 0.256 | 10.634 | |
| runScranSNN | 0.662 | 0.000 | 0.662 | |
| runScrublet | 0.000 | 0.002 | 0.002 | |
| runSingleR | 0.053 | 0.001 | 0.054 | |
| runWilcox | 1.051 | 0.000 | 1.051 | |
| runZINBWaVE | 0.002 | 0.000 | 0.002 | |
| sampleSummaryStats | 0.416 | 0.004 | 0.420 | |
| scaterCPM | 0.174 | 0.012 | 0.186 | |
| scaterPCA | 0.823 | 0.008 | 0.831 | |
| scaterlogNormCounts | 0.883 | 0.024 | 0.907 | |
| sce | 0.000 | 0.002 | 0.002 | |
| scranModelGeneVar | 0.260 | 0.018 | 0.277 | |
| sctkListGeneSetCollections | 0.199 | 0.004 | 0.203 | |
| sctkPythonInstallConda | 0 | 0 | 0 | |
| sctkPythonInstallVirtualEnv | 0 | 0 | 0 | |
| selectSCTKConda | 0 | 0 | 0 | |
| selectSCTKVirtualEnvironment | 0.001 | 0.000 | 0.001 | |
| setSCTKDisplayRow | 0.456 | 0.008 | 0.464 | |
| seuratComputeHeatmap | 0.002 | 0.000 | 0.002 | |
| seuratComputeJackStraw | 0.002 | 0.000 | 0.002 | |
| seuratElbowPlot | 0.002 | 0.000 | 0.002 | |
| seuratFindClusters | 0.002 | 0.000 | 0.002 | |
| seuratFindHVG | 0.001 | 0.000 | 0.002 | |
| seuratICA | 0.001 | 0.000 | 0.001 | |
| seuratJackStrawPlot | 0.001 | 0.000 | 0.001 | |
| seuratNormalizeData | 0.000 | 0.001 | 0.001 | |
| seuratPCA | 0.000 | 0.001 | 0.001 | |
| seuratPlotHVG | 0.000 | 0.002 | 0.001 | |
| seuratReductionPlot | 0.000 | 0.001 | 0.001 | |
| seuratRunUMAP | 0.000 | 0.001 | 0.002 | |
| seuratSCTransform | 2.962 | 0.026 | 2.988 | |
| seuratScaleData | 0.000 | 0.002 | 0.002 | |
| singleCellTK | 0.000 | 0.001 | 0.001 | |
| subDiffEx | 0.596 | 0.009 | 0.605 | |
| subsetSCECols | 0.215 | 0.004 | 0.219 | |
| subsetSCERows | 0.668 | 0.000 | 0.669 | |
| summarizeSCE | 0.062 | 0.000 | 0.062 | |
| trimCounts | 0.311 | 0.000 | 0.310 | |
| visPlot | 0.638 | 0.000 | 0.639 | |