Yichen Wang
| Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 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 -0400 (Wed, 27 Oct 2021) |
| Back to Multiple platform build/check report for BioC 3.14 |
|
This page was generated on 2022-04-13 12:07:22 -0400 (Wed, 13 Apr 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4324 |
| tokay2 | Windows Server 2012 R2 Standard | x64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4077 |
| machv2 | macOS 10.14.6 Mojave | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 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 | ||||
|
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. |
| Package 1807/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| singleCellTK 2.4.0 (landing page) Yichen Wang
| nebbiolo2 | Linux (Ubuntu 20.04.4 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: 2.4.0 |
| Command: set _R_CHECK_FORCE_SUGGESTS_=0&& C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:singleCellTK.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings singleCellTK_2.4.0.tar.gz |
| StartedAt: 2022-04-13 03:03:19 -0400 (Wed, 13 Apr 2022) |
| EndedAt: 2022-04-13 03:17:27 -0400 (Wed, 13 Apr 2022) |
| EllapsedTime: 847.8 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: singleCellTK.Rcheck |
| Warnings: NA |
##############################################################################
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###
### Running command:
###
### set _R_CHECK_FORCE_SUGGESTS_=0&& C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:singleCellTK.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings singleCellTK_2.4.0.tar.gz
###
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##############################################################################
* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/singleCellTK.Rcheck'
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 whether package 'singleCellTK' can be installed ... OK
* checking installed package size ... NOTE
installed size is 7.8Mb
sub-directories of 1Mb or more:
extdata 1.5Mb
html 1.2Mb
shiny 2.7Mb
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... ERROR
Running examples in 'singleCellTK-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: enrichRSCE
> ### Title: enrichR Given a list of genes this function runs the enrichR()
> ### to perform Gene enrichment
> ### Aliases: enrichRSCE
>
> ### ** Examples
>
> enrichRSCE(mouseBrainSubsetSCE, "Cmtm5", "GO_Cellular_Component_2017")
EnrichR website not responding
Error in enrichRSCE(mouseBrainSubsetSCE, "Cmtm5", "GO_Cellular_Component_2017") :
database 'GO_Cellular_Component_2017' does not exist.
Execution halted
** running examples for arch 'x64' ... ERROR
Running examples in 'singleCellTK-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: enrichRSCE
> ### Title: enrichR Given a list of genes this function runs the enrichR()
> ### to perform Gene enrichment
> ### Aliases: enrichRSCE
>
> ### ** Examples
>
> enrichRSCE(mouseBrainSubsetSCE, "Cmtm5", "GO_Cellular_Component_2017")
EnrichR website not responding
Error in enrichRSCE(mouseBrainSubsetSCE, "Cmtm5", "GO_Cellular_Component_2017") :
database 'GO_Cellular_Component_2017' does not exist.
Execution halted
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'spelling.R'
Running 'testthat.R'
OK
** running tests for arch 'x64' ...
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 ERRORs, 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.14-bioc/meat/singleCellTK.Rcheck/00check.log'
for details.
singleCellTK.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/singleCellTK_2.4.0.tar.gz && rm -rf singleCellTK.buildbin-libdir && mkdir singleCellTK.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=singleCellTK.buildbin-libdir singleCellTK_2.4.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL singleCellTK_2.4.0.zip && rm singleCellTK_2.4.0.tar.gz singleCellTK_2.4.0.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
3 42.2M 3 1641k 0 0 1695k 0 0:00:25 --:--:-- 0:00:25 1695k
10 42.2M 10 4401k 0 0 2247k 0 0:00:19 0:00:01 0:00:18 2247k
18 42.2M 18 8142k 0 0 2750k 0 0:00:15 0:00:02 0:00:13 2750k
27 42.2M 27 11.6M 0 0 3008k 0 0:00:14 0:00:03 0:00:11 3008k
34 42.2M 34 14.5M 0 0 3007k 0 0:00:14 0:00:04 0:00:10 3006k
43 42.2M 43 18.5M 0 0 3178k 0 0:00:13 0:00:05 0:00:08 3465k
55 42.2M 55 23.2M 0 0 3419k 0 0:00:12 0:00:06 0:00:06 3877k
68 42.2M 68 29.0M 0 0 3726k 0 0:00:11 0:00:07 0:00:04 4302k
84 42.2M 84 35.5M 0 0 4055k 0 0:00:10 0:00:08 0:00:02 4882k
93 42.2M 93 39.6M 0 0 4070k 0 0:00:10 0:00:09 0:00:01 5123k
100 42.2M 100 42.2M 0 0 4106k 0 0:00:10 0:00:10 --:--:-- 5317k
install for i386
* 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
converting help for package 'singleCellTK'
finding HTML links ... done
MitoGenes html
SEG html
calcEffectSizes html
combineSCE html
computeHeatmap html
computeZScore html
constructSCE html
convertSCEToSeurat html
convertSeuratToSCE html
dataAnnotationColor html
finding level-2 HTML links ... done
dedupRowNames html
detectCellOutlier html
diffAbundanceFET html
discreteColorPalette html
distinctColors html
dot-addSeuratToMetaDataSCE html
dot-checkDiffExpResultExists html
dot-computeSignificantPC html
dot-extractSCEAnnotation html
dot-formatDEAList html
dot-getComponentNames html
dot-ggBar html
dot-ggDensity html
dot-ggScatter html
dot-ggViolin html
dot-sce2adata html
dot-seuratGetVariableFeatures html
dot-seuratInvalidate html
dot-updateAssaySCE html
downSampleCells html
downSampleDepth html
enrichRSCE html
expData-ANY-character-method html
expData-set-ANY-character-CharacterOrNullOrMissing-logical-method
html
expData-set html
expData html
expDataNames-ANY-method html
expDataNames html
expDeleteDataTag html
expSetDataTag html
expTaggedData html
exportSCE html
exportSCEToSeurat html
exportSCEtoAnnData html
exportSCEtoFlatFile html
featureIndex html
findMarkerDiffExp html
findMarkerTopTable html
generateHTANMeta html
generateMeta html
generateSimulatedData html
getBiomarker html
getDEGTopTable html
getMSigDBTable html
getSceParams html
getTSNE html
getTopHVG html
getUMAP html
importAlevin html
importAnnData html
importBUStools html
importCellRanger html
importCellRangerV2Sample html
importCellRangerV3Sample html
importDropEst html
importExampleData html
importFromFiles html
importGeneSetsFromCollection html
importGeneSetsFromGMT html
importGeneSetsFromList html
importGeneSetsFromMSigDB html
importMitoGeneSet html
importMultipleSources html
importOptimus html
importSEQC html
importSTARsolo html
iterateSimulations html
mergeSCEColData html
mouseBrainSubsetSCE html
msigdb_table html
plotBarcodeRankDropsResults html
plotBarcodeRankScatter html
plotBatchCorrCompare html
plotBatchVariance html
plotBcdsResults html
plotClusterAbundance html
plotCxdsResults html
plotDEGHeatmap html
plotDEGRegression html
plotDEGViolin html
plotDecontXResults html
plotDimRed html
plotDoubletFinderResults html
plotEmptyDropsResults html
plotEmptyDropsScatter html
plotMASTThresholdGenes html
plotMarkerDiffExp html
plotPCA html
plotRunPerCellQCResults html
plotSCEBarAssayData html
plotSCEBarColData html
plotSCEBatchFeatureMean html
plotSCEDensity html
plotSCEDensityAssayData html
plotSCEDensityColData html
plotSCEDimReduceColData html
plotSCEDimReduceFeatures html
plotSCEHeatmap html
plotSCEScatter html
plotSCEViolin html
plotSCEViolinAssayData html
plotSCEViolinColData html
plotScDblFinderResults html
plotScdsHybridResults html
plotScrubletResults html
plotTSNE html
plotTopHVG html
plotUMAP html
qcInputProcess html
readSingleCellMatrix html
reportCellQC html
reportDiffExp html
reportDropletQC html
reportFindMarker html
reportQCTool html
retrieveSCEIndex html
runANOVA html
runBBKNN html
runBarcodeRankDrops html
runBcds html
runCellQC html
runComBatSeq html
runCxds html
runCxdsBcdsHybrid html
runDEAnalysis html
runDESeq2 html
runDecontX html
runDimReduce html
runDoubletFinder html
runDropletQC html
runEmptyDrops html
runFastMNN html
runFeatureSelection html
runGSVA html
runKMeans html
runLimmaBC html
runLimmaDE html
runMAST html
runMNNCorrect html
runNormalization html
runPerCellQC html
runSCANORAMA html
runSCMerge html
runScDblFinder html
runScranSNN html
runScrublet html
runSingleR html
runVAM html
runWilcox html
runZINBWaVE html
sampleSummaryStats html
scaterCPM html
scaterPCA html
scaterlogNormCounts html
sce html
sceBatches html
scranModelGeneVar html
sctkListGeneSetCollections html
sctkPythonInstallConda html
sctkPythonInstallVirtualEnv html
selectSCTKConda html
selectSCTKVirtualEnvironment html
setSCTKDisplayRow html
seuratComputeHeatmap html
seuratComputeJackStraw html
seuratElbowPlot html
seuratFindClusters html
seuratFindHVG html
seuratFindMarkers html
seuratGenePlot html
seuratHeatmapPlot html
seuratICA html
seuratIntegration html
seuratJackStrawPlot html
seuratNormalizeData html
seuratPCA html
seuratPlotHVG html
seuratReductionPlot html
seuratReport html
seuratRunTSNE html
seuratRunUMAP html
seuratSCTransform html
seuratScaleData html
seuratVariableFeatures html
simpleLog html
singleCellTK html
subDiffEx html
subsetSCECols html
subsetSCERows html
summarizeSCE html
trimCounts html
** 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
install for x64
* installing *source* package 'singleCellTK' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'singleCellTK' as singleCellTK_2.4.0.zip
* DONE (singleCellTK)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'singleCellTK' successfully unpacked and MD5 sums checked
|
singleCellTK.Rcheck/tests_i386/spelling.Rout
R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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
0.28 0.06 0.32
|
singleCellTK.Rcheck/tests_x64/spelling.Rout
R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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
0.21 0.07 0.29
|
|
singleCellTK.Rcheck/tests_i386/testthat.Rout
R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
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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Calculating gene variances
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[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
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[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Estimating GSVA scores for 34 gene sets.
Estimating ECDFs with Gaussian kernels
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Performing log-normalization
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[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating gene variances
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
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[----|----|----|----|----|----|----|----|----|----|
**************************************************|
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[03:11:05] 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.
[03:11:08] 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.
[03:11:41] 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%
|
|======================================================================| 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 15 | SKIP 0 | PASS 126 ]
[ FAIL 0 | WARN 15 | SKIP 0 | PASS 126 ]
>
> proc.time()
user system elapsed
234.73 8.28 247.29
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singleCellTK.Rcheck/tests_x64/testthat.Rout
R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
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
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Calculating gene variances
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[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
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[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Estimating GSVA scores for 34 gene sets.
Estimating ECDFs with Gaussian kernels
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Performing log-normalization
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Calculating gene variances
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Calculating feature variances of standardized and clipped values
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[03:15:18] 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.
[03:15:20] 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.
[03:15:47] 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
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[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Performing log-normalization
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[----|----|----|----|----|----|----|----|----|----|
**************************************************|
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Calculating gene variances
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[----|----|----|----|----|----|----|----|----|----|
**************************************************|
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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**************************************************|
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[----|----|----|----|----|----|----|----|----|----|
**************************************************|
[ FAIL 0 | WARN 15 | SKIP 0 | PASS 126 ]
[ FAIL 0 | WARN 15 | SKIP 0 | PASS 126 ]
>
> proc.time()
user system elapsed
247.39 4.78 253.68
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singleCellTK.Rcheck/examples_i386/singleCellTK-Ex.timings
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singleCellTK.Rcheck/examples_x64/singleCellTK-Ex.timings
|