| Back to Multiple platform build/check report for BioC 3.12 |
|
This page was generated on 2021-05-06 12:33:39 -0400 (Thu, 06 May 2021).
|
To the developers/maintainers of the singleCellTK package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1725/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| singleCellTK 2.0.0 (landing page) Yusuke Koga
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | ERROR | OK | |||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | ERROR | OK | |||||||||
| Package: singleCellTK |
| Version: 2.0.0 |
| Command: set _R_CHECK_FORCE_SUGGESTS_=0&& C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:singleCellTK.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings singleCellTK_2.0.0.tar.gz |
| StartedAt: 2021-05-06 07:02:02 -0400 (Thu, 06 May 2021) |
| EndedAt: 2021-05-06 07:11:37 -0400 (Thu, 06 May 2021) |
| EllapsedTime: 575.3 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-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:singleCellTK.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings singleCellTK_2.0.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/singleCellTK.Rcheck'
* using R version 4.0.5 (2021-03-31)
* 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 '2.0.0'
* 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 5.0Mb
sub-directories of 1Mb or more:
extdata 1.5Mb
* 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:
'BiocGenerics' 'ggplotify' 'kableExtra' 'shinyBS' 'shinyFiles'
'shinyWidgets' 'shinyjqui' 'shinythemes'
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 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: importGeneSetsFromMSigDB
> ### Title: Imports gene sets from MSigDB
> ### Aliases: importGeneSetsFromMSigDB
>
> ### ** Examples
>
> data(scExample)
> sce <- importGeneSetsFromMSigDB(inSCE = sce,
+ categoryIDs = "H",
+ species = "Homo sapiens",
+ mapping = "gene_symbol",
+ by = "feature_name")
Thu May 06 07:08:45 2021 .. Importing 'H' gene sets (n = 50)
Error in validObject(.Object) :
invalid class "GeneSet" object: gene symbols must be unique
Calls: importGeneSetsFromMSigDB ... <Anonymous> -> initialize -> initialize -> validObject
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: importGeneSetsFromMSigDB
> ### Title: Imports gene sets from MSigDB
> ### Aliases: importGeneSetsFromMSigDB
>
> ### ** Examples
>
> data(scExample)
> sce <- importGeneSetsFromMSigDB(inSCE = sce,
+ categoryIDs = "H",
+ species = "Homo sapiens",
+ mapping = "gene_symbol",
+ by = "feature_name")
Thu May 06 07:09:51 2021 .. Importing 'H' gene sets (n = 50)
Error in validObject(.Object) :
invalid class "GeneSet" object: gene symbols must be unique
Calls: importGeneSetsFromMSigDB ... <Anonymous> -> initialize -> initialize -> validObject
Execution halted
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'spelling.R'
Running 'testthat.R'
ERROR
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
10. \-Seurat:::FindNeighbors.Seurat(seurat, dims = seuratPcs, verbose = verbose)
11. +-SeuratObject::`DefaultAssay<-`(object = `*tmp*`, value = assay)
12. \-SeuratObject:::`DefaultAssay<-.Graph`(object = `*tmp*`, value = assay)
13. \-SeuratObject:::UpdateSlots(object = object)
14. +-base::do.call(what = "new", args = object.list)
15. \-methods::new(...)
16. +-methods::initialize(value, ...)
17. \-Matrix:::initialize(value, ...)
18. +-methods::callNextMethod()
19. \-methods:::.nextMethod(.Object = .Object, ... = ...)
20. \-methods::validObject(.Object)
[ FAIL 2 | WARN 0 | SKIP 0 | PASS 25 ]
Error: Test failures
Execution halted
** running tests for arch 'x64' ...
Running 'spelling.R'
Running 'testthat.R'
ERROR
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
10. \-Seurat:::FindNeighbors.Seurat(seurat, dims = seuratPcs, verbose = verbose)
11. +-SeuratObject::`DefaultAssay<-`(object = `*tmp*`, value = assay)
12. \-SeuratObject:::`DefaultAssay<-.Graph`(object = `*tmp*`, value = assay)
13. \-SeuratObject:::UpdateSlots(object = object)
14. +-base::do.call(what = "new", args = object.list)
15. \-methods::new(...)
16. +-methods::initialize(value, ...)
17. \-Matrix:::initialize(value, ...)
18. +-methods::callNextMethod()
19. \-methods:::.nextMethod(.Object = .Object, ... = ...)
20. \-methods::validObject(.Object)
[ FAIL 2 | WARN 0 | SKIP 0 | PASS 25 ]
Error: Test failures
Execution halted
* 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: 4 ERRORs, 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.12-bioc/meat/singleCellTK.Rcheck/00check.log'
for details.
singleCellTK.Rcheck/00install.out
##############################################################################
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/singleCellTK_2.0.0.tar.gz && rm -rf singleCellTK.buildbin-libdir && mkdir singleCellTK.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=singleCellTK.buildbin-libdir singleCellTK_2.0.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL singleCellTK_2.0.0.zip && rm singleCellTK_2.0.0.tar.gz singleCellTK_2.0.0.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
100 2511k 100 2511k 0 0 41.3M 0 --:--:-- --:--:-- --:--:-- 42.2M
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
SEG html
calcEffectSizes html
combineSCE html
computeZScore html
constructSCE html
convertGeneIDs html
finding level-2 HTML links ... done
convertSCEToSeurat html
convertSeuratToSCE html
dataAnnotationColor 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
exportSCE html
exportSCEtoAnnData html
exportSCEtoFlatFile html
featureIndex html
featureNameDedup html
findMarkerDiffExp html
generateMeta html
generateSimulatedData html
getBiomarker html
getMSigDBTable html
getPCA html
getSceParams html
getTSNE html
getTopHVG html
getUMAP html
gsvaSCE 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
importMultipleSources html
importOptimus html
importSEQC html
importSTARsolo html
iterateSimulations html
mergeSCEColData html
mouseBrainSubsetSCE html
msigdb_table html
plotBarcodeRankDropsResults html
plotBarcodeRankScatter html
plotBatchVariance html
plotBcdsResults html
plotBiomarker html
plotCxdsResults html
plotDEGHeatmap html
plotDEGRegression html
plotDEGViolin html
plotDecontXResults html
plotDoubletCellsResults 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
plotScdsHybridResults html
plotScrubletResults html
plotTSNE html
plotUMAP html
qcInputProcess html
readSingleCellMatrix html
reportCellQC html
reportDiffExp html
reportDropletQC html
reportQCTool html
retrieveSCEIndex html
runANOVA html
runBBKNN html
runBarcodeRankDrops html
runBcds html
runCellQC html
runComBat html
runCxds html
runCxdsBcdsHybrid html
runDEAnalysis html
runDESeq2 html
runDecontX html
runDoubletCells html
runDoubletFinder html
runDropletQC html
runEmptyDrops html
runFastMNN html
runKMeans html
runLimmaBC html
runLimmaDE html
runMAST html
runMNNCorrect html
runPerCellQC html
runSCANORAMA html
runSCMerge html
runScranSNN html
runScrublet html
runZINBWaVE html
sampleSummaryStats html
scater_logNormCounts html
sce html
sceBatches html
scran_modelGeneVar html
sctkListGeneSetCollections html
sctkPythonInstallConda html
sctkPythonInstallVirtualEnv html
selectSCTKConda html
selectSCTKVirtualEnvironment html
seuratComputeHeatmap html
seuratComputeJackStraw html
seuratElbowPlot html
seuratFindClusters html
seuratFindHVG html
seuratHeatmapPlot html
seuratICA html
seuratIntegration html
seuratJackStrawPlot html
seuratNormalizeData html
seuratPCA html
seuratPlotHVG html
seuratReductionPlot html
seuratRunTSNE html
seuratRunUMAP html
seuratSCTransform html
seuratScaleData html
simpleLog html
singleCellTK html
subDiffEx html
subsetSCECols html
subsetSCERows html
summarizeSCE html
trimCounts html
visPlot 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_2.0.0.zip
* DONE (singleCellTK)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'singleCellTK' successfully unpacked and MD5 sums checked
|
singleCellTK.Rcheck/tests_i386/spelling.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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
0.18 0.03 0.20
|
singleCellTK.Rcheck/tests_x64/spelling.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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
0.18 0.01 0.18
|
|
singleCellTK.Rcheck/tests_i386/testthat.Rout.fail
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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
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 object is masked from 'package:base':
expand.grid
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
Attaching package: 'singleCellTK'
The following object is masked from 'package:BiocGenerics':
plotPCA
>
> test_check("singleCellTK")
== Failed tests ================================================================
-- Error (test-import.R:107:3): Testing importGeneSetFromMSigDB ----------------
Error: invalid class "GeneSet" object: gene symbols must be unique
Backtrace:
x
1. \-singleCellTK::importGeneSetsFromMSigDB(...) test-import.R:107:2
2. +-GSEABase::GeneSet(...)
3. \-GSEABase::GeneSet(...)
4. +-base::do.call(new, c("GeneSet", list(... = ..., setIdentifier = setIdentifier)))
5. \-(function (Class, ...) ...
6. +-methods::initialize(value, ...)
7. \-methods::initialize(value, ...)
8. \-methods::validObject(.Object)
-- Error (test-qc.R:52:1): (code run outside of `test_that()`) -----------------
Error: invalid class "Graph" object: superclass "Mnumeric" not defined in the environment of the object's class
Backtrace:
x
1. \-singleCellTK::runCellQC(...) test-qc.R:52:0
2. +-base::do.call(...)
3. \-(function (inSCE, useAssay = "counts", sample = NULL, seed = 12345, ...
4. +-base::suppressMessages(...)
5. | \-base::withCallingHandlers(...)
6. +-withr::with_seed(...)
7. | \-withr::with_preserve_seed(...)
8. \-singleCellTK:::.runDoubletFinder(...)
9. +-Seurat::FindNeighbors(seurat, dims = seuratPcs, verbose = verbose)
10. \-Seurat:::FindNeighbors.Seurat(seurat, dims = seuratPcs, verbose = verbose)
11. +-SeuratObject::`DefaultAssay<-`(object = `*tmp*`, value = assay)
12. \-SeuratObject:::`DefaultAssay<-.Graph`(object = `*tmp*`, value = assay)
13. \-SeuratObject:::UpdateSlots(object = object)
14. +-base::do.call(what = "new", args = object.list)
15. \-methods::new(...)
16. +-methods::initialize(value, ...)
17. \-Matrix:::initialize(value, ...)
18. +-methods::callNextMethod()
19. \-methods:::.nextMethod(.Object = .Object, ... = ...)
20. \-methods::validObject(.Object)
[ FAIL 2 | WARN 0 | SKIP 0 | PASS 25 ]
Error: Test failures
Execution halted
|
singleCellTK.Rcheck/tests_x64/testthat.Rout.fail
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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
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 object is masked from 'package:base':
expand.grid
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
Attaching package: 'singleCellTK'
The following object is masked from 'package:BiocGenerics':
plotPCA
>
> test_check("singleCellTK")
== Failed tests ================================================================
-- Error (test-import.R:107:3): Testing importGeneSetFromMSigDB ----------------
Error: invalid class "GeneSet" object: gene symbols must be unique
Backtrace:
x
1. \-singleCellTK::importGeneSetsFromMSigDB(...) test-import.R:107:2
2. +-GSEABase::GeneSet(...)
3. \-GSEABase::GeneSet(...)
4. +-base::do.call(new, c("GeneSet", list(... = ..., setIdentifier = setIdentifier)))
5. \-(function (Class, ...) ...
6. +-methods::initialize(value, ...)
7. \-methods::initialize(value, ...)
8. \-methods::validObject(.Object)
-- Error (test-qc.R:52:1): (code run outside of `test_that()`) -----------------
Error: invalid class "Graph" object: superclass "Mnumeric" not defined in the environment of the object's class
Backtrace:
x
1. \-singleCellTK::runCellQC(...) test-qc.R:52:0
2. +-base::do.call(...)
3. \-(function (inSCE, useAssay = "counts", sample = NULL, seed = 12345, ...
4. +-base::suppressMessages(...)
5. | \-base::withCallingHandlers(...)
6. +-withr::with_seed(...)
7. | \-withr::with_preserve_seed(...)
8. \-singleCellTK:::.runDoubletFinder(...)
9. +-Seurat::FindNeighbors(seurat, dims = seuratPcs, verbose = verbose)
10. \-Seurat:::FindNeighbors.Seurat(seurat, dims = seuratPcs, verbose = verbose)
11. +-SeuratObject::`DefaultAssay<-`(object = `*tmp*`, value = assay)
12. \-SeuratObject:::`DefaultAssay<-.Graph`(object = `*tmp*`, value = assay)
13. \-SeuratObject:::UpdateSlots(object = object)
14. +-base::do.call(what = "new", args = object.list)
15. \-methods::new(...)
16. +-methods::initialize(value, ...)
17. \-Matrix:::initialize(value, ...)
18. +-methods::callNextMethod()
19. \-methods:::.nextMethod(.Object = .Object, ... = ...)
20. \-methods::validObject(.Object)
[ FAIL 2 | WARN 0 | SKIP 0 | PASS 25 ]
Error: Test failures
Execution halted
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singleCellTK.Rcheck/examples_i386/singleCellTK-Ex.timings
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singleCellTK.Rcheck/examples_x64/singleCellTK-Ex.timings
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