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CHECK report for singleCellTK on merida1

This page was generated on 2021-05-05 12:15:27 -0400 (Wed, 05 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 1725/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
singleCellTK 2.0.0  (landing page)
Yusuke Koga
Snapshot Date: 2021-05-04 14:50:13 -0400 (Tue, 04 May 2021)
URL: https://git.bioconductor.org/packages/singleCellTK
Branch: RELEASE_3_12
Last Commit: e97b135
Last Changed Date: 2020-10-27 11:34:50 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    ERROR  
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    ERROR    OK  
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    ERROR    OK  

Summary

Package: singleCellTK
Version: 2.0.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:singleCellTK.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings singleCellTK_2.0.0.tar.gz
StartedAt: 2021-05-05 06:59:58 -0400 (Wed, 05 May 2021)
EndedAt: 2021-05-05 07:07:25 -0400 (Wed, 05 May 2021)
EllapsedTime: 446.8 seconds
RetCode: 1
Status:   ERROR  
CheckDir: singleCellTK.Rcheck
Warnings: NA

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:singleCellTK.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings singleCellTK_2.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/singleCellTK.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-apple-darwin17.0 (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 ‘2.0.0’
* 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 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 ... 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 ... ERROR
Running examples in ‘singleCellTK-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotDoubletFinderResults
> ### Title: Plots for runDoubletFinder outputs.
> ### Aliases: plotDoubletFinderResults
> 
> ### ** Examples
> 
> data(scExample, package="singleCellTK")
> sce <- subsetSCECols(sce, colData = "type != 'EmptyDroplet'")
> sce <- getUMAP(inSCE=sce, useAssay="counts", reducedDimName="UMAP")
> sce <- runDoubletFinder(sce)
Wed May  5 07:06:18 2021 ... Running 'doubletFinder'
Error in validObject(.Object) : 
  invalid class “Graph” object: superclass "Mnumeric" not defined in the environment of the object's class
Calls: runDoubletFinder ... initialize -> callNextMethod -> .nextMethod -> validObject
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  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 1 | WARN 0 | SKIP 0 | PASS 26 ]
  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: 2 ERRORs, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.12-bioc/meat/singleCellTK.Rcheck/00check.log’
for details.


Installation output

singleCellTK.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL singleCellTK
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/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 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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 
  0.272   0.075   0.321 

singleCellTK.Rcheck/tests/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-apple-darwin17.0 (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
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-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:
     █
  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 1 | WARN 0 | SKIP 0 | PASS 26 ]
Error: Test failures
Execution halted

Example timings

singleCellTK.Rcheck/singleCellTK-Ex.timings

nameusersystemelapsed
SEG0.0030.0020.006
calcEffectSizes0.3780.0090.388
combineSCE1.6810.0151.697
computeZScore0.4300.0190.451
convertGeneIDs2.9970.4563.458
convertSCEToSeurat3.1620.1923.390
convertSeuratToSCE0.2850.0040.290
discreteColorPalette0.0110.0020.013
distinctColors0.0030.0000.003
downSampleCells3.9980.2734.277
downSampleDepth0.4380.0290.467
enrichRSCE0.0000.0010.000
exportSCE0.0010.0020.003
exportSCEtoAnnData0.1510.0010.152
exportSCEtoFlatFile0.1670.0040.171
featureIndex0.0200.0020.022
generateMeta0.0670.0130.080
generateSimulatedData0.0470.0030.050
getBiomarker0.0160.0010.017
getPCA0.9490.0400.991
getTSNE0.3240.0160.341
getTopHVG0.6610.0190.681
getUMAP3.2960.0503.344
importAnnData0.0010.0010.001
importBUStools0.1680.0040.172
importCellRanger0.7200.0280.792
importCellRangerV2Sample0.1570.0020.159
importCellRangerV3Sample0.2830.0110.296
importDropEst0.2410.0020.244
importExampleData18.844 1.34521.107
importGeneSetsFromCollection1.0930.0821.175
importGeneSetsFromGMT0.0670.0030.070
importGeneSetsFromList0.1370.0080.146
importGeneSetsFromMSigDB4.3470.2624.618
importOptimus0.0020.0010.003
importSEQC0.2070.0060.213
importSTARsolo0.2480.0190.267
iterateSimulations0.0680.0020.070
mergeSCEColData0.4110.0150.429
mouseBrainSubsetSCE0.0010.0020.005
msigdb_table0.0020.0020.004
plotBarcodeRankDropsResults0.8690.0100.880
plotBarcodeRankScatter0.6680.0130.685
plotBatchVariance000
plotBcdsResults8.2350.1558.426
plotBiomarker0.6200.0250.647
plotCxdsResults5.5520.0795.657
plotDEGHeatmap0.0020.0010.002
plotDecontXResults11.742 0.16412.033
plotDoubletCellsResults17.173 0.54517.838