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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
###
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* 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: 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  6 06:24:53 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 ‘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: 2 ERRORs, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.12-bioc/meat/singleCellTK.Rcheck/00check.log’
for details.

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

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 
  0.250   0.068   0.298 

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-import.R:107:3): Testing importGeneSetFromMSigDB ────────────────
Error: invalid class "GeneSet" object: gene symbols must be unique
Backtrace:
    █
 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:
     █
  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