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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Voyager.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Voyager_1.0.10.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/Voyager.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Voyager/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Voyager’ version ‘1.0.10’
* 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 ‘Voyager’ 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 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
ElbowPlot     7.196  1.022   8.737
moranPlot     7.091  0.282   7.599
plotCellBin2D 5.943  0.288   6.486
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  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

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL Voyager
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library’
* installing *source* package ‘Voyager’ ...
** using staged installation
** R
** data
** 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 (Voyager)

R version 4.2.3 (2023-03-15) -- "Shortstop Beagle"
Copyright (C) 2023 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(Voyager)
> 
> test_check("Voyager")
Loading required package: SingleCellExperiment
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, aperm, 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: scuttle
Loading required package: ggplot2

Attaching package: 'Matrix'

The following object is masked from 'package:S4Vectors':

    expand

snapshotDate(): 2022-10-31
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
Linking to GEOS 3.10.2, GDAL 3.4.2, PROJ 8.2.1; sf_use_s2() is TRUE
snapshotDate(): 2022-10-31
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
snapshotDate(): 2022-10-31
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
snapshotDate(): 2022-10-31
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
snapshotDate(): 2022-10-31
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
[ FAIL 0 | WARN 0 | SKIP 20 | PASS 101 ]

══ Skipped tests ═══════════════════════════════════════════════════════════════
• On CRAN (20)

[ FAIL 0 | WARN 0 | SKIP 20 | PASS 101 ]
Deleting unused snapshots:
• plot/also-plot-annotgeometry.svg
• plot/cell-density-hex.svg
• plot/change-the-number-of-columns.svg
• plot/coldata-bin2d-with-hexbin.svg
• plot/coldata-freqpoly-multiple-variables.svg
• plot/coldata-histogram-multiple-variables.svg
• plot/discrete-represented-as-color.svg
• plot/discrete-represented-as-point-shapes.svg
• plot/divergent-scale-annot-also-on-divergent-scale.svg
• plot/divergent-scale-annot-not-on-divergent-scale.svg
• plot/divergent-scale-with-scattermore.svg
• plot/divergent-scale.svg
• plot/elbowplot-more-pcs-than-available.svg
• plot/elbowplot-with-10-of-the-20-pcs.svg
• plot/gene-expression.svg
• plot/moran-plot-don-t-plot-influential.svg
• plot/moran-plot-hex-bin.svg
• plot/moranplot-not-filled-coldata.svg
• plot/multiple-variables-color-by.svg
• plot/multiple-variables-fill-by.svg
• plot/one-variable-color-by.svg
• plot/one-variable-fill-by.svg
• plot/plot-2-features.svg
• plot/plot-a-categorical-attribute.svg
• plot/plot-a-type-in-annotgeometry-but-not-assay-or-coldata.svg
• plot/plot-another-column.svg
• plot/plot-coldata.svg
• plot/plot-colgeometry.svg
• plot/plot-ii-for-annotgeometry-alone.svg
• plot/plot-ii-for-gene-on-top-of-an-annotation.svg
• plot/plot-multiple-coldata-columns.svg
• plot/plot-with-annotgeometry-colored-outlines-of-polygons.svg
• plot/plot-with-annotgeometry-with-new-fill-scale.svg
• plot/plot-with-annotgeometry.svg
• plot/plotcorrelogram-categorical-color-by.svg
• plot/plotcorrelogram-coldata-i.svg
• plot/plotcorrelogram-continuous-color-by.svg
• plot/plotcorrelogram-one-gene-c.svg
• plot/plotcorrelogram-one-gene-corr.svg
• plot/plotcorrelogram-specify-gene-and-coldata-i.svg
• plot/plotdimloadings-not-balanced.svg
• plot/plotlocalresult-with-illegal-gene-name.svg
• plot/rowdata-bin2d-with-subset-and-default-legend.svg
• plot/rowdata-bin2d-with-subset.svg
• plot/rowdata-bin2d.svg
• plot/with-subset-freqpoly.svg
• plot/with-subset.svg
> 
> proc.time()
   user  system elapsed 
 47.709   3.008  52.175