##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Voyager.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings Voyager_1.1.6.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/Voyager.Rcheck'
* using R Under development (unstable) (2022-12-25 r83502 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 10.4.0
    GNU Fortran (GCC) 10.4.0
* running under: Windows Server x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'Voyager/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'Voyager' version '1.1.6'
* 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 '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 ... NOTE
.plot_dimdata_hist : <anonymous>: no visible global function definition
  for 'vars'
plotColDataHistogram: no visible global function definition for 'vars'
plotRowDataHistogram: no visible global function definition for 'vars'
Undefined global functions or variables:
  vars
* 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     5.72   1.41    7.28
plotCellBin2D 5.76   0.47    6.70
moranPlot     5.22   0.28    5.88
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 ERROR
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  • 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.svg
  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: 1 ERROR, 1 NOTE
See
  'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/Voyager.Rcheck/00check.log'
for details.

##############################################################################
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###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL Voyager
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.17-bioc/R/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 Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences"
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(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

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: scuttle
Loading required package: ggplot2

Attaching package: 'Matrix'

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

    expand

snapshotDate(): 2022-12-16
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
Linking to GEOS 3.9.3, GDAL 3.5.2, PROJ 8.2.1; sf_use_s2() is TRUE
snapshotDate(): 2022-12-16
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
[ FAIL 1 | WARN 0 | SKIP 15 | PASS 96 ]

══ Skipped tests ═══════════════════════════════════════════════════════════════
• On CRAN (15)

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-plot.R:416'): (code run outside of `test_that()`) ──────────────
Error in `(function (classes, fdef, mtable) 
{
    methods <- .findInheritedMethods(classes, fdef, mtable)
    if (length(methods) == 1L) 
        return(methods[[1L]])
    else if (length(methods) == 0L) {
        cnames <- paste0("\"", vapply(classes, as.character, 
            ""), "\"", collapse = ", ")
        stop(gettextf("unable to find an inherited method for function %s for signature %s", 
            sQuote(fdef@generic), sQuote(cnames)), domain = NA)
    }
    else stop("Internal error in finding inherited methods; didn't return a unique method", 
        domain = NA)
})(list(structure("SpatialFeatureExperiment", package = "SpatialFeatureExperiment")), 
    new("standardGeneric", .Data = function (x, objects = list(), 
        use.names = TRUE, ignore.mcols = FALSE, check = TRUE) 
    standardGeneric("bindCOLS"), generic = structure("bindCOLS", package = "S4Vectors"), 
        package = "S4Vectors", group = list(), valueClass = character(0), 
        signature = "x", default = NULL, skeleton = (function (x, 
            objects = list(), use.names = TRUE, ignore.mcols = FALSE, 
            check = TRUE) 
        stop(gettextf("invalid call in method dispatch to '%s' (no default method)", 
            "bindCOLS"), domain = NA))(x, objects, use.names, 
            ignore.mcols, check)), <environment>)`: unable to find an inherited method for function 'bindCOLS' for signature '"SpatialFeatureExperiment"'
Backtrace:
    ▆
 1. └─base::cbind(sfe_cosmx2a, sfe_cosmx2b) at test-plot.R:416:0
 2.   └─S4Vectors::cbind(deparse.level, ...)
 3.     └─S4Vectors::bindCOLS(objects[[1L]], objects = objects[-1L])
 4.       └─methods (local) `<fn>`(`<list>`, `<stndrdGn>`, `<env>`)

[ FAIL 1 | WARN 0 | SKIP 15 | PASS 96 ]
Deleting unused snapshots:
• plot/also-plot-annotgeometry.svg
• plot/cell-density-hex.new.svg
• plot/cell-density-hex.svg
• plot/cell-density-rectangular.svg
• plot/coldata-bin2d-for-multiple-samples.svg
• plot/coldata-bin2d-with-hexbin.new.svg
• plot/coldata-bin2d-with-hexbin.svg
• plot/coldata-bin2d.svg
• plot/coldata-histogram-multiple-variables.svg
• plot/coldata-histogram-one-variable.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.new.svg
• plot/moran-plot-hex-bin.svg
• plot/moran-plot-rectangular-bin.svg
• plot/moranplot-not-filled-coldata.svg
• plot/multiple-samples.svg
• plot/multiple-variables-facetting.svg
• plot/multiple-variables-fill-by.svg
• plot/one-variable-facetting.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-annotgeometry-1-sample.svg
• plot/plot-annotgeometry-2-samples.svg
• plot/plot-another-column.svg
• plot/plot-coldata.svg
• plot/plot-colgeometry-1-sample.svg
• plot/plot-colgeometry-2-samples.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.svg
Error: Test failures
Execution halted