##############################################################################
##############################################################################
###
### 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_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/Voyager.Rcheck’
* using R version 4.3.2 Patched (2023-11-01 r85457)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.3 (clang-1403.0.22.14.1)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Voyager/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Voyager’ version ‘1.4.0’
* 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 ‘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 ... ERROR
Running examples in ‘Voyager-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ElbowPlot
> ### Title: Plot the elbow plot or scree plot for PCA
> ### Aliases: ElbowPlot
> 
> ### ** Examples
> 
> library(SFEData)
> library(scater)
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 object is masked from ‘package:utils’:

    findMatches

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
> sfe <- McKellarMuscleData("small")
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
Error: failed to load resource
  name: EH7561
  title: Small demo subset of mouse skeletal muscle Visium data
  reason: unknown input format
Execution halted
* 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/plotcellbin2d-with-bbox.svg
  • plot/plotcorrelogram-categorical-color-by.svg
  • plot/plotcorrelogram-coldata-i.svg
  • plot/plotcorrelogram-continuous-color-by.svg
  • plot/plotcorrelogram-multiple-samples.svg
  • plot/plotcorrelogram-one-gene-c.svg
  • plot/plotcorrelogram-one-gene-corr.svg
  • plot/plotcorrelogram-one-gene-i.svg
  • plot/plotcorrelogram-specify-gene-and-coldata-i.svg
  • plot/plotdimloadings-balanced.svg
  • plot/plotdimloadings-not-balanced.svg
  • plot/with-subset-freqpoly.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: 2 ERRORs
See
  ‘/Users/biocbuild/bbs-3.18-bioc/meat/Voyager.Rcheck/00check.log’
for details.

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/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 4.3.2 Patched (2023-11-01 r85457) -- "Eye Holes"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20 (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: spData
To access larger datasets in this package, install the spDataLarge
package with: `install.packages('spDataLarge',
repos='https://nowosad.github.io/drat/', type='source')`
Loading required package: sf
Linking to GEOS 3.11.0, GDAL 3.5.3, PROJ 9.1.0; sf_use_s2() is TRUE
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 object is masked from 'package:utils':

    findMatches

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: 'SpatialFeatureExperiment'

The following object is masked from 'package:ggplot2':

    unit

see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache

Attaching package: 'Matrix'

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

    expand

see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
[ FAIL 7 | WARN 0 | SKIP 0 | PASS 163 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-bivariate.R:8:1'): (code run outside of `test_that()`) ─────────
Error: failed to load resource
  name: EH7561
  title: Small demo subset of mouse skeletal muscle Visium data
  reason: unknown input format
Backtrace:
     ▆
  1. └─SFEData::McKellarMuscleData("small") at test-bivariate.R:8:1
  2.   ├─ds[[id, force = force, verbose = verbose]]
  3.   └─ds[[id, force = force, verbose = verbose]]
  4.     └─ExperimentHub (local) .local(x, i, j = j, ...)
  5.       ├─methods::callNextMethod(x, i, j, ..., force = force, verbose = verbose)
  6.       │ └─base::eval(call, callEnv)
  7.       │   └─base::eval(call, callEnv)
  8.       └─AnnotationHub (local) .nextMethod(x, i, j, ..., force = force, verbose = verbose)
  9.         └─AnnotationHub (local) .local(x, i, j = j, ...)
 10.           └─AnnotationHub:::.Hub_get1(x[idx], force = force, verbose = verbose)
 11.             └─base::tryCatch(...)
 12.               └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 13.                 └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 14.                   └─value[[3L]](cond)
── Error ('test-featureData.R:6:1'): (code run outside of `test_that()`) ───────
Error: failed to load resource
  name: EH7561
  title: Small demo subset of mouse skeletal muscle Visium data
  reason: unknown input format
Backtrace:
     ▆
  1. └─SFEData::McKellarMuscleData("small") at test-featureData.R:6:1
  2.   ├─ds[[id, force = force, verbose = verbose]]
  3.   └─ds[[id, force = force, verbose = verbose]]
  4.     └─ExperimentHub (local) .local(x, i, j = j, ...)
  5.       ├─methods::callNextMethod(x, i, j, ..., force = force, verbose = verbose)
  6.       │ └─base::eval(call, callEnv)
  7.       │   └─base::eval(call, callEnv)
  8.       └─AnnotationHub (local) .nextMethod(x, i, j, ..., force = force, verbose = verbose)
  9.         └─AnnotationHub (local) .local(x, i, j = j, ...)
 10.           └─AnnotationHub:::.Hub_get1(x[idx], force = force, verbose = verbose)
 11.             └─base::tryCatch(...)
 12.               └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 13.                 └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 14.                   └─value[[3L]](cond)
── Error ('test-gstat.R:13:1'): (code run outside of `test_that()`) ────────────
Error: failed to load resource
  name: EH7561
  title: Small demo subset of mouse skeletal muscle Visium data
  reason: unknown input format
Backtrace:
     ▆
  1. └─SFEData::McKellarMuscleData("small") at test-gstat.R:13:1
  2.   ├─ds[[id, force = force, verbose = verbose]]
  3.   └─ds[[id, force = force, verbose = verbose]]
  4.     └─ExperimentHub (local) .local(x, i, j = j, ...)
  5.       ├─methods::callNextMethod(x, i, j, ..., force = force, verbose = verbose)
  6.       │ └─base::eval(call, callEnv)
  7.       │   └─base::eval(call, callEnv)
  8.       └─AnnotationHub (local) .nextMethod(x, i, j, ..., force = force, verbose = verbose)
  9.         └─AnnotationHub (local) .local(x, i, j = j, ...)
 10.           └─AnnotationHub:::.Hub_get1(x[idx], force = force, verbose = verbose)
 11.             └─base::tryCatch(...)
 12.               └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 13.                 └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 14.                   └─value[[3L]](cond)
── Error ('test-multivariate.R:4:1'): (code run outside of `test_that()`) ──────
Error: failed to load resource
  name: EH7561
  title: Small demo subset of mouse skeletal muscle Visium data
  reason: unknown input format
Backtrace:
     ▆
  1. └─SFEData::McKellarMuscleData("small") at test-multivariate.R:4:1
  2.   ├─ds[[id, force = force, verbose = verbose]]
  3.   └─ds[[id, force = force, verbose = verbose]]
  4.     └─ExperimentHub (local) .local(x, i, j = j, ...)
  5.       ├─methods::callNextMethod(x, i, j, ..., force = force, verbose = verbose)
  6.       │ └─base::eval(call, callEnv)
  7.       │   └─base::eval(call, callEnv)
  8.       └─AnnotationHub (local) .nextMethod(x, i, j, ..., force = force, verbose = verbose)
  9.         └─AnnotationHub (local) .local(x, i, j = j, ...)
 10.           └─AnnotationHub:::.Hub_get1(x[idx], force = force, verbose = verbose)
 11.             └─base::tryCatch(...)
 12.               └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 13.                 └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 14.                   └─value[[3L]](cond)
── Error ('test-plot.R:138:1'): (code run outside of `test_that()`) ────────────
Error: failed to load resource
  name: EH7561
  title: Small demo subset of mouse skeletal muscle Visium data
  reason: unknown input format
Backtrace:
     ▆
  1. └─SFEData::McKellarMuscleData("small") at test-plot.R:138:1
  2.   ├─ds[[id, force = force, verbose = verbose]]
  3.   └─ds[[id, force = force, verbose = verbose]]
  4.     └─ExperimentHub (local) .local(x, i, j = j, ...)
  5.       ├─methods::callNextMethod(x, i, j, ..., force = force, verbose = verbose)
  6.       │ └─base::eval(call, callEnv)
  7.       │   └─base::eval(call, callEnv)
  8.       └─AnnotationHub (local) .nextMethod(x, i, j, ..., force = force, verbose = verbose)
  9.         └─AnnotationHub (local) .local(x, i, j = j, ...)
 10.           └─AnnotationHub:::.Hub_get1(x[idx], force = force, verbose = verbose)
 11.             └─base::tryCatch(...)
 12.               └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 13.                 └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 14.                   └─value[[3L]](cond)
── Error ('test-spatial-misc.R:5:1'): (code run outside of `test_that()`) ──────
Error: failed to load resource
  name: EH7561
  title: Small demo subset of mouse skeletal muscle Visium data
  reason: unknown input format
Backtrace:
     ▆
  1. └─SFEData::McKellarMuscleData("small") at test-spatial-misc.R:5:1
  2.   ├─ds[[id, force = force, verbose = verbose]]
  3.   └─ds[[id, force = force, verbose = verbose]]
  4.     └─ExperimentHub (local) .local(x, i, j = j, ...)
  5.       ├─methods::callNextMethod(x, i, j, ..., force = force, verbose = verbose)
  6.       │ └─base::eval(call, callEnv)
  7.       │   └─base::eval(call, callEnv)
  8.       └─AnnotationHub (local) .nextMethod(x, i, j, ..., force = force, verbose = verbose)
  9.         └─AnnotationHub (local) .local(x, i, j = j, ...)
 10.           └─AnnotationHub:::.Hub_get1(x[idx], force = force, verbose = verbose)
 11.             └─base::tryCatch(...)
 12.               └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 13.                 └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 14.                   └─value[[3L]](cond)
── Error ('test-univariate.R:296:1'): (code run outside of `test_that()`) ──────
Error: failed to load resource
  name: EH7561
  title: Small demo subset of mouse skeletal muscle Visium data
  reason: unknown input format
Backtrace:
     ▆
  1. └─SFEData::McKellarMuscleData("small") at test-univariate.R:296:1
  2.   ├─ds[[id, force = force, verbose = verbose]]
  3.   └─ds[[id, force = force, verbose = verbose]]
  4.     └─ExperimentHub (local) .local(x, i, j = j, ...)
  5.       ├─methods::callNextMethod(x, i, j, ..., force = force, verbose = verbose)
  6.       │ └─base::eval(call, callEnv)
  7.       │   └─base::eval(call, callEnv)
  8.       └─AnnotationHub (local) .nextMethod(x, i, j, ..., force = force, verbose = verbose)
  9.         └─AnnotationHub (local) .local(x, i, j = j, ...)
 10.           └─AnnotationHub:::.Hub_get1(x[idx], force = force, verbose = verbose)
 11.             └─base::tryCatch(...)
 12.               └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 13.                 └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 14.                   └─value[[3L]](cond)

[ FAIL 7 | WARN 0 | SKIP 0 | PASS 163 ]
Deleting unused snapshots:
• bivariate/plot-cross-variogram-map.svg
• bivariate/plot-cross-variograms-no-np.svg
• bivariate/plot-cross-variograms-with-anisotropy.svg
• bivariate/plot-cross-variograms.svg
• gstat/multiple-samples-multiple-features.svg
• gstat/multiple-samples-one-feature.svg
• gstat/one-sample-one-feature-variogram-map.svg
• gstat/plot-np.svg
• plot/both-positive-and-negative.svg
• plot/cell-density-hex.svg
• plot/cell-density-rectangular.svg
• plot/change-the-number-of-columns.svg
• plot/cluster-by-gene-instead.svg
• plot/coldata-freqpoly-multiple-variables.svg
• plot/coldata-freqpoly-one-variable.svg
• plot/coldata-histogram-multiple-variables.svg
• plot/coldata-histogram-one-variable.svg
• plot/correlograms-for-multispati-pcs-one-component.svg
• plot/correlograms-for-multispati-pcs.svg
• plot/elbowplot-default.svg
• plot/elbowplot-more-pcs-than-available.svg
• plot/elbowplot-with-10-of-the-20-pcs.svg
• plot/facetting-by-sample.svg
• plot/illegal-symbol-freqpoly.svg
• plot/illegal-symbol.svg
• plot/moran-plot-don-t-plot-influential.svg
• plot/moran-plot-hex-bin.svg
• plot/moran-plot-rectangular-bin.svg
• plot/multiple-samples.svg
• plot/multiple-variables-color-by.svg
• plot/multiple-variables-facetting.svg
• plot/multiple-variables-fill-by.svg
• plot/multispati-loadings-2-samples.svg
• plot/not-facetting-multispati-elbow-negative-only.svg
• plot/not-facetting-multispati-elbow-positive-only.svg
• plot/one-variable-color-by.svg
• plot/one-variable-facetting.svg
• plot/one-variable-fill-by.svg
• plot/plotcellbin2d-with-bbox.svg
• plot/plotcorrelogram-categorical-color-by.svg
• plot/plotcorrelogram-coldata-i.svg
• plot/plotcorrelogram-continuous-color-by.svg
• plot/plotcorrelogram-multiple-samples.svg
• plot/plotcorrelogram-one-gene-c.svg
• plot/plotcorrelogram-one-gene-corr.svg
• plot/plotcorrelogram-one-gene-i.svg
• plot/plotcorrelogram-specify-gene-and-coldata-i.svg
• plot/plotdimloadings-balanced.svg
• plot/plotdimloadings-not-balanced.svg
• plot/with-subset-freqpoly.svg
• plot/with-subset.svg
Error: Test failures
Execution halted