##############################################################################
##############################################################################
###
### 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_1.9.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/Voyager.Rcheck’
* using R Under development (unstable) (2024-11-20 r87352)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Voyager/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Voyager’ version ‘1.9.2’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 22 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* 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 code 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 ... WARNING
'::' or ':::' import not declared from: ‘spatialreg’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.get_tx_df: no visible binding for global variable ‘cell_col’
.get_tx_df: no visible global function definition for ‘getTechTxFields’
.get_tx_df: no visible global function definition for
  ‘gdalParquetAvailable’
.get_tx_df : <anonymous>: no visible global function definition for
  ‘gdalParquetAvailable’
.get_tx_df : <anonymous>: no visible global function definition for
  ‘rowGeometryNames’
.get_tx_df : <anonymous>: no visible global function definition for
  ‘st_is_empty’
.get_tx_df : <anonymous>: no visible global function definition for
  ‘readSelectTx’
.plot_var_sf: no visible binding for global variable ‘gene’
plotTxBin2D: no visible binding for global variable ‘X’
plotTxBin2D: no visible binding for global variable ‘Y’
Undefined global functions or variables:
  X Y cell_col gdalParquetAvailable gene getTechTxFields readSelectTx
  rowGeometryNames st_is_empty
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  calculateBivariate.Rd: lee, lee.mc, lee.test, localmoran_bv,
    BiocParallelParam, colGraphNames, colGeometryNames, localResults
  calculateMultivariate.Rd: localC, colGraphNames, BiocParallelParam,
    reducedDim
  calculateUnivariate.Rd: BiocParallelParam, colGeometry,
    annotGeometry, colGraphNames, colGeometryNames, annotGeometryNames,
    annotGraphNames, reducedDimNames, geometryFeatureData,
    colFeatureData
  clusterCorrelograms.Rd: BlusterParam-class, reducedDimNames
  clusterMoranPlot.Rd: BlusterParam-class
  clusterVariograms.Rd: BlusterParam-class, reducedDimNames
  moranPlot.Rd: colGeometryNames, geom_bin2d, geom_hex, geom_density2d
  plotCellBin2D.Rd: geom_bin2d, geom_hex, wrap_plots
  plotColDataHistogram.Rd: facet_grid
  plotColGraph.Rd: colGeometryNames, wrap_plots
  plotCorrelogram.Rd: colFeatureData, colGeometryNames,
    reducedDimNames, moran.test, geary.test
  plotGeometry.Rd: colGeometryNames, wrap_plots, formatTxSpots, imgData
  plotImage.Rd: wrap_plots
  plotLocalResult.Rd: colGeometryNames, wrap_plots, formatTxSpots,
    imgData, geom_bin2d, geom_hex
  plotMoranMC.Rd: colGeometryNames, reducedDimNames, geom_density,
    geom_histogram, geom_freqpoly
  plotSpatialFeature.Rd: colGeometryNames, wrap_plots, formatTxSpots,
    imgData, geom_bin2d, geom_hex
  plotTxBin2D.Rd: geom_bin2d, geom_hex, wrap_plots, formatTxSpots
  plotVariogram.Rd: colFeatureData, colGeometryNames, reducedDimNames
  plotVariogramMap.Rd: colGeometryNames, reducedDimNames
  spatialReducedDim.Rd: colGeometryNames, wrap_plots, formatTxSpots,
    imgData, geom_bin2d, geom_hex
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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: plotImage
> ### Title: Show image without plotting geometries
> ### Aliases: plotImage
> 
> ### ** Examples
> 
> library(SFEData)
> library(SpatialFeatureExperiment)
> fn <- XeniumOutput("v2", file_path = "xenium_example")
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /Users/biocbuild/bbs-3.21-bioc/meat/Voyager.Rcheck/xenium_example/xenium2 
> # Weird RBioFormats null pointer error the first time it's run
> try(sfe <- readXenium(fn))
Error in readXenium(fn) : The package "arrow" is required.
> sfe <- readXenium(fn)
Error in readXenium(fn) : The package "arrow" is required.
Calls: readXenium -> check_installed
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
calculateMultivariate 47.852  0.978  49.326
calculateBivariate    13.407  0.475  14.119
ElbowPlot              7.565  1.463  12.486
clusterVariograms      7.884  0.209  11.429
plotCellBin2D          5.822  0.284   6.305
plotGeometry           5.427  0.269   6.120
plotCrossVariogram     3.217  0.150   5.563
plotCrossVariogramMap  3.206  0.147   6.867
* 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/not-facetting-multispati-elbow-negative-only.svg
  • plot/one-variable-color-by.svg
  • plot/one-variable-facetting.svg
  • plot/one-variable-fill-by.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/with-subset-freqpoly.svg
  • plot/with-subset.svg
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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 WARNING, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.21-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/4.5-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 Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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)
Loading required package: SpatialFeatureExperiment

Attaching package: 'SpatialFeatureExperiment'

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

    scale

> 
> 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
Loading required package: generics

Attaching package: 'generics'

The following objects are masked from 'package:base':

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


Attaching package: 'BiocGenerics'

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

    saveRDS

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, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, 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: 'ggplot2'

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

    unit

Loading required package: Matrix

Attaching package: 'Matrix'

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

    expand

Loading required package: S4Arrays
Loading required package: abind

Attaching package: 'S4Arrays'

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

    abind

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

    rowsum

Loading required package: SparseArray

Attaching package: 'DelayedArray'

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

    scale

The following objects are masked from 'package:base':

    apply, scale, sweep

see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
BioFormats library version 7.3.0
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /private/tmp/RtmpT8xXNQ/fileb7fb39a8fda2/xenium2/xenium2 
Error in readXenium(fp) : The package "arrow" is required.
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
gstat does not fit anisotropic variograms. Variogram model is fitted to the whole dataset.
Only one cluster is present. Not using color_by.
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
The downloaded files are in /private/tmp/RtmpT8xXNQ/fileb7fb447f7d53/xenium2 
>>> Must use gene symbols as row names when adding transcript spots.
Error in readXenium(fn, add_molecules = TRUE) : 
  The package "arrow" is required.
>>> Must use gene symbols as row names when adding transcript spots.

Attaching package: 'EBImage'

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

    abind

The following object is masked from 'package:S4Arrays':

    abind

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

    abind

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

    resize

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

    channel

The following objects are masked from 'package:GenomicRanges':

    resize, tile

The following objects are masked from 'package:IRanges':

    resize, tile

The following objects are masked from 'package:SpatialFeatureExperiment':

    affine, rotate, translate, transpose

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
Coordinate system already present. Adding new coordinate system, which will replace the existing one.
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
beginning bbox testssee ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
trying URL 'https://cf.10xgenomics.com/samples/spatial-exp/2.0.0/Visium_Mouse_Olfactory_Bulb/Visium_Mouse_Olfactory_Bulb_filtered_feature_bc_matrix.h5'
Content type 'binary/octet-stream' length 7521734 bytes (7.2 MB)
==================================================
downloaded 7.2 MB

trying URL 'https://cf.10xgenomics.com/samples/spatial-exp/2.0.0/Visium_Mouse_Olfactory_Bulb/Visium_Mouse_Olfactory_Bulb_spatial.tar.gz'
Content type 'application/x-tar' length 7806681 bytes (7.4 MB)
==================================================
downloaded 7.4 MB

>>> 10X Visium data will be loaded: outs

>>> Adding spatial neighborhood graph to sample01

see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /Users/biocbuild/bbs-3.21-bioc/meat/Voyager.Rcheck/tests/testthat/vizgen_cellbound 
>>> 1 `.parquet` files exist:
/Users/biocbuild/bbs-3.21-bioc/meat/Voyager.Rcheck/tests/testthat/vizgen_cellbound/cell_boundaries.parquet
>>> using -> /Users/biocbuild/bbs-3.21-bioc/meat/Voyager.Rcheck/tests/testthat/vizgen_cellbound/cell_boundaries.parquet
>>> Cell segmentations are found in `.parquet` file
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 3 | WARN 0 | SKIP 17 | PASS 546 ]

══ Skipped tests (17) ══════════════════════════════════════════════════════════
• On CRAN (17): 'test-bivariate.R:130:5', 'test-bivariate.R:151:5',
  'test-gstat.R:187:5', 'test-plot.R:358:5', 'test-plot.R:404:5',
  'test-plot.R:441:5', 'test-plot.R:459:5', 'test-plot.R:473:5',
  'test-plot.R:477:5', 'test-plot.R:527:5', 'test-plot.R:605:5',
  'test-plot.R:638:5', 'test-plot.R:660:5', 'test-plot.R:820:5',
  'test-plot.R:855:5', 'test-plot.R:866:5', 'test-plot.R:926:5'

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-bivariate.R:267:1'): (code run outside of `test_that()`) ───────
<rlib_error_package_not_found/rlang_error/error/condition>
Error in `readXenium(fp)`: The package "arrow" is required.
Backtrace:
    ▆
 1. └─SpatialFeatureExperiment::readXenium(fp) at test-bivariate.R:267:1
 2.   └─rlang::check_installed("arrow")
── Error ('test-plot-transcripts.R:16:1'): (code run outside of `test_that()`) ──
<rlib_error_package_not_found/rlang_error/error/condition>
Error in `readXenium(fn, add_molecules = TRUE)`: The package "arrow" is required.
Backtrace:
    ▆
 1. └─SpatialFeatureExperiment::readXenium(fn, add_molecules = TRUE) at test-plot-transcripts.R:16:1
 2.   └─rlang::check_installed("arrow")
── Error ('test-plot.R:970:1'): (code run outside of `test_that()`) ────────────
Error in `dyn.load(file, DLLpath = DLLpath, ...)`: unable to load shared object '/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/arrow/libs/arrow.so':
  dlopen(/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/arrow/libs/arrow.so, 0x0006): symbol not found in flat namespace (_ZSTD_compress)
Backtrace:
    ▆
 1. ├─SpatialFeatureExperiment::readVizgen(dir_use, z = 3L, image = "PolyT") at test-plot.R:970:1
 2. │ └─sfarrow::st_read_parquet(fn)
 3. └─base::loadNamespace(x)
 4.   └─base::library.dynam(lib, package, package.lib)
 5.     └─base::dyn.load(file, DLLpath = DLLpath, ...)

[ FAIL 3 | WARN 0 | SKIP 17 | PASS 546 ]
Deleting unused snapshots:
• bivariate/plot-cross-variograms-no-np.svg
• bivariate/plot-cross-variograms-with-anisotropy.svg
• gstat/multiple-samples-multiple-features.svg
• gstat/multiple-samples-one-feature.svg
• gstat/plot-np.svg
• plot/both-positive-and-negative.svg
• plot/change-the-number-of-columns.svg
• plot/cluster-by-gene-instead.svg
• plot/coldata-freqpoly-multiple-variables.svg
• plot/coldata-histogram-multiple-variables.svg
• plot/correlograms-for-multispati-pcs-one-component.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/multiple-samples.svg
• plot/multiple-variables-color-by.svg
• plot/multiple-variables-facetting.svg
• plot/multiple-variables-fill-by.svg
• plot/not-facetting-multispati-elbow-negative-only.svg
• plot/one-variable-color-by.svg
• plot/one-variable-facetting.svg
• plot/one-variable-fill-by.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/with-subset-freqpoly.svg
• plot/with-subset.svg
Error: Test failures
Execution halted