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### Running command:
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###   /home/biocbuild/R/R/bin/R CMD check --install=check:Voyager.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings Voyager_1.8.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/Voyager.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14)
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Voyager/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Voyager’ version ‘1.8.1’
* 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 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 loading without being on the library search path ... 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
.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 ... 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: 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
/usr/bin/gtar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/gtar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/gtar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/gtar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/gtar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/gtar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/gtar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/gtar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/gtar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/gtar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/gtar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
The downloaded files are in /home/biocbuild/bbs-3.20-bioc/meat/Voyager.Rcheck/xenium_example/xenium2 
> # Weird RBioFormats null pointer error the first time it's run
> try(sfe <- readXenium(fn))
Error in getPixelSize(file) : The package "RBioFormats" is required.
> sfe <- readXenium(fn)
Error in getPixelSize(file) : The package "RBioFormats" is required.
Calls: readXenium ... .get_fullres_scale_factor -> getPixelSize -> check_installed
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/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 NOTE
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/Voyager.Rcheck/00check.log’
for details.