##############################################################################
##############################################################################
###
### 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_1.7.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/Voyager.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-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 Ventura 13.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Voyager/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Voyager’ version ‘1.7.2’
* 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 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
.add_fd_dimData: no visible global function definition for ‘mcols’
.add_fd_dimData: no visible global function definition for ‘mcols<-’
.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 mcols mcols<-
  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: plotMoranMC
> ### Title: Plot Moran/Geary Monte Carlo results
> ### Aliases: plotMoranMC
> 
> ### ** Examples
> 
> library(SpatialFeatureExperiment)
> library(SFEData)
> sfe <- McKellarMuscleData("small")
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
> colGraph(sfe, "visium") <- findVisiumGraph(sfe)
> sfe <- colDataUnivariate(sfe, type = "moran.mc", "nCounts", nsim = 100)
Error in mcols(dimData(x)) : could not find function "mcols"
Calls: colDataUnivariate -> fun -> .set_fd_fun -> .add_fd_dimData
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* 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: 1 ERROR, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/Voyager.Rcheck/00check.log’
for details.