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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SpatialFeatureExperiment.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SpatialFeatureExperiment_1.7.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/SpatialFeatureExperiment.Rcheck’
* using R version 4.4.0 Patched (2024-04-24 r86482)
* 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 12.7.4
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SpatialFeatureExperiment/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SpatialFeatureExperiment’ version ‘1.7.0’
* 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 ‘SpatialFeatureExperiment’ 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: ‘Biobase’
Unexported objects imported by ':::' calls:
  ‘S4Vectors:::disableValidity’ ‘SpatialExperiment:::.get_img_idx’
  ‘spdep:::minmax.listw’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.no_raw_bytes: no visible binding for global variable ‘xoa_version’
.no_raw_bytes: no visible binding for global variable ‘major_version’
.no_raw_bytes: no visible binding for global variable ‘minor_version’
.no_raw_bytes: no visible binding for global variable
  ‘instrument_version’
.seu_to_sfe : <anonymous>: no visible binding for '<<-' assignment to
  ‘assays_sfe_out’
.seu_to_sfe : <anonymous>: no visible binding for '<<-' assignment to
  ‘sfe_out’
.seu_to_sfe : <anonymous>: no visible global function definition for
  ‘reducedDim<-’
.seu_to_sfe : <anonymous>: no visible global function definition for
  ‘slot<-’
.seu_to_sfe : <anonymous>: no visible global function definition for
  ‘altExp<-’
.seu_to_sfe: no visible binding for '<<-' assignment to ‘obj_list_test’
addTxTech: no visible binding for global variable ‘gene_col’
addTxTech: no visible binding for global variable ‘cell_col’
addTxTech: no visible binding for global variable ‘fn’
formatTxTech: no visible binding for global variable ‘gene_col’
formatTxTech: no visible binding for global variable ‘cell_col’
formatTxTech: no visible binding for global variable ‘fn’
readXenium: no visible binding for global variable ‘xoa_version’
readXenium: no visible binding for global variable ‘major_version’
readXenium: no visible binding for global variable ‘minor_version’
readXenium: no visible binding for global variable ‘instrument_version’
reducedDimFeatureData<-: no visible global function definition for
  ‘reducedDim<-’
Undefined global functions or variables:
  altExp<- cell_col fn gene_col instrument_version major_version
  minor_version reducedDim<- slot<- xoa_version
Consider adding
  importFrom("methods", "slot<-")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 ‘SpatialFeatureExperiment-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: formatTxTech
> ### Title: Read and process transcript spots for specific commercial
> ###   technologies
> ### Aliases: formatTxTech addTxTech
> 
> ### ** Examples
> 
> library(SFEData)
> fp <- tempdir()
> dir_use <- XeniumOutput("v2", file_path = file.path(fp, "xenium_test"))
Error: record not found in database
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:
  Backtrace:
      ▆
   1. └─SFEData::XeniumOutput("v2", file_path = file.path(fp, "xenium_test")) at test-read.R:727:5
   2.   ├─ds[[id, force = force, verbose = verbose]]
   3.   └─ds[[id, force = force, verbose = verbose]]
   4.     └─ExperimentHub (local) .local(x, i, j = j, ...)
  ── Error ('test-utils.R:56:1'): (code run outside of `test_that()`) ────────────
  Error in `names(fn) <- datasets`: 'names' attribute [2] must be the same length as the vector [1]
  Backtrace:
      ▆
   1. └─SFEData::XeniumOutput("v1", file_path = file.path(fp, "xenium_test")) at test-utils.R:56:1
  
  [ FAIL 20 | WARN 2 | SKIP 2 | PASS 812 ]
  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, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/SpatialFeatureExperiment.Rcheck/00check.log’
for details.