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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_1.12.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/SpatialFeatureExperiment.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SpatialFeatureExperiment/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SpatialFeatureExperiment’ version ‘1.12.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 21 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 ‘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 whether startup messages can be suppressed ... OK
* checking dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
  ‘S4Vectors:::disableValidity’ ‘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
.seu_to_sfe: warning in do.call(setdiff, arg = assays_n): partial
  argument match of 'arg' to 'args'
.seu_to_sfe: warning in do.call(intersect, arg = assays_n): partial
  argument match of 'arg' to 'args'
.seu_to_sfe : <anonymous>: warning in do.call(setdiff, arg = assays_n):
  partial argument match of 'arg' to 'args'
.filter_polygons: no visible binding for global variable ‘gmax’
.filter_polygons: no visible binding for global variable ‘area’
.filter_polygons: no visible binding for global variable ‘name’
.filter_polygons: no visible binding for global variable ‘gi’
.filter_polygons: no visible binding for global variable ‘.N’
.filter_polygons: no visible binding for global variable ‘i’
.filter_polygons: no visible binding for global variable ‘.I’
.filter_polygons: no visible binding for global variable ‘ID_row’
.get_tb1: no visible global function definition for ‘clahe’
.get_tb1_concave: no visible global function definition for
  ‘st_concave_hull’
.mols2geo: no visible global function definition for ‘txtProgressBar’
.mols2geo: no visible binding for global variable ‘gene’
.mols2geo: no visible global function definition for ‘syms’
.mols2geo: no visible global function definition for ‘write_parquet’
.mols2geo: no visible global function definition for
  ‘setTxtProgressBar’
.mols2geo_split: no visible binding for global variable ‘grp’
aggregateTx: no visible binding for global variable ‘gene’
aggregateTx : <anonymous>: no visible binding for global variable
  ‘gene’
findVisiumHDGraph: no visible binding for global variable ‘..cols’
formatTxSpots: no visible binding for global variable ‘rng’
Undefined global functions or variables:
  ..cols .I .N ID_row area clahe gene gi gmax grp i name rng
  setTxtProgressBar st_concave_hull syms txtProgressBar write_parquet
Consider adding
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
* 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:
  SpatialFeatureExperiment-coercion.Rd: DataFrame
  SpatialFeatureExperiment.Rd: DataFrame
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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                  user system elapsed
Img-set-SpatialExperiment-method 6.415  0.498   6.084
formatTxSpots                    4.873  0.400   5.852
* 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:
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-aggregate.R:75:5'): aggregateTxTech for Vizgen ───────────────
  all(st_area(colGeometry(sfe)) == 400) is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  ── Failure ('test-formatTxSpots.R:15:5'): Read MERFISH transcript spots into rowGeometries ──
  y < 10 is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  
  [ FAIL 2 | WARN 1 | SKIP 10 | PASS 1252 ]
  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: 1 ERROR, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.22-bioc/meat/SpatialFeatureExperiment.Rcheck/00check.log’
for details.