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### Running command:
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###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:SpatialFeatureExperiment.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings SpatialFeatureExperiment_1.6.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck’
* using R version 4.4.0 beta (2024-04-15 r86425)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 10.3.1
    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 ‘SpatialFeatureExperiment/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SpatialFeatureExperiment’ version ‘1.6.0’
* 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 loading without being on the library search path ... 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
.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’
reducedDimFeatureData<-: no visible global function definition for
  ‘reducedDim<-’
showAsCell,SpatRasterImage: no visible binding for global variable ‘d’
Undefined global functions or variables:
  altExp<- d reducedDim<- slot<-
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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                                       user system elapsed
formatTxSpots                                        21.852  1.897  52.597
removeEmptySpace                                     10.094  0.250  16.401
dimGeometries                                         7.871  0.199  28.261
spatialGraphs                                         7.467  0.108  38.483
findVisiumGraph                                       7.098  0.312  46.773
cbind-SpatialFeatureExperiment-method                 6.557  0.349  41.317
findSpatialNeighbors-SpatialFeatureExperiment-method  6.729  0.128  33.982
SFE-transform                                         5.545  1.069  19.544
crop                                                  5.445  0.230  13.842
SFE-image                                             5.015  0.296  17.745
readVizgen                                            5.146  0.130  60.427
readCosMX                                             4.346  0.061  14.660
getParams                                             3.820  0.128  17.476
colFeatureData                                        3.756  0.112  10.577
SpatialFeatureExperiment-subset                       2.855  0.490  17.933
annotSummary                                          2.675  0.531  11.475
annotOp                                               2.708  0.479  11.023
annotPred                                             2.539  0.587  14.302
unit-SpatialFeatureExperiment-method                  2.961  0.052  15.085
bbox-SpatialFeatureExperiment-method                  2.626  0.221  14.216
annotGeometries                                       2.548  0.260  37.351
updateObject                                          2.723  0.064  13.233
colGeometries                                         2.686  0.096  13.947
show-SpatialFeatureExperiment-method                  2.630  0.072  24.647
sampleIDs                                             2.646  0.028  14.395
changeSampleIDs                                       2.502  0.126  20.476
* 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. ├─sfe1[, rep(FALSE, ncol(sfe1))] at test-subset.R:198:5
   2. └─sfe1[, rep(FALSE, ncol(sfe1))]
   3.   └─SpatialFeatureExperiment::`rowGeometries<-`(...)
   4.     └─SpatialFeatureExperiment::.check_sample_id(x, sample_id, one = FALSE)
  ── 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 = "xenium_test") at test-utils.R:56:1
  
  [ FAIL 10 | WARN 0 | SKIP 2 | PASS 784 ]
  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, 1 WARNING, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck/00check.log’
for details.