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### Running command:
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###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:SpatialFeatureExperiment.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings SpatialFeatureExperiment_1.7.1.tar.gz
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* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/SpatialFeatureExperiment.Rcheck'
* using R version 4.4.1 (2024-06-14 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'SpatialFeatureExperiment/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'SpatialFeatureExperiment' version '1.7.1'
* 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 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 ... NOTE
Unexported objects imported by ':::' calls:
  'S4Vectors:::disableValidity' 'SpatialExperiment:::.get_img_idx'
  'SpatialExperiment:::.read_xyz' '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'
.aggregate_sample_tx: no visible binding for global variable '.N'
.aggregate_sample_tx: no visible global function definition for '.'
.aggregate_sample_tx: no visible binding for global variable 'gene'
.aggregate_sample_tx: no visible binding for global variable 'L1'
.aggregate_sample_tx: no visible binding for global variable 'grid_id'
.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'
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'
aggregateTx: no visible binding for global variable '.N'
aggregateTx: no visible global function definition for '.'
aggregateTx: no visible binding for global variable 'gene'
aggregateTx: no visible binding for global variable 'grid_id'
aggregateTxTech: no visible binding for global variable 'gene_col'
aggregateTxTech: no visible binding for global variable 'cell_col'
aggregateTxTech: no visible binding for global variable 'fn'
aggregateTxTech: no visible binding for global variable 'xoa_version'
aggregateTxTech: no visible binding for global variable 'major_version'
aggregateTxTech: no visible binding for global variable 'minor_version'
aggregateTxTech: no visible binding for global variable
  'instrument_version'
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'
readVizgen: no visible binding for global variable 'img_df'
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'
readXenium: no visible binding for global variable 'img_df'
Undefined global functions or variables:
  . .N L1 cell_col fn gene gene_col grid_id img_df instrument_version
  major_version minor_version xoa_version
* 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
Img-set-SpatialExperiment-method                     19.98   3.23   22.38
formatTxSpots                                        18.43   2.11   21.96
rowGeometries                                        11.49   0.71   12.61
readXenium                                           11.43   0.69   12.46
dimGeometries                                         8.55   0.64    9.53
removeEmptySpace                                      8.28   0.58    9.30
spatialGraphs                                         7.16   0.62    8.00
cbind-SpatialFeatureExperiment-method                 6.53   0.55    7.29
findVisiumGraph                                       6.11   0.59    6.97
findSpatialNeighbors-SpatialFeatureExperiment-method  6.00   0.64    6.89
SFE-transform                                         4.53   0.38    5.01
SpatialFeatureExperiment-coercion                     2.74   0.16    8.10
* 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 ... WARNING
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! LaTeX Error: Unicode character └ (U+2514)
               not set up for use with LaTeX.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
! LaTeX Error: Unicode character ─ (U+2500)
               not set up for use with LaTeX.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
! LaTeX Error: Unicode character ─ (U+2500)
               not set up for use with LaTeX.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
! LaTeX Error: Unicode character ├ (U+251C)
               not set up for use with LaTeX.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
! LaTeX Error: Unicode character ─ (U+2500)
               not set up for use with LaTeX.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
! LaTeX Error: Unicode character ─ (U+2500)
               not set up for use with LaTeX.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
! LaTeX Error: Unicode character ├ (U+251C)
               not set up for use with LaTeX.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
! LaTeX Error: Unicode character ─ (U+2500)
               not set up for use with LaTeX.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
! LaTeX Error: Unicode character ─ (U+2500)
               not set up for use with LaTeX.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
! LaTeX Error: Unicode character └ (U+2514)
               not set up for use with LaTeX.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
! LaTeX Error: Unicode character ─ (U+2500)
               not set up for use with LaTeX.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
! LaTeX Error: Unicode character ─ (U+2500)
               not set up for use with LaTeX.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
* checking PDF version of manual without index ... ERROR
* DONE

Status: 1 ERROR, 1 WARNING, 2 NOTEs
See
  'F:/biocbuild/bbs-3.20-bioc/meat/SpatialFeatureExperiment.Rcheck/00check.log'
for details.