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### Running command:
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###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:spatialLIBD.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings spatialLIBD_1.19.6.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.21-data-experiment/meat/spatialLIBD.Rcheck’
* using R Under development (unstable) (2024-10-21 r87258)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘spatialLIBD/DESCRIPTION’ ... OK
* this is package ‘spatialLIBD’ version ‘1.19.6’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 36 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 ‘spatialLIBD’ 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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:
  check_sce.Rd: SingleCellExperiment-class
  check_sce_layer.Rd: SingleCellExperiment-class
  fetch_data.Rd: SingleCellExperiment-class
  layer_boxplot.Rd: SingleCellExperiment-class
  read10xVisiumWrapper.Rd: SpatialExperiment-class
  run_app.Rd: SingleCellExperiment-class
  sce_to_spe.Rd: SingleCellExperiment-class
  sig_genes_extract.Rd: SingleCellExperiment-class
  sig_genes_extract_all.Rd: SingleCellExperiment-class
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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                           user system elapsed
add_images               22.626  5.027  65.532
vis_gene                 23.975  2.414  26.779
img_update_all           18.549  2.304  21.904
vis_clus                 17.752  1.960  20.094
add_qc_metrics           14.974  3.297  18.432
add_key                  14.749  2.837  18.038
vis_grid_clus            14.610  2.010  17.047
vis_grid_gene            14.841  1.738  16.943
vis_clus_p               14.826  1.752  16.947
vis_gene_p               14.572  1.500  16.463
check_spe                14.296  1.600  16.246
cluster_import           14.458  1.325  16.126
img_update               13.625  1.704  15.650
cluster_export           13.629  1.619  15.599
img_edit                 13.521  1.448  15.489
frame_limits             13.274  1.599  15.842
sce_to_spe               13.103  1.467  14.974
geom_spatial             13.191  1.340  14.894
gene_set_enrichment_plot  7.934  0.433   8.670
layer_stat_cor_plot       4.704  0.679  13.423
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.21-data-experiment/meat/spatialLIBD.Rcheck/00check.log’
for details.