############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:spatialLIBD.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings spatialLIBD_1.21.5.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.22-data-experiment/meat/spatialLIBD.Rcheck’ * using R version 4.5.1 (2025-06-13) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 * running under: Ubuntu 24.04.2 LTS * using session charset: UTF-8 * checking for file ‘spatialLIBD/DESCRIPTION’ ... OK * this is package ‘spatialLIBD’ version ‘1.21.5’ * 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 vis_gene 27.475 3.697 31.704 vis_clus 21.054 2.964 24.801 add_images 20.313 2.219 23.555 img_update_all 19.164 2.404 21.929 add_qc_metrics 16.472 2.900 19.572 vis_grid_clus 16.083 2.845 19.553 vis_grid_gene 16.259 2.580 19.615 vis_clus_p 15.926 2.088 18.638 cluster_export 15.841 2.063 18.436 vis_image 15.578 2.181 18.292 cluster_import 15.995 1.682 18.322 add_key 15.932 1.385 17.847 vis_gene_p 14.980 1.811 17.537 img_edit 14.661 2.043 17.446 frame_limits 14.261 1.998 16.794 img_update 14.354 1.841 16.726 geom_spatial 14.423 1.666 16.595 check_spe 14.225 1.683 16.341 sce_to_spe 14.111 1.455 16.083 gene_set_enrichment_plot 7.890 0.836 9.072 layer_stat_cor_plot 4.243 0.643 5.215 sig_genes_extract_all 3.233 0.320 5.254 * 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-3.22-data-experiment/meat/spatialLIBD.Rcheck/00check.log’ for details.