############################################################################## ############################################################################## ### ### Running command: ### ### /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_1.8.6.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/SpatialFeatureExperiment.Rcheck’ * using R version 4.4.3 (2025-02-28) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘SpatialFeatureExperiment/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘SpatialFeatureExperiment’ version ‘1.8.6’ * 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 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 : : warning in do.call(setdiff, arg = assays_n): partial argument match of 'arg' to 'args' .filter_polygons: no visible binding for global variable ‘ID_row’ .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’ .read10xVisium: no visible global function definition for ‘spatialCoordsNames<-’ 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 global function definition for ‘tail’ 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’ findVisiumHDGraph: no visible binding for global variable ‘..cols’ 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: ..cols ID_row cell_col fn gene_col img_df instrument_version major_version minor_version spatialCoordsNames<- tail xoa_version Consider adding importFrom("utils", "tail") to your NAMESPACE file. * 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 35.087 1.787 38.209 Img-set-SpatialExperiment-method 31.287 3.237 33.311 readXenium 16.838 0.765 17.626 rowGeometries 16.065 0.728 17.120 removeEmptySpace 11.997 0.459 12.799 spatialGraphs 10.071 0.450 11.026 dimGeometries 9.771 0.470 10.997 cbind-SpatialFeatureExperiment-method 8.229 0.472 9.498 findVisiumGraph 8.156 0.470 9.048 findSpatialNeighbors-SpatialFeatureExperiment-method 8.091 0.446 9.044 crop 6.888 0.259 7.603 SFE-transform 6.433 0.304 7.203 getParams 6.052 0.345 6.636 getPixelSize 5.899 0.455 5.802 formatTxTech 5.775 0.527 6.701 readVizgen 5.608 0.296 6.490 colFeatureData 5.187 0.362 6.034 SpatialFeatureExperiment-coercion 5.182 0.187 5.518 * 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 ... OK * DONE Status: 2 NOTEs See ‘/Users/biocbuild/bbs-3.20-bioc/meat/SpatialFeatureExperiment.Rcheck/00check.log’ for details.