############################################################################## ############################################################################## ### ### 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_1.12.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/SpatialFeatureExperiment.Rcheck’ * using R version 4.5.2 (2025-10-31) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 14.2.0 * 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 ‘1.12.1’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... INFO Imports includes 21 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 ‘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 ‘gmax’ .filter_polygons: no visible binding for global variable ‘area’ .filter_polygons: no visible binding for global variable ‘name’ .filter_polygons: no visible binding for global variable ‘gi’ .filter_polygons: no visible binding for global variable ‘.N’ .filter_polygons: no visible binding for global variable ‘i’ .filter_polygons: no visible binding for global variable ‘.I’ .filter_polygons: no visible binding for global variable ‘ID_row’ .get_tb1: no visible global function definition for ‘clahe’ .get_tb1_concave: no visible global function definition for ‘st_concave_hull’ .mols2geo: no visible global function definition for ‘txtProgressBar’ .mols2geo: no visible binding for global variable ‘gene’ .mols2geo: no visible global function definition for ‘syms’ .mols2geo: no visible global function definition for ‘write_parquet’ .mols2geo: no visible global function definition for ‘setTxtProgressBar’ .mols2geo_split: no visible binding for global variable ‘grp’ aggregateTx: no visible binding for global variable ‘gene’ aggregateTx : : no visible binding for global variable ‘gene’ findVisiumHDGraph: no visible binding for global variable ‘..cols’ formatTxSpots: no visible binding for global variable ‘rng’ Undefined global functions or variables: ..cols .I .N ID_row area clahe gene gi gmax grp i name rng setTxtProgressBar st_concave_hull syms txtProgressBar write_parquet Consider adding importFrom("utils", "setTxtProgressBar", "txtProgressBar") to your NAMESPACE file. * 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: SpatialFeatureExperiment-coercion.Rd: DataFrame SpatialFeatureExperiment.Rd: DataFrame 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 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 33.513 1.869 38.282 Img-set-SpatialExperiment-method 27.951 2.229 28.769 readXenium 18.420 0.830 20.165 rowGeometries 15.993 0.686 17.581 removeEmptySpace 12.148 0.439 13.550 spatialGraphs 9.771 0.488 11.033 dimGeometries 9.591 0.456 10.959 findSpatialNeighbors 9.339 0.471 10.588 findVisiumGraph 8.172 0.479 9.825 cbind-SpatialFeatureExperiment-method 8.010 0.465 8.934 formatTxTech 6.643 0.546 7.702 colFeatureData 6.107 0.358 7.052 SFE-transform 5.844 0.338 45.014 getPixelSize 5.392 0.454 5.180 readVizgen 5.427 0.289 6.676 crop 5.463 0.234 6.277 getParams 4.694 0.308 5.426 annotOp 4.330 0.240 9.238 SpatialFeatureExperiment-subset 3.558 0.264 24.251 annotGeometries 3.420 0.258 24.097 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’