############################################################################## ############################################################################## ### ### 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 Patched (2025-11-04 r88984) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 16.0.0 (clang-1600.0.26.6) GNU Fortran (GCC) 14.2.0 * running under: macOS Ventura 13.7.8 * 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 24.778 1.528 42.298 Img-set-SpatialExperiment-method 21.669 1.259 33.103 readXenium 14.987 0.644 23.998 rowGeometries 13.904 0.636 22.813 spatialGraphs 13.233 0.433 21.056 cbind-SpatialFeatureExperiment-method 13.189 0.443 22.070 findSpatialNeighbors 12.122 0.445 20.251 findVisiumGraph 11.438 0.414 19.116 removeEmptySpace 10.687 0.405 18.534 dimGeometries 9.015 0.416 14.217 annotSummary 7.338 0.233 12.229 formatTxTech 6.996 0.454 11.684 annotOp 5.526 0.206 9.441 bbox-SpatialFeatureExperiment-method 5.370 0.217 9.012 readVizgen 5.251 0.261 8.832 getPixelSize 5.125 0.355 7.367 SFE-transform 5.089 0.225 8.123 colFeatureData 4.918 0.297 8.675 changeSampleIDs 4.720 0.204 8.197 getParams 4.559 0.258 7.998 show-SpatialFeatureExperiment-method 4.359 0.197 8.002 readCosMX 4.274 0.226 7.446 updateObject 4.224 0.199 7.800 annotPred 4.202 0.205 7.325 colGeometries 4.099 0.213 7.121 crop 4.050 0.208 7.356 unit-SpatialFeatureExperiment-method 3.926 0.198 7.173 SFE-image 3.360 0.203 6.431 SpatialFeatureExperiment-subset 3.197 0.223 5.597 annotGeometries 2.967 0.215 5.768 sampleIDs 2.744 0.189 5.411 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’