############################################################################## ############################################################################## ### ### 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_1.6.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck’ * using R version 4.4.0 (2024-04-24) * 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 12.7.4 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘SpatialFeatureExperiment/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘SpatialFeatureExperiment’ version ‘1.6.1’ * 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 dependencies in R code ... NOTE Unexported objects imported by ':::' calls: ‘S4Vectors:::disableValidity’ ‘SpatialExperiment:::.get_img_idx’ ‘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 .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’ 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’ 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’ 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’ Undefined global functions or variables: cell_col fn gene_col instrument_version major_version minor_version xoa_version * 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 32.877 2.029 42.134 Img-set-SpatialExperiment-method 26.859 2.762 32.737 rowGeometries 16.896 0.783 19.446 readXenium 15.179 0.694 17.503 removeEmptySpace 13.468 0.557 16.195 dimGeometries 12.058 0.518 14.252 spatialGraphs 10.767 0.502 12.776 cbind-SpatialFeatureExperiment-method 9.159 0.460 10.775 findVisiumGraph 8.317 0.485 10.215 findSpatialNeighbors-SpatialFeatureExperiment-method 8.182 0.490 12.816 addVisiumSpotPoly 7.399 0.177 8.176 formatTxTech 6.567 0.593 8.289 readVizgen 6.474 0.311 7.746 crop 6.340 0.275 7.543 SFE-transform 6.263 0.321 7.265 SpatialFeatureExperiment-coercion 6.186 0.206 6.864 getPixelSize 5.748 0.479 6.123 read10xVisiumSFE 5.950 0.078 6.715 saveRDS-SpatialFeatureExperiment-method 5.789 0.060 6.337 colFeatureData 5.387 0.336 6.596 getParams 4.995 0.323 6.116 readCosMX 4.902 0.265 5.940 sampleIDs 4.602 0.290 5.615 annotOp 4.404 0.237 5.145 annotSummary 4.369 0.240 5.164 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’