############################################################################## ############################################################################## ### ### 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 32.660 2.065 67.028 Img-set-SpatialExperiment-method 27.287 2.959 37.473 rowGeometries 17.320 0.789 19.544 readXenium 15.102 0.664 16.993 removeEmptySpace 13.455 0.537 15.243 dimGeometries 12.091 0.499 14.358 spatialGraphs 10.740 0.506 12.474 findSpatialNeighbors-SpatialFeatureExperiment-method 9.536 0.489 11.754 cbind-SpatialFeatureExperiment-method 9.179 0.479 11.168 findVisiumGraph 9.024 0.485 11.048 addVisiumSpotPoly 7.522 0.205 8.573 formatTxTech 6.717 0.581 8.025 readVizgen 6.559 0.300 7.638 SpatialFeatureExperiment-coercion 6.439 0.225 7.569 SFE-transform 6.237 0.326 7.560 crop 6.255 0.267 7.532 saveRDS-SpatialFeatureExperiment-method 5.906 0.063 6.500 read10xVisiumSFE 5.897 0.067 6.480 getPixelSize 5.320 0.482 5.431 colFeatureData 5.396 0.344 6.741 readCosMX 4.976 0.268 5.922 annotOp 4.926 0.252 6.052 getParams 4.842 0.318 5.805 sampleIDs 4.603 0.302 5.477 annotSummary 4.459 0.247 5.388 colGeometries 4.083 0.245 5.081 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’