############################################################################## ############################################################################## ### ### 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: aarch64-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 Ventura 13.6.5 * 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 23.510 1.659 41.469 Img-set-SpatialExperiment-method 18.118 1.833 26.659 rowGeometries 13.301 0.725 19.640 removeEmptySpace 11.567 0.424 16.759 spatialGraphs 10.906 0.528 16.957 readXenium 10.561 0.591 15.811 dimGeometries 10.621 0.513 16.168 findSpatialNeighbors-SpatialFeatureExperiment-method 10.385 0.508 15.684 cbind-SpatialFeatureExperiment-method 9.835 0.536 15.184 findVisiumGraph 9.198 0.490 13.335 getParams 6.653 0.321 10.000 getPixelSize 5.550 0.442 8.106 formatTxTech 5.573 0.417 8.888 readVizgen 5.353 0.298 8.353 colFeatureData 5.258 0.341 8.406 crop 5.221 0.305 7.977 annotOp 4.920 0.261 7.444 annotSummary 4.901 0.247 7.694 SFE-transform 4.550 0.271 6.742 readCosMX 4.363 0.260 6.828 updateObject 4.355 0.242 6.638 colGeometries 4.027 0.246 6.438 unit-SpatialFeatureExperiment-method 3.960 0.237 6.261 sampleIDs 3.790 0.252 5.963 changeSampleIDs 3.545 0.241 5.483 SpatialFeatureExperiment-subset 3.495 0.242 5.379 annotPred 3.475 0.244 5.569 show-SpatialFeatureExperiment-method 3.461 0.245 5.577 bbox-SpatialFeatureExperiment-method 3.395 0.229 5.605 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: `expected`: TRUE ── Failure ('test-read.R:721:5'): readXenium XOA v2, use csv files ───────────── mean(v$lyr.1, na.rm = TRUE) > 0.9 is not TRUE `actual`: FALSE `expected`: TRUE ── Failure ('test-read.R:741:5'): readXenium, flip image ─────────────────────── mean(v$lyr.1, na.rm = TRUE) > 0.9 is not TRUE `actual`: FALSE `expected`: TRUE [ FAIL 6 | WARN 0 | SKIP 3 | PASS 1079 ] Error: Test failures Execution halted * 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: 1 ERROR, 2 NOTEs See ‘/Users/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck/00check.log’ for details.