############################################################################## ############################################################################## ### ### 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_1.8.6.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/SpatialFeatureExperiment.Rcheck’ * using R version 4.4.2 (2024-10-31) * 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 13.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘SpatialFeatureExperiment/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘SpatialFeatureExperiment’ version ‘1.8.6’ * 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 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 ‘ID_row’ .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’ .read10xVisium: no visible global function definition for ‘spatialCoordsNames<-’ 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’ aggregateTx: no visible global function definition for ‘tail’ aggregateTxTech: no visible binding for global variable ‘gene_col’ aggregateTxTech: no visible binding for global variable ‘cell_col’ aggregateTxTech: no visible binding for global variable ‘fn’ aggregateTxTech: no visible binding for global variable ‘xoa_version’ aggregateTxTech: no visible binding for global variable ‘major_version’ aggregateTxTech: no visible binding for global variable ‘minor_version’ aggregateTxTech: no visible binding for global variable ‘instrument_version’ findVisiumHDGraph: no visible binding for global variable ‘..cols’ 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’ readVizgen: no visible binding for global variable ‘img_df’ 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’ readXenium: no visible binding for global variable ‘img_df’ Undefined global functions or variables: ..cols ID_row cell_col fn gene_col img_df instrument_version major_version minor_version spatialCoordsNames<- tail xoa_version Consider adding importFrom("utils", "tail") to your NAMESPACE file. * 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 23.397 1.255 26.452 Img-set-SpatialExperiment-method 21.249 1.844 22.970 readXenium 13.619 0.639 14.275 rowGeometries 12.956 0.707 13.767 spatialGraphs 11.142 0.395 13.205 removeEmptySpace 10.169 0.389 11.661 cbind-SpatialFeatureExperiment-method 9.253 0.381 11.397 findSpatialNeighbors-SpatialFeatureExperiment-method 9.022 0.370 11.306 findVisiumGraph 8.625 0.354 10.625 dimGeometries 7.950 0.357 9.979 getPixelSize 6.239 0.347 6.878 formatTxTech 5.751 0.453 6.513 getParams 5.901 0.280 7.215 readVizgen 5.656 0.263 6.334 updateObject 5.592 0.203 6.755 colGeometries 5.384 0.226 6.444 colFeatureData 4.866 0.296 6.097 annotSummary 4.803 0.188 5.803 annotOp 4.563 0.195 5.575 SFE-transform 4.497 0.218 5.516 listw2sparse 4.244 0.192 5.269 * 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: 'test-read.R:158:5', 'test-read.R:168:5', 'test-read.R:175:5', 'test-read.R:187:5' • gdalParquetAvailable() is not TRUE (3): 'test-formatTxSpots.R:113:5', 'test-formatTxSpots.R:140:5', 'test-formatTxSpots.R:157:5' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-formatTxSpots.R:13:5'): Read MERFISH transcript spots into rowGeometries ── sum(v$mosaic_PolyT_z3 < 30, na.rm = TRUE) < 10 is not TRUE `actual`: FALSE `expected`: TRUE [ FAIL 1 | WARN 0 | SKIP 10 | PASS 1256 ] 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-3.20-bioc/meat/SpatialFeatureExperiment.Rcheck/00check.log’ for details.