############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:SpatialFeatureExperiment.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings SpatialFeatureExperiment_1.12.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/SpatialFeatureExperiment.Rcheck’ * using R version 4.5.0 (2025-04-11) * using platform: aarch64-unknown-linux-gnu * R was compiled by aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0 GNU Fortran (GCC) 14.2.0 * running under: openEuler 24.03 (LTS) * 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 loading without being on the library search path ... 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 23.770 0.781 35.189 Img-set-SpatialExperiment-method 20.445 1.146 28.238 readXenium 12.507 0.540 19.614 rowGeometries 11.852 0.305 18.732 dimGeometries 8.103 0.467 20.905 findSpatialNeighbors 7.761 0.543 17.337 removeEmptySpace 8.042 0.218 12.655 spatialGraphs 7.743 0.204 14.873 findVisiumGraph 6.539 0.284 14.662 cbind-SpatialFeatureExperiment-method 6.492 0.165 14.501 formatTxTech 5.293 0.336 9.962 getPixelSize 4.785 0.178 9.367 colFeatureData 4.644 0.133 10.375 crop 4.471 0.292 10.001 readVizgen 4.483 0.128 9.301 SFE-transform 4.035 0.066 8.101 annotOp 3.749 0.067 8.191 updateObject 3.643 0.124 8.236 getParams 3.462 0.105 8.276 bbox-SpatialFeatureExperiment-method 3.448 0.083 6.698 colGeometries 3.425 0.059 7.691 readCosMX 3.211 0.125 8.576 changeSampleIDs 3.166 0.080 7.486 annotSummary 2.979 0.095 7.600 unit-SpatialFeatureExperiment-method 2.781 0.071 7.182 SpatialFeatureExperiment-subset 2.683 0.059 7.656 SFE-image 2.669 0.056 6.854 show-SpatialFeatureExperiment-method 2.661 0.063 7.450 annotPred 2.610 0.100 7.196 sampleIDs 2.599 0.056 6.677 annotGeometries 2.551 0.071 6.758 * 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: ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-aggregate.R:75:5'): aggregateTxTech for Vizgen ─────────────── all(st_area(colGeometry(sfe)) == 400) is not TRUE `actual`: FALSE `expected`: TRUE ── Failure ('test-formatTxSpots.R:15:5'): Read MERFISH transcript spots into rowGeometries ── y < 10 is not TRUE `actual`: FALSE `expected`: TRUE [ FAIL 2 | WARN 1 | SKIP 10 | PASS 1252 ] 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, 3 NOTEs See ‘/home/biocbuild/bbs-3.22-bioc/meat/SpatialFeatureExperiment.Rcheck/00check.log’ for details.