############################################################################## ############################################################################## ### ### 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_1.7.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/SpatialFeatureExperiment.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: aarch64-unknown-linux-gnu * R was compiled by gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14) GNU Fortran (GCC) 10.3.1 * running under: openEuler 22.03 (LTS-SP1) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘SpatialFeatureExperiment/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘SpatialFeatureExperiment’ version ‘1.7.0’ * 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 loading without being on the library search path ... 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 22.889 1.184 28.603 Img-set-SpatialExperiment-method 21.011 2.483 25.361 readXenium 15.038 0.991 17.417 rowGeometries 14.316 0.850 17.381 removeEmptySpace 11.534 0.308 14.575 dimGeometries 9.794 0.418 15.319 cbind-SpatialFeatureExperiment-method 8.525 1.353 14.532 spatialGraphs 8.842 0.228 13.547 findVisiumGraph 8.276 0.391 13.220 findSpatialNeighbors-SpatialFeatureExperiment-method 7.732 0.299 13.054 crop 6.848 0.226 9.335 colFeatureData 5.903 1.006 9.219 getPixelSize 6.438 0.383 8.397 annotPred 5.526 0.419 8.229 SFE-transform 5.150 0.687 8.087 readVizgen 5.068 0.139 7.580 formatTxTech 4.750 0.269 7.410 bbox-SpatialFeatureExperiment-method 4.391 0.459 7.126 updateObject 4.748 0.065 7.057 getParams 4.180 0.312 7.210 readCosMX 3.862 0.213 6.848 changeSampleIDs 3.225 0.438 5.942 annotOp 3.268 0.290 5.960 colGeometries 2.813 0.347 5.464 show-SpatialFeatureExperiment-method 2.970 0.056 5.965 SpatialFeatureExperiment-subset 2.759 0.267 5.759 SFE-image 2.779 0.211 5.706 annotSummary 2.672 0.315 5.376 annotGeometries 2.655 0.323 5.746 unit-SpatialFeatureExperiment-method 2.874 0.051 5.154 sampleIDs 2.533 0.104 5.443 * 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:727:5'): readXenium XOA v2, use csv files ───────────── mean(v$lyr.1, na.rm = TRUE) > 0.9 is not TRUE `actual`: FALSE `expected`: TRUE ── Failure ('test-read.R:748:5'): readXenium, flip image ─────────────────────── mean(v$lyr.1, na.rm = TRUE) > 0.9 is not TRUE `actual`: FALSE `expected`: TRUE [ FAIL 16 | WARN 2 | SKIP 3 | PASS 1041 ] 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 ‘/home/biocbuild/bbs-3.20-bioc/meat/SpatialFeatureExperiment.Rcheck/00check.log’ for details.