############################################################################## ############################################################################## ### ### 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_1.7.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/SpatialFeatureExperiment.Rcheck’ * using R version 4.4.1 RC (2024-06-06 r86719) * 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 12.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘SpatialFeatureExperiment/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘SpatialFeatureExperiment’ version ‘1.7.0’ * 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 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 19.126 1.155 20.811 Img-set-SpatialExperiment-method 17.796 2.044 20.741 readXenium 11.540 0.672 12.211 rowGeometries 11.307 0.643 12.161 spatialGraphs 7.929 0.354 8.653 removeEmptySpace 7.862 0.366 8.469 dimGeometries 7.449 0.357 8.157 findVisiumGraph 6.734 0.319 7.495 findSpatialNeighbors-SpatialFeatureExperiment-method 6.648 0.331 7.323 cbind-SpatialFeatureExperiment-method 6.447 0.325 7.093 formatTxTech 4.775 0.420 5.372 sampleIDs 2.453 0.162 5.980 * 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: 2. │ └─testthat:::expect_condition_matching(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. └─SpatialFeatureExperiment::readXenium(fn) 8. └─arrow::read_parquet(fn_meta) 9. └─base::tryCatch(reader$ReadTable(), error = read_compressed_error) 10. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 11. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 12. └─value[[3L]](cond) [ FAIL 1 | WARN 2 | SKIP 3 | PASS 1088 ] 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.