############################################################################## ############################################################################## ### ### Running command: ### ### E:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:SpatialFeatureExperiment.install-out.txt --library=E:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings SpatialFeatureExperiment_1.6.1.tar.gz ### ############################################################################## ############################################################################## * using log directory 'E:/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck' * using R version 4.4.1 (2024-06-14 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * 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 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 21.00 1.58 25.55 Img-set-SpatialExperiment-method 18.84 3.24 21.38 rowGeometries 9.22 0.53 11.74 dimGeometries 8.78 0.58 9.57 readXenium 8.81 0.53 9.81 removeEmptySpace 8.36 0.53 9.59 spatialGraphs 7.32 0.73 8.25 findSpatialNeighbors-SpatialFeatureExperiment-method 7.03 0.53 7.78 cbind-SpatialFeatureExperiment-method 6.34 0.45 7.19 findVisiumGraph 6.17 0.55 6.97 formatTxTech 5.17 0.45 6.01 getParams 4.56 0.42 5.11 readVizgen 4.63 0.25 5.13 SFE-image 2.25 0.25 10.44 * 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: ── Failure ('test-read.R:535:5'): readCosMX, split z, split cell compartments ── time_note > time_check is not TRUE `actual`: `expected`: TRUE ── Failure ('test-read.R:536:5'): readCosMX, split z, split cell compartments ── rowGeometryNames(sfe) (`actual`) and rgns[1:4] (`expected`) don't have the same values. * Only in `expected`: "txSpots" * Only in `actual`: "Nuclear_z0", "None_z0", "Membrane_z0", "Cytoplasm_z0" [ FAIL 44 | WARN 27 | SKIP 4 | PASS 1037 ] 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 'E:/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck/00check.log' for details.