############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:RegionalST.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings RegionalST_1.5.3.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/RegionalST.Rcheck’ * using R Under development (unstable) (2024-10-21 r87258) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * checking for file ‘RegionalST/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘RegionalST’ version ‘1.5.3’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' 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 ‘RegionalST’ 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 Namespace in Imports field not imported from: ‘BiocStyle’ All declared Imports should be used. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE GetCellTypeSpecificDE_withProp: no visible binding for global variable ‘OneRegOut1’ GetCellTypeSpecificDE_withProp: no visible binding for global variable ‘twoCenter’ GetCellTypeSpecificDE_withProp: no visible binding for global variable ‘OneRegOut2’ Undefined global functions or variables: OneRegOut1 OneRegOut2 twoCenter * 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 files in ‘vignettes’ ... OK * checking examples ... ERROR Running examples in ‘RegionalST-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: RankCenterByEntropy > ### Title: Automatically rank ROI centers based on entropy > ### Aliases: RankCenterByEntropy > > ### ** Examples > > data("example_sce") > example_sce <- mySpatialPreprocess(example_sce, platform="Visium") > weight <- data.frame(celltype = c("Cancer Epithelial", "CAFs", "T-cells", "Endothelial", + "PVL", "Myeloid", "B-cells", "Normal Epithelial", "Plasmablasts"), + weight = c(0.25,0.05, + 0.25,0.05, + 0.025,0.05, + 0.25,0.05,0.025)) > example_sce <- RankCenterByEntropy(example_sce, weight, label = "celltype", + selectN = round(length(example_sce$spot)/10), + topN = 3, min_radius = 10, + radius_vec = c(10,15), + doPlot = TRUE) Processing to Radius = 10 | | | 0% | |== | 3% | |==== | 7% | |====== | 10% | |======== | 13% | |========== | 17% | |============ | 20% | |============== | 23% | |================ | 27% | |================== | 30% | |==================== | 33% | |====================== | 37% | |======================== | 40% | |========================== | 43% | |============================ | 47% | |============================== | 50% | |================================ | 53% | |================================== | 57% | |==================================== | 60% | |====================================== | 63% | |======================================== | 67% | |========================================== | 70% | |============================================ | 73% | |============================================== | 77% | |================================================ | 80% | |================================================== | 83% | |==================================================== | 87% | |====================================================== | 90% | |======================================================== | 93% | |========================================================== | 97% | |============================================================| 100% Error in cor(sce$array_col, sce$pxl_col_in_fullres) : supply both 'x' and 'y' or a matrix-like 'x' Calls: RankCenterByEntropy ... eval -> -> .make_vertices -> .flip_axis -> cor Execution halted Examples with CPU (user + system) or elapsed time > 5s user system elapsed GetCrossRegionalDE_raw 7.038 0.368 7.408 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: 7. └─stats::cor(sce$array_col, sce$pxl_col_in_fullres) ── Error ('test-PlotOneSelectCenter.R:5:1'): (code run outside of `test_that()`) ── Error in `cor(sce$array_col, sce$pxl_col_in_fullres)`: supply both 'x' and 'y' or a matrix-like 'x' Backtrace: ▆ 1. └─RegionalST::PlotOneSelectedCenter(example_sce, ploti = 1) at test-PlotOneSelectCenter.R:5:1 2. └─RegionalST::FindRegionalCells(...) 3. └─BayesSpace::featurePlot(...) 4. └─BayesSpace:::.make_vertices(...) 5. └─BayesSpace:::.flip_axis(sce, platform) 6. └─stats::cor(sce$array_col, sce$pxl_col_in_fullres) [ FAIL 2 | WARN 3 | SKIP 0 | PASS 3 ] Error: Test failures Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 2 ERRORs, 2 NOTEs See ‘/home/biocbuild/bbs-3.21-bioc/meat/RegionalST.Rcheck/00check.log’ for details.