* using log directory 'd:/Rcompile/CRANpkg/local/4.0/DUBStepR.Rcheck' * using R version 4.0.5 (2021-03-31) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * checking for file 'DUBStepR/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'DUBStepR' version '1.2.0' * 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 whether package 'DUBStepR' 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 R 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 use of S3 registration ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... [8s] OK * 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 installed files from 'inst/doc' ... OK * checking files in 'vignettes' ... OK * checking examples ... [5s] ERROR Running examples in 'DUBStepR-Ex.R' failed The error most likely occurred in: > ### Name: DUBStepR > ### Title: DUBStepR - Obtain a list of feature genes to characterise cell > ### types > ### Aliases: DUBStepR > > ### ** Examples > > res <- DUBStepR(input.data = pbmc_norm_small_data) Running DUBStepR... Dimensions of input data: 230 x 80 Expression Filtering Done. Mitochondrial, Ribosomal and Pseudo Genes Filtering Done. Dimensions of filtered data: 218 x 80 Computing GGC... Done. Running Stepwise Regression... | | | 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% Done. Adding correlated features... | | | 0% | |== | 3% | |==== | 6% | |====== | 9% | |======== | 12% | |========== | 15% | |============ | 18% | |============== | 21% | |================ | 24% | |=================== | 26% | |===================== | 29% | |======================= | 32% | |========================= | 35% | |=========================== | 38% | |============================= | 41% | |=============================== | 44% | |================================= | 47% | |=================================== | 50% | |===================================== | 53% | |======================================= | 56% | |========================================= | 59% | |=========================================== | 62% | |============================================= | 65% | |=============================================== | 68% | |================================================= | 71% | |=================================================== | 74% | |====================================================== | 76% | |======================================================== | 79% | |========================================================== | 82% | |============================================================ | 85% | |============================================================== | 88% | |================================================================ | 91% | |================================================================== | 94% | |==================================================================== | 97% | |======================================================================| 100% Done. Determining optimal feature set... Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace 'Matrix' 1.3-2 is already loaded, but >= 1.3.3 is required Calls: DUBStepR -> getOptimalFeatureSet Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes in 'inst/doc' ... OK * checking re-building of vignette outputs ... [5s] WARNING Error(s) in re-building vignettes: --- re-building 'dub-vignette.Rmd' using rmarkdown Loading required package: DUBStepR Quitting from lines 50-52 (dub-vignette.Rmd) Error: processing vignette 'dub-vignette.Rmd' failed with diagnostics: package or namespace load failed for 'Seurat' in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): namespace 'Matrix' 1.3-2 is already loaded, but >= 1.3.3 is required --- failed re-building 'dub-vignette.Rmd' SUMMARY: processing the following file failed: 'dub-vignette.Rmd' Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... OK * DONE Status: 1 ERROR, 1 WARNING