* using log directory 'd:/Rcompile/CRANpkg/local/3.6/DUBStepR.Rcheck' * using R version 3.6.3 (2020-02-29) * 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 '1.1.1' * 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 '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 ... [6s] 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 ... 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: 219 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% | |=========== | 16% | |============= | 19% | |=============== | 22% | |================== | 25% | |==================== | 28% | |====================== | 31% | |======================== | 34% | |========================== | 38% | |============================ | 41% | |=============================== | 44% | |================================= | 47% | |=================================== | 50% | |===================================== | 53% | |======================================= | 56% | |========================================== | 59% | |============================================ | 62% | |============================================== | 66% | |================================================ | 69% | |================================================== | 72% | |==================================================== | 75% | |======================================================= | 78% | |========================================================= | 81% | |=========================================================== | 84% | |============================================================= | 88% | |=============================================================== | 91% | |================================================================== | 94% | |==================================================================== | 97% | |======================================================================| 100% Done. Determining optimal feature set... Error: object 'markvario' is not exported by 'namespace:spatstat' Execution halted runtime error R6031 - Attempt to initialize the CRT more than once. This indicates a bug in your application. * checking for unstated dependencies in vignettes ... OK * checking package vignettes in 'inst/doc' ... OK * checking re-building of vignette outputs ... [75s] WARNING Error(s) in re-building vignettes: --- re-building 'dub-vignette.Rmd' using rmarkdown Installing package into 'D:/temp/Rtmp2JXPwM/RLIBS_b90c52e2570d' (as 'lib' is unspecified) installing the source package 'DUBStepR' trying URL 'https://cloud.r-project.org/src/contrib/DUBStepR_1.1.1.tar.gz' Content type 'application/x-gzip' length 2837180 bytes (2.7 MB) ================================================== downloaded 2.7 MB * installing *source* package 'DUBStepR' ... ** package 'DUBStepR' successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location *** arch - i386 *** arch - x64 ** testing if installed package can be loaded from final location *** arch - i386 *** arch - x64 ** testing if installed package keeps a record of temporary installation path * DONE (DUBStepR) The downloaded source packages are in 'D:\temp\RtmpAXJF1Y\downloaded_packages' Quitting from lines 57-60 (dub-vignette.Rmd) Error: processing vignette 'dub-vignette.Rmd' failed with diagnostics: package or namespace load failed for 'Seurat': object 'markvario' is not exported by 'namespace:spatstat' --- failed re-building 'dub-vignette.Rmd' SUMMARY: processing the following file failed: 'dub-vignette.Rmd' Error: Vignette re-building failed. Execution halted runtime error R6031 - Attempt to initialize the CRT more than once. This indicates a bug in your application. * checking PDF version of manual ... OK * DONE Status: 1 ERROR, 1 WARNING