* using log directory 'd:/Rcompile/CRANpkg/local/4.2/BCDAG.Rcheck' * using R version 4.2.3 (2023-03-15 ucrt) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: UTF-8 * checking for file 'BCDAG/DESCRIPTION' ... OK * this is package 'BCDAG' version '1.0.0' * 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 'BCDAG' 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 ... [4s] OK * checking Rd files ... [1s] 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 LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking installed files from 'inst/doc' ... OK * checking files in 'vignettes' ... OK * checking examples ... [24s] ERROR Running examples in 'BCDAG-Ex.R' failed The error most likely occurred in: > ### Name: summary.bcdag > ### Title: bcdag object summaries > ### Aliases: summary.bcdag > > ### ** Examples > > n <- 1000 > q <- 4 > DAG <- matrix(c(0,1,1,0,0,0,0,0,0,0,0,0,0,1,1,0), nrow = q) > > L <- DAG > L[L != 0] <- runif(q, 0.2, 1) > diag(L) <- c(1,1,1,1) > D <- diag(1, q) > Sigma <- t(solve(L))%*%D%*%solve(L) > > a <- 6 > g <- 1/1000 > U <- g*diag(1,q) > w = 0.2 > > set.seed(1) > X <- mvtnorm::rmvnorm(n, sigma = Sigma) > > out <- learn_DAG(1000, 0, X, a, U, w, fast = TRUE, collapse = TRUE, save.memory = FALSE) Sampling DAGs... | | | 0% | | | 1% | |= | 1% | |= | 2% | |== | 2% | |== | 3% | |== | 4% | |=== | 4% | |=== | 5% | |==== | 5% | |==== | 6% | |===== | 7% | |===== | 8% | |====== | 8% | |====== | 9% | |======= | 9% | |======= | 10% | |======= | 11% | |======== | 11% | |======== | 12% | |========= | 12% | |========= | 13% | |========= | 14% | |========== | 14% | |========== | 15% | |=========== | 15% | |=========== | 16% | |============ | 16% | |============ | 17% | |============ | 18% | |============= | 18% | |============= | 19% | |============== | 19% | |============== | 20% | |============== | 21% | |=============== | 21% | |=============== | 22% | |================ | 22% | |================ | 23% | |================ | 24% | |================= | 24% | |================= | 25% | |================== | 25% | |================== | 26% | |=================== | 26% | |=================== | 27% | |=================== | 28% | |==================== | 28% | |==================== | 29% | |===================== | 29% | |===================== | 30% | |===================== | 31% | |====================== | 31% | |====================== | 32% | |======================= | 32% | |======================= | 33% | |======================= | 34% | |======================== | 34% | |======================== | 35% | |========================= | 35% | |========================= | 36% | |========================== | 36% | |========================== | 37% | |========================== | 38% | |=========================== | 38% | |=========================== | 39% | |============================ | 39% | |============================ | 40% | |============================ | 41% | |============================= | 41% | |============================= | 42% | |============================== | 42% | |============================== | 43% | |=============================== | 44% | |=============================== | 45% | |================================ | 45% | |================================ | 46% | |================================= | 46% | |================================= | 47% | |================================= | 48% | |================================== | 48% | |================================== | 49% | |=================================== | 49% | |=================================== | 50% | |=================================== | 51% | |==================================== | 51% | |==================================== | 52% | |===================================== | 52% | |===================================== | 53% | |===================================== | 54% | |====================================== | 54% | |====================================== | 55% | |======================================= | 55% | |======================================= | 56% | |======================================== | 57% | |======================================== | 58% | |========================================= | 58% | |========================================= | 59% | |========================================== | 59% | |========================================== | 60% | |========================================== | 61% | |=========================================== | 61% | |=========================================== | 62% | |============================================ | 62% | |============================================ | 63% | |============================================ | 64% | |============================================= | 64% | |============================================= | 65% | |============================================== | 65% | |============================================== | 66% | |=============================================== | 66% | |=============================================== | 67% | |=============================================== | 68% | |================================================ | 68% | |================================================ | 69% | |================================================= | 69% | |================================================= | 70% | |================================================= | 71% | |================================================== | 71% | |================================================== | 72% | |=================================================== | 72% | |=================================================== | 73% | |=================================================== | 74% | |==================================================== | 74% | |==================================================== | 75% | |===================================================== | 75% | |===================================================== | 76% | |====================================================== | 76% | |====================================================== | 77% | |====================================================== | 78% | |======================================================= | 78% | |======================================================= | 79% | |======================================================== | 79% | |======================================================== | 80% | |======================================================== | 81% | |========================================================= | 81% | |========================================================= | 82% | |========================================================== | 82% | |========================================================== | 83% | |========================================================== | 84% | |=========================================================== | 84% | |=========================================================== | 85% | |============================================================ | 85% | |============================================================ | 86% | |============================================================= | 86% | |============================================================= | 87% | |============================================================= | 88% | |============================================================== | 88% | |============================================================== | 89% | |=============================================================== | 89% | |=============================================================== | 90% | |=============================================================== | 91% | |================================================================ | 91% | |================================================================ | 92% | |================================================================= | 92% | |================================================================= | 93% | |================================================================== | 94% | |================================================================== | 95% | |=================================================================== | 95% | |=================================================================== | 96% | |==================================================================== | 96% | |==================================================================== | 97% | |==================================================================== | 98% | |===================================================================== | 98% | |===================================================================== | 99% | |======================================================================| 99% | |======================================================================| 100%> summary(out) A collapsed bcdag object containing 1000 draws from the posterior distribution of DAGs. (Burnin = 0 ). Prior hyperparameters: w = 0.2 a = 6 U = [,1] [,2] [,3] [,4] [1,] 0.001 0.000 0.000 0.000 [2,] 0.000 0.001 0.000 0.000 [3,] 0.000 0.000 0.001 0.000 [4,] 0.000 0.000 0.000 0.001 Error in h(simpleError(msg, call)) : error in evaluating the argument 'x' in selecting a method for function 'plot': no method or default for coercing "matrix" to "graphNEL" Calls: summary -> summary.bcdag -> -> Execution halted * checking for unstated dependencies in 'tests' ... OK * checking tests ... [6s] OK Running 'testthat.R' [6s] * checking for unstated dependencies in vignettes ... OK * checking package vignettes in 'inst/doc' ... OK * checking re-building of vignette outputs ... [291s] ERROR Error(s) in re-building vignettes: --- re-building 'bcdag_generatedata.Rmd' using rmarkdown --- finished re-building 'bcdag_generatedata.Rmd' --- re-building 'bcdag_getfamily.Rmd' using rmarkdown Quitting from lines 96-97 [unnamed-chunk-7] (bcdag_getfamily.Rmd) Error: processing vignette 'bcdag_getfamily.Rmd' failed with diagnostics: error in evaluating the argument 'x' in selecting a method for function 'plot': no method or default for coercing "matrix" to "graphNEL" --- failed re-building 'bcdag_getfamily.Rmd' --- re-building 'bcdag_learnDAG.Rmd' using rmarkdown --- finished re-building 'bcdag_learnDAG.Rmd' SUMMARY: processing the following file failed: 'bcdag_getfamily.Rmd' Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... OK * DONE Status: 2 ERRORs