* using log directory ‘/srv/hornik/tmp/CRAN_pretest/pimbayes.Rcheck’ * using R Under development (unstable) (2025-03-20 r88016) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 19.1.7 (1+b1) Debian flang-new version 19.1.7 (1+b1) * running under: Debian GNU/Linux trixie/sid * using session charset: UTF-8 * checking for file ‘pimbayes/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘pimbayes’ version ‘0.1.0’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [3s/11s] NOTE Maintainer: ‘Seren Lee ’ New submission Possibly misspelled words in DESCRIPTION: Gustafson (9:43) ISTP (8:188, 9:5) Pigeson (10:71) Spall (11:125) Surjanovic (10:90) al (10:104) algorthm (9:10) et (10:101) jl (10:79) reparameterization (8:168) The Title field should be in title case. Current version is: ‘Comprehensive tools for Bayesian inference with partially identified models’ In title case that is: ‘Comprehensive Tools for Bayesian Inference with Partially Identified Models’ * 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 executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking serialization versions ... OK * checking whether package ‘pimbayes’ can be installed ... [2s/2s] OK * checking package directory ... OK * checking for future file timestamps ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... NOTE Non-standard files/directories found at top level: ‘LICENSE.md’ ‘data-raw’ * 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 ... [0s/0s] OK * checking whether the package can be loaded with stated dependencies ... [0s/0s] OK * checking whether the package can be unloaded cleanly ... [0s/0s] OK * checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK * checking whether the namespace can be unloaded cleanly ... [0s/0s] OK * checking loading without being on the library search path ... [0s/0s] 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 ... [3s/3s] OK * checking Rd files ... [0s/0s] OK * checking Rd metadata ... OK * checking Rd line widths ... NOTE Rd file 'sampling.Rd': \examples lines wider than 100 characters: pr[i] <- (y[i]) * inprod(x[i,1:p2], pr_xy1[1:p2]) + abs(y[i]-1) * inprod(x[i,1:p2], pr_xy0[1:p2]) These lines will be truncated in the PDF manual. * 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 ... [0s/0s] OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking sizes of PDF files under ‘inst/doc’ ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... [10s/10s] ERROR Running examples in ‘pimbayes-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: sampling > ### Title: Posterior sampling of given JAGS (BUGS) code and data > ### Aliases: sampling > > ### ** Examples > > jags_code <- + "model{ + y[1:4] ~ dmulti(eta[1:4], n) + eta[1:4] <- c(se*pi[1]+(1-sp)*pi[3], + se*pi[2]+(1-sp)*pi[4], + sp*pi[3]+(1-se)*pi[1], + (1-se)*pi[2]+sp*pi[4]) + pi[1:4] ~ ddirch(c(1,1,1,1)) + se ~ dbeta(25,3) + sp ~ dbeta(30,1.5) + }" > data(small_cross) > data = list(y = small_cross, n = sum(small_cross)) > sampling(jags_code, data, "cross", N = 15000) /home/hornik/.bashrc: line 5: ulimit: stack size: cannot modify limit: Operation not permitted Warning in system2("bash", "-l -c 'which julia'", stdout = TRUE) : running command ''bash' -l -c 'which julia'' had status 1 sh: 1: NA: not found Error in julia_setup() : Julia is not found. Calls: sampling ... -> -> -> julia_setup Execution halted Examples with CPU (user + system) or elapsed time > 5s user system elapsed istp.manual 6.141 0.024 6.166 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... [1s/1s] OK Running ‘testthat.R’ [1s/1s] * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [10s/10s] ERROR Error(s) in re-building vignettes: ... --- re-building ‘Diagnosing-identification.Rmd’ using rmarkdown --- finished re-building ‘Diagnosing-identification.Rmd’ --- re-building ‘Sampling-cross-manual.Rmd’ using rmarkdown --- finished re-building ‘Sampling-cross-manual.Rmd’ --- re-building ‘Sampling-cross.Rmd’ using rmarkdown /home/hornik/.bashrc: line 5: ulimit: stack size: cannot modify limit: Operation not permitted sh: 1: NA: not found Quitting from Sampling-cross.Rmd:70-76 [unnamed-chunk-4] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error in `julia_setup()`: ! Julia is not found. --- Backtrace: ▆ 1. └─pimbayes::sampling(jags_code, data, type = "cross", N = 1000) 2. └─pimbayes:::istp.cross(jags_code, data, N) 3. └─pimbayes:::prepare_cross(jags_code, data) 4. └─pimbayes:::parse_jags_code(jags_code, data) 5. └─JuliaCall::julia_library("JuliaBUGS") 6. └─julia$command(paste0("using ", pkg_name)) 7. └─julia$call(...) 8. └─julia$do.call(func_name, list(...), need_return, show_value) 9. └─JuliaCall::julia_setup() ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'Sampling-cross.Rmd' failed with diagnostics: Julia is not found. --- failed re-building ‘Sampling-cross.Rmd’ --- re-building ‘Sampling-pigeons.Rmd’ using rmarkdown /home/hornik/.bashrc: line 5: ulimit: stack size: cannot modify limit: Operation not permitted sh: 1: NA: not found Quitting from Sampling-pigeons.Rmd:34-36 [unnamed-chunk-2] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error in `julia_setup()`: ! Julia is not found. --- Backtrace: x 1. \-pimbayes::init_julia_session_multi(threads = 4) 2. \-JuliaCall::julia_eval("Threads.nthreads()") 3. \-julia$call("JuliaCall.eval_string", cmd, need_return = match.arg(need_return)) 4. \-julia$do.call(func_name, list(...), need_return, show_value) 5. \-JuliaCall::julia_setup() ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'Sampling-pigeons.Rmd' failed with diagnostics: Julia is not found. --- failed re-building ‘Sampling-pigeons.Rmd’ --- re-building ‘Sampling-sat.Rmd’ using rmarkdown /home/hornik/.bashrc: line 5: ulimit: stack size: cannot modify limit: Operation not permitted sh: 1: NA: not found Quitting from Sampling-sat.Rmd:101-111 [unnamed-chunk-4] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error in `julia_setup()`: ! Julia is not found. --- Backtrace: ▆ 1. └─pimbayes::sampling(jags_code, data, type = "sat", N = 1000) 2. └─pimbayes:::istp.sat(jags_code, data, N) 3. └─pimbayes:::prepare_sat(jags_code, data) 4. └─pimbayes:::parse_jags_code(jags_code, data) 5. └─JuliaCall::julia_library("JuliaBUGS") 6. └─julia$command(paste0("using ", pkg_name)) 7. └─julia$call(...) 8. └─julia$do.call(func_name, list(...), need_return, show_value) 9. └─JuliaCall::julia_setup() ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'Sampling-sat.Rmd' failed with diagnostics: Julia is not found. --- failed re-building ‘Sampling-sat.Rmd’ SUMMARY: processing the following files failed: ‘Sampling-cross.Rmd’ ‘Sampling-pigeons.Rmd’ ‘Sampling-sat.Rmd’ Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... [2s/2s] OK * checking HTML version of manual ... [0s/0s] OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 2 ERRORs, 3 NOTEs