• using R version 4.5.1 Patched (2025-07-14 r88411)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     gcc-14 (Debian 14.2.0-19) 14.2.0     GNU Fortran (Debian 14.2.0-19) 14.2.0
• running under: Debian GNU/Linux 13 (trixie)
• using session charset: UTF-8
• checking for file ‘MRFcov/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘MRFcov’ version ‘1.0.39’
• 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 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 ‘MRFcov’ can be installed ... OK See the install log for details.
• checking package directory ... OK
• checking for future file timestamps ... 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 ... [2s/2s] OK
• checking whether the package can be loaded with stated dependencies ... [2s/3s] OK
• checking whether the package can be unloaded cleanly ... [2s/2s] OK
• checking whether the namespace can be loaded with stated dependencies ... [2s/2s] OK
• checking whether the namespace can be unloaded cleanly ... [2s/2s] OK
• checking loading without being on the library search path ... [2s/2s] OK
• checking whether startup messages can be suppressed ... [2s/3s] 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 ... [19s/27s] OK
• checking Rd files ... [0s/1s] OK
• checking Rd metadata ... OK
• checking Rd line widths ... 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 ... [0s/0s] 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 ... [10s/12s] OK
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [18s/22s] OK   Running ‘testthat.R’ [18s/22s]
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [69s/92s] ERROR Error(s) in re-building vignettes:   ... --- re-building ‘Bird_Parasite_CRF.Rmd’ using rmarkdown Quitting from Bird_Parasite_CRF.Rmd:295-302 [unnamed-chunk-40] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error in `if (preds[x, i] == 0) ...`: ! missing value where TRUE/FALSE needed --- Backtrace:     ▆  1. └─MRFcov::predict_MRFnetworks(...)  2. └─base::lapply(...)  3. └─MRFcov (local) FUN(X[[i]], ...) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'Bird_Parasite_CRF.Rmd' failed with diagnostics: missing value where TRUE/FALSE needed --- failed re-building ‘Bird_Parasite_CRF.Rmd’ --- re-building ‘CRF_data_prep.Rmd’ using rmarkdown --- finished re-building ‘CRF_data_prep.Rmd’ --- re-building ‘Gaussian_Poisson_CRFs.Rmd’ using rmarkdown --- finished re-building ‘Gaussian_Poisson_CRFs.Rmd’ SUMMARY: processing the following file failed:   ‘Bird_Parasite_CRF.Rmd’ Error: Vignette re-building failed. Execution halted
• checking PDF version of manual ... [5s/6s] OK
• checking HTML version of manual ... [1s/2s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 1 ERROR