* using log directory ‘/Volumes/Builds/packages/big-sur-arm64/results/4.5/MGDrivE2.Rcheck’ * using R version 4.5.0 beta (2025-03-29 r88069) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 14.2.0 * running under: macOS Ventura 13.4 * using session charset: UTF-8 * checking for file ‘MGDrivE2/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘MGDrivE2’ version ‘2.1.0’ * 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 executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘MGDrivE2’ can be installed ... [6s/7s] OK See 'https://www.r-project.org/nosvn/R.check/r-release-macos-arm64/MGDrivE2-00install.html' for details. * 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 code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... [1s/1s] OK * checking whether the package can be loaded with stated dependencies ... [1s/1s] OK * checking whether the package can be unloaded cleanly ... [1s/1s] OK * checking whether the namespace can be loaded with stated dependencies ... [1s/1s] OK * checking whether the namespace can be unloaded cleanly ... [1s/1s] OK * checking loading without being on the library search path ... [1s/1s] OK * checking whether startup messages can be suppressed ... [1s/1s] 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 ... [7s/9s] OK * checking Rd files ... [0s/0s] NOTE checkRd: (-1) summarize_stats_CSV.Rd:81: Lost braces; missing escapes or markup? 81 | {stage}\emph{Mean}(patchNum).csv and {stage}\emph{Quantile}(quantNum)_(patchNum).csv. | ^ checkRd: (-1) summarize_stats_CSV.Rd:81: Lost braces; missing escapes or markup? 81 | {stage}\emph{Mean}(patchNum).csv and {stage}\emph{Quantile}(quantNum)_(patchNum).csv. | ^ checkRd: (-1) summarize_stats_CSV_decoupled.Rd:84: Lost braces; missing escapes or markup? 84 | {stage}\emph{Mean}(patchNum).csv and {stage}\emph{Quantile}(quantNum)_(patchNum).csv. | ^ checkRd: (-1) summarize_stats_CSV_decoupled.Rd:84: Lost braces; missing escapes or markup? 84 | {stage}\emph{Mean}(patchNum).csv and {stage}\emph{Quantile}(quantNum)_(patchNum).csv. | ^ * 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 ... [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 ... [1s/1s] OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [67s/78s] ERROR Error(s) in re-building vignettes: --- re-building ‘advanced_topics.Rmd’ using rmarkdown --- finished re-building ‘advanced_topics.Rmd’ --- re-building ‘epi-SEIR.Rmd’ using rmarkdown --- finished re-building ‘epi-SEIR.Rmd’ --- re-building ‘epi-network.Rmd’ using rmarkdown --- finished re-building ‘epi-network.Rmd’ --- re-building ‘epi-node-Imperial-decoupled.Rmd’ using rmarkdown --- finished re-building ‘epi-node-Imperial-decoupled.Rmd’ --- re-building ‘epi-node-SIS-decoupled.Rmd’ using rmarkdown --- finished re-building ‘epi-node-SIS-decoupled.Rmd’ --- re-building ‘epi-node.Rmd’ using rmarkdown --- finished re-building ‘epi-node.Rmd’ --- re-building ‘inhomogeneous.Rmd’ using rmarkdown Quitting from inhomogeneous.Rmd:41-50 [unnamed-chunk-2] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error in `library()`: ! there is no package called 'MGDrivE' --- Backtrace: ▆ 1. └─base::library(MGDrivE) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'inhomogeneous.Rmd' failed with diagnostics: there is no package called 'MGDrivE' --- failed re-building ‘inhomogeneous.Rmd’ --- re-building ‘lifecycle-network.Rmd’ using rmarkdown Quitting from lifecycle-network.Rmd:34-46 [unnamed-chunk-2] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error in `library()`: ! there is no package called 'MGDrivE' --- Backtrace: ▆ 1. └─base::library(MGDrivE) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'lifecycle-network.Rmd' failed with diagnostics: there is no package called 'MGDrivE' --- failed re-building ‘lifecycle-network.Rmd’ --- re-building ‘lifecycle-node.Rmd’ using rmarkdown Quitting from lifecycle-node.Rmd:42-52 [unnamed-chunk-2] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error in `library()`: ! there is no package called 'MGDrivE' --- Backtrace: ▆ 1. └─base::library(MGDrivE) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'lifecycle-node.Rmd' failed with diagnostics: there is no package called 'MGDrivE' --- failed re-building ‘lifecycle-node.Rmd’ SUMMARY: processing the following files failed: ‘inhomogeneous.Rmd’ ‘lifecycle-network.Rmd’ ‘lifecycle-node.Rmd’ Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... [6s/7s] OK * DONE Status: 1 ERROR, 1 NOTE * using check arguments '--no-clean-on-error ' * elapsed time (check, wall clock): 2:10