• using R version 4.4.0 (2024-04-24)
• using platform: x86_64-apple-darwin20
• R was compiled by     Apple clang version 14.0.0 (clang-1400.0.29.202)     GNU Fortran (GCC) 12.2.0
• running under: macOS Ventura 13.3.1
• 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 ... [9s/13s] OK See the install log 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 ... [14s/14s] OK
• checking Rd files ... [1s/1s] 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 ... [111s/142s] 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 lines 42-50 [unnamed-chunk-2] (inhomogeneous.Rmd) 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 lines 35-46 [unnamed-chunk-2] (lifecycle-network.Rmd) 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 lines 43-52 [unnamed-chunk-2] (lifecycle-node.Rmd) 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 ... [8s/9s] OK
• DONE Status: 1 ERROR, 1 NOTE
• using check arguments '--no-clean-on-error '