• using R Under development (unstable) (2025-06-25 r88360)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     Debian clang version 19.1.7 (3+b1)     Debian flang-new version 19.1.7 (3+b1)
• running under: Debian GNU/Linux 13 (trixie)
• 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 CRAN incoming feasibility ... [1s/2s] OK
• checking package namespace information ... OK
• checking package dependencies ... INFO Package suggested but not available for checking: ‘MGDrivE’
• 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 ‘MGDrivE2’ 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/2s] 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/2s] 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 ... [35s/40s] 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 line widths ... OK
• checking Rd cross-references ... NOTE Unknown package ‘MGDrivE’ in Rd xrefs
• 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/1s] 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 ... [2s/2s] OK
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [26s/34s] ERROR Error(s) in re-building vignettes:   ... --- re-building ‘advanced_topics.Rmd’ using rmarkdown Quitting from advanced_topics.Rmd:88-98 [unnamed-chunk-3] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error in `library()`: ! there is no package called 'MGDrivE' --- Backtrace:     ▆  1. └─base::library(MGDrivE) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'advanced_topics.Rmd' failed with diagnostics: there is no package called 'MGDrivE' --- failed re-building ‘advanced_topics.Rmd’ --- re-building ‘epi-SEIR.Rmd’ using rmarkdown Quitting from epi-SEIR.Rmd:44-56 [unnamed-chunk-2] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error in `library()`: ! there is no package called 'MGDrivE' --- Backtrace:     ▆  1. └─base::library(MGDrivE) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'epi-SEIR.Rmd' failed with diagnostics: there is no package called 'MGDrivE' --- failed re-building ‘epi-SEIR.Rmd’ --- re-building ‘epi-network.Rmd’ using rmarkdown Quitting from epi-network.Rmd:35-47 [unnamed-chunk-2] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error in `library()`: ! there is no package called 'MGDrivE' --- Backtrace:     ▆  1. └─base::library(MGDrivE) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'epi-network.Rmd' failed with diagnostics: there is no package called 'MGDrivE' --- failed re-building ‘epi-network.Rmd’ --- re-building ‘epi-node-Imperial-decoupled.Rmd’ using rmarkdown Quitting from epi-node-Imperial-decoupled.Rmd:35-45 [unnamed-chunk-2] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error in `library()`: ! there is no package called 'MGDrivE' --- Backtrace:     ▆  1. └─base::library(MGDrivE) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'epi-node-Imperial-decoupled.Rmd' failed with diagnostics: there is no package called 'MGDrivE' --- failed re-building ‘epi-node-Imperial-decoupled.Rmd’ --- re-building ‘epi-node-SIS-decoupled.Rmd’ using rmarkdown Quitting from epi-node-SIS-decoupled.Rmd:37-47 [unnamed-chunk-2] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error in `library()`: ! there is no package called 'MGDrivE' --- Backtrace:     ▆  1. └─base::library(MGDrivE) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'epi-node-SIS-decoupled.Rmd' failed with diagnostics: there is no package called 'MGDrivE' --- failed re-building ‘epi-node-SIS-decoupled.Rmd’ --- re-building ‘epi-node.Rmd’ using rmarkdown Quitting from epi-node.Rmd:36-46 [unnamed-chunk-2] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error in `library()`: ! there is no package called 'MGDrivE' --- Backtrace:     ▆  1. └─base::library(MGDrivE) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'epi-node.Rmd' failed with diagnostics: there is no package called 'MGDrivE' --- failed re-building ‘epi-node.Rmd’ --- re-building ‘inhomogeneous.Rmd’ using rmarkdown Quitting from inhomogeneous.Rmd:41-50 [unnamed-chunk-2] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> 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/rlang_error> 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/rlang_error> 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:   ‘advanced_topics.Rmd’ ‘epi-SEIR.Rmd’ ‘epi-network.Rmd’   ‘epi-node-Imperial-decoupled.Rmd’ ‘epi-node-SIS-decoupled.Rmd’   ‘epi-node.Rmd’ ‘inhomogeneous.Rmd’ ‘lifecycle-network.Rmd’   ‘lifecycle-node.Rmd’ Error: Vignette re-building failed. Execution halted
• checking PDF version of manual ... [8s/10s] OK
• checking HTML version of manual ... [5s/7s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 1 ERROR, 2 NOTEs