* using log directory ‘/data/gannet/ripley/R/packages/tests-Suggests/pagoo.Rcheck’ * using R Under development (unstable) (2024-04-19 r86451) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc-13 (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Fedora Linux 36 (Workstation Edition) * using session charset: UTF-8 * using option ‘--no-stop-on-test-error’ * checking for file ‘pagoo/DESCRIPTION’ ... OK * this is package ‘pagoo’ version ‘0.3.17’ * 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 ‘pagoo’ can be installed ... [46s/60s] 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 ... [12s/14s] OK * checking whether the package can be loaded with stated dependencies ... [13s/17s] OK * checking whether the package can be unloaded cleanly ... [12s/16s] OK * checking whether the namespace can be loaded with stated dependencies ... [11s/13s] OK * checking whether the namespace can be unloaded cleanly ... [12s/15s] OK * checking loading without being on the library search path ... [12s/15s] 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 ... [51s/69s] OK * checking Rd files ... NOTE checkRd: (-1) pagoo.Rd:107-110: Lost braces in \itemize; meant \describe ? checkRd: (-1) pagoo.Rd:112-115: Lost braces in \itemize; meant \describe ? checkRd: (-1) pagoo.Rd:117-119: Lost braces in \itemize; meant \describe ? checkRd: (-1) pagoo.Rd:121-125: Lost braces in \itemize; meant \describe ? checkRd: (-1) pagoo.Rd:127-129: Lost braces in \itemize; meant \describe ? checkRd: (-1) pagoo.Rd:131-133: Lost braces in \itemize; meant \describe ? checkRd: (-1) pagoo.Rd:135: Lost braces in \itemize; meant \describe ? checkRd: (-1) pagoo.Rd:137-138: Lost braces in \itemize; meant \describe ? checkRd: (-1) pagoo.Rd:140-141: Lost braces in \itemize; meant \describe ? checkRd: (-1) pagoo.Rd:143-146: Lost braces in \itemize; meant \describe ? checkRd: (-1) pagoo.Rd:148-149: Lost braces in \itemize; meant \describe ? checkRd: (-1) pagoo.Rd:151-152: Lost braces in \itemize; meant \describe ? checkRd: (-1) pagoo.Rd:154-157: Lost braces in \itemize; meant \describe ? checkRd: (-1) pagoo.Rd:159-160: Lost braces in \itemize; meant \describe ? checkRd: (-1) pagoo.Rd:162-163: Lost braces in \itemize; meant \describe ? checkRd: (-1) pagoo.Rd:165-167: Lost braces in \itemize; meant \describe ? checkRd: (-1) pagoo.Rd:169-170: Lost braces in \itemize; meant \describe ? checkRd: (-1) pagoo.Rd:172-173: Lost braces in \itemize; meant \describe ? * 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 installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... [13s/17s] OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ [55s/72s] [55s/72s] OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [102s/136s] ERROR Error(s) in re-building vignettes: --- re-building ‘Input.Rmd’ using rmarkdown --- finished re-building ‘Input.Rmd’ --- re-building ‘Methods_Plots.Rmd’ using rmarkdown Quitting from lines at lines 75-77 [unnamed-chunk-5] (Methods_Plots.Rmd) Error: processing vignette 'Methods_Plots.Rmd' failed with diagnostics: there is no package called 'patchwork' --- failed re-building ‘Methods_Plots.Rmd’ --- re-building ‘Querying_Data.Rmd’ using rmarkdown --- finished re-building ‘Querying_Data.Rmd’ --- re-building ‘Recipes.Rmd’ using rmarkdown Quitting from lines at lines 29-75 [unnamed-chunk-2] (Recipes.Rmd) Error: processing vignette 'Recipes.Rmd' failed with diagnostics: there is no package called 'patchwork' --- failed re-building ‘Recipes.Rmd’ --- re-building ‘Subseting.Rmd’ using rmarkdown --- finished re-building ‘Subseting.Rmd’ --- re-building ‘pagoo.Rmd’ using rmarkdown ** Processing: /data/gannet/ripley/R/packages/tests-Suggests/pagoo.Rcheck/vign_test/pagoo/vignettes/pagoo_files/figure-html/unnamed-chunk-6-1.png 288x288 pixels, 8 bits/pixel, 241 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 3350 bytes Input file size = 4163 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 2957 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 2957 Output IDAT size = 2957 bytes (393 bytes decrease) Output file size = 3035 bytes (1128 bytes = 27.10% decrease) --- finished re-building ‘pagoo.Rmd’ SUMMARY: processing the following files failed: ‘Methods_Plots.Rmd’ ‘Recipes.Rmd’ Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... OK * checking HTML version of manual ... OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 1 ERROR, 1 NOTE See ‘/data/gannet/ripley/R/packages/tests-Suggests/pagoo.Rcheck/00check.log’ for details. Command exited with non-zero status 1 Time 11:03.78, 450.13 + 45.35