* using log directory ‘/data/gannet/ripley/R/packages/tests-clang/simtrial.Rcheck’ * using R Under development (unstable) (2024-05-02 r86508) * using platform: x86_64-pc-linux-gnu * R was compiled by clang version 18.1.5 flang-new version 18.1.5 * running under: Fedora Linux 36 (Workstation Edition) * using session charset: UTF-8 * using option ‘--no-stop-on-test-error’ * checking for file ‘simtrial/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘simtrial’ version ‘0.3.2’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... NOTE Package suggested but not available for checking: ‘bshazard’ * 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 ‘simtrial’ can be installed ... [62s/192s] OK See 'https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-fedora-clang/simtrial-00install.html' for details. * used C++ compiler: ‘clang version 18.1.5’ * 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 ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... 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 ... [21s/43s] OK * checking Rd files ... 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 ... OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking pragmas in C/C++ headers and code ... OK * checking compilation flags used ... OK * checking compiled code ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... [26s/49s] OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... [59s/82s] OK Running ‘testthat.R’ [59s/82s] * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [125s/158s] ERROR Error(s) in re-building vignettes: --- re-building ‘arbitrary-hazard.Rmd’ using rmarkdown Quitting from lines at lines 20-26 [unnamed-chunk-2] (arbitrary-hazard.Rmd) Error: processing vignette 'arbitrary-hazard.Rmd' failed with diagnostics: there is no package called 'bshazard' --- failed re-building ‘arbitrary-hazard.Rmd’ --- re-building ‘modest-wlrt.Rmd’ using rmarkdown ** Processing: /data/gannet/ripley/R/packages/tests-clang/simtrial.Rcheck/vign_test/simtrial/vignettes/modest-wlrt_files/figure-html/unnamed-chunk-4-1.png 720x384 pixels, 3x8 bits/pixel, RGB Input IDAT size = 18833 bytes Input file size = 18935 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 14375 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 = 14375 Output IDAT size = 14375 bytes (4458 bytes decrease) Output file size = 14453 bytes (4482 bytes = 23.67% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-clang/simtrial.Rcheck/vign_test/simtrial/vignettes/modest-wlrt_files/figure-html/unnamed-chunk-9-1.png 720x384 pixels, 3x8 bits/pixel, RGB Input IDAT size = 16854 bytes Input file size = 16956 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 12730 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 = 12730 Output IDAT size = 12730 bytes (4124 bytes decrease) Output file size = 12808 bytes (4148 bytes = 24.46% decrease) --- finished re-building ‘modest-wlrt.Rmd’ --- re-building ‘parallel.Rmd’ using rmarkdown ** Processing: /data/gannet/ripley/R/packages/tests-clang/simtrial.Rcheck/vign_test/simtrial/vignettes/parallel_files/figure-html/enrollments-1.png 576x384 pixels, 3x8 bits/pixel, RGB Input IDAT size = 21441 bytes Input file size = 21543 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 17503 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 = 17503 Output IDAT size = 17503 bytes (3938 bytes decrease) Output file size = 17581 bytes (3962 bytes = 18.39% decrease) --- finished re-building ‘parallel.Rmd’ --- re-building ‘pvalue-maxcombo.Rmd’ using rmarkdown --- finished re-building ‘pvalue-maxcombo.Rmd’ --- re-building ‘routines.Rmd’ using rmarkdown ** Processing: /data/gannet/ripley/R/packages/tests-clang/simtrial.Rcheck/vign_test/simtrial/vignettes/routines_files/figure-html/unnamed-chunk-6-1.png 576x288 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 7038 bytes Input file size = 7896 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 6310 zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 6288 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 = 1 f = 0 IDAT size = 6288 Output IDAT size = 6288 bytes (750 bytes decrease) Output file size = 6366 bytes (1530 bytes = 19.38% decrease) --- finished re-building ‘routines.Rmd’ --- re-building ‘workflow.Rmd’ using rmarkdown --- finished re-building ‘workflow.Rmd’ SUMMARY: processing the following file failed: ‘arbitrary-hazard.Rmd’ Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... [11s/12s] 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