• using R Under development (unstable) (2025-02-28 r87848)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     clang version 20.1.0-rc3     flang version 20.1.0-rc3
• running under: Fedora Linux 40 (Workstation Edition)
• using session charset: UTF-8
• using option ‘--no-stop-on-test-error’
• checking for file ‘GUILDS/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘GUILDS’ version ‘1.4.6’
• 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 ‘GUILDS’ can be installed ... [27s/57s] OK See the install log for details.
• used C++ compiler: ‘clang version 20.1.0-rc3’
• 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 ... [12s/31s] 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 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 ... [8s/30s] ERROR Running examples in ‘GUILDS-Ex.R’ failed The error most likely occurred in: > ### Name: maxLikelihood.Guilds.Conditional > ### Title: Maximization of the loglikelihood under the Guilds Model, > ### conditioned on guild size. > ### Aliases: maxLikelihood.Guilds.Conditional > > ### ** Examples > > theta = 20 > alpha = 0.1 > initParams <- c(theta, alpha) > maxLikelihood.Guilds.Conditional(initParams, + model = "D0", + sadx = 1:20, + sady = 1:20, + verbose = TRUE) Error in if (fnew <= fmin) { : missing value where TRUE/FALSE needed Calls: maxLikelihood.Guilds.Conditional ... eval_f -> conditional.LogLik -> logLikguilds -> <Anonymous> Execution halted
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [23s/81s] OK   Running ‘testthat.R’ [23s/80s]
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [30m/39m] ERROR Error(s) in re-building vignettes: --- re-building ‘GUILDS.Rmd’ using rmarkdown ** Processing: /data/gannet/ripley/R/packages/tests-clang/GUILDS.Rcheck/vign_test/GUILDS/vignettes/GUILDS_files/figure-html/unnamed-chunk-1-1.png 576x288 pixels, 8 bits/pixel, 246 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 2947 bytes Input file size = 3775 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 2454   zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 2452   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 = 2452 Output IDAT size = 2452 bytes (495 bytes decrease) Output file size = 2530 bytes (1245 bytes = 32.98% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-clang/GUILDS.Rcheck/vign_test/GUILDS/vignettes/GUILDS_files/figure-html/unnamed-chunk-2-1.png 576x288 pixels, 8 bits/pixel, 255 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 4642 bytes Input file size = 5497 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 3998   zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 3970   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 = 3970 Output IDAT size = 3970 bytes (672 bytes decrease) Output file size = 4048 bytes (1449 bytes = 26.36% decrease)
• 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: 2 ERRORs