* using log directory ‘/data/gannet/ripley/R/packages/tests-Suggests/zenplots.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 ‘zenplots/DESCRIPTION’ ... OK * this is package ‘zenplots’ version ‘1.0.6’ * 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 ‘zenplots’ can be installed ... [19s/22s] OK * used C compiler: ‘gcc-13 (GCC) 13.2.0’ * 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 ... [23s/23s] 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 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 ... ERROR Running examples in ‘zenplots-Ex.R’ failed The error most likely occurred in: > ### Name: graph_pairs > ### Title: Turn pairs or paths into a graph > ### Aliases: graph_pairs > > ### ** Examples > > ## To display the graphs constructed the packages > ## graph and Rgraphviz packages need to be loaded > library(graph) Loading required package: BiocGenerics Attaching package: ‘BiocGenerics’ The following objects are masked from ‘package:stats’: IQR, mad, sd, var, xtabs The following objects are masked from ‘package:base’: Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply, union, unique, unsplit, which.max, which.min > library(Rgraphviz) Error in library(Rgraphviz) : there is no package called ‘Rgraphviz’ Execution halted * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ [12s/12s] [13s/13s] OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [12s/12s] ERROR Error(s) in re-building vignettes: --- re-building ‘intro.Rmd’ using rmarkdown Quitting from lines at lines 98-102 [unnamed-chunk-7] (intro.Rmd) Error: processing vignette 'intro.Rmd' failed with diagnostics: there is no package called 'Rgraphviz' --- failed re-building ‘intro.Rmd’ --- re-building ‘selected_features.Rmd’ using rmarkdown ** Processing: /data/gannet/ripley/R/packages/tests-Suggests/zenplots.Rcheck/vign_test/zenplots/vignettes/selected_features_files/figure-html/unnamed-chunk-2-1.png 576x768 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 43726 bytes Input file size = 44644 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 41670 zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 41365 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 IDAT size = 41008 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 = 3 f = 0 IDAT size = 41008 Output IDAT size = 41008 bytes (2718 bytes decrease) Output file size = 41086 bytes (3558 bytes = 7.97% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-Suggests/zenplots.Rcheck/vign_test/zenplots/vignettes/selected_features_files/figure-html/unnamed-chunk-3-1.png 576x768 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 10399 bytes Input file size = 11269 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 9094 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 = 9094 Output IDAT size = 9094 bytes (1305 bytes decrease) Output file size = 9172 bytes (2097 bytes = 18.61% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-Suggests/zenplots.Rcheck/vign_test/zenplots/vignettes/selected_features_files/figure-html/unnamed-chunk-7-1.png 768x1276 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 20322 bytes Input file size = 21204 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 18364 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 = 18364 Output IDAT size = 18364 bytes (1958 bytes decrease) Output file size = 18442 bytes (2762 bytes = 13.03% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-Suggests/zenplots.Rcheck/vign_test/zenplots/vignettes/selected_features_files/figure-html/unnamed-chunk-8-1.png 768x768 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 17673 bytes Input file size = 18555 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 15985 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 = 15985 Output IDAT size = 15985 bytes (1688 bytes decrease) Output file size = 16063 bytes (2492 bytes = 13.43% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-Suggests/zenplots.Rcheck/vign_test/zenplots/vignettes/selected_features_files/figure-html/unnamed-chunk-9-1.png 768x633 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 17300 bytes Input file size = 18182 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 15548 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 = 15548 Output IDAT size = 15548 bytes (1752 bytes decrease) Output file size = 15626 bytes (2556 bytes = 14.06% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-Suggests/zenplots.Rcheck/vign_test/zenplots/vignettes/selected_features_files/figure-html/unnamed-chunk-10-1.png 768x518 pixels, 8 bits/pixel, 255 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 12859 bytes Input file size = 13726 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 11635 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 = 11635 Output IDAT size = 11635 bytes (1224 bytes decrease) Output file size = 11713 bytes (2013 bytes = 14.67% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-Suggests/zenplots.Rcheck/vign_test/zenplots/vignettes/selected_features_files/figure-html/unnamed-chunk-11-1.png 576x960 pixels, 8 bits/pixel, 253 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 10034 bytes Input file size = 10895 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 8677 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 = 8677 Output IDAT size = 8677 bytes (1357 bytes decrease) Output file size = 8755 bytes (2140 bytes = 19.64% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-Suggests/zenplots.Rcheck/vign_test/zenplots/vignettes/selected_features_files/figure-html/unnamed-chunk-12-1.png 576x672 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 9332 bytes Input file size = 10202 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7750 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 = 7750 Output IDAT size = 7750 bytes (1582 bytes decrease) Output file size = 7828 bytes (2374 bytes = 23.27% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-Suggests/zenplots.Rcheck/vign_test/zenplots/vignettes/selected_features_files/figure-html/unnamed-chunk-20-1.png 576x864 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 104190 bytes Input file size = 105192 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 100252 zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 100164 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 = 100164 Output IDAT size = 100164 bytes (4026 bytes decrease) Output file size = 100242 bytes (4950 bytes = 4.71% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-Suggests/zenplots.Rcheck/vign_test/zenplots/vignettes/selected_features_files/figure-html/unnamed-chunk-23-1.png 576x768 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 66445 bytes Input file size = 67399 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 63860 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 = 63860 Output IDAT size = 63860 bytes (2585 bytes decrease) Output file size = 63938 bytes (3461 bytes = 5.14% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-Suggests/zenplots.Rcheck/vign_test/zenplots/vignettes/selected_features_files/figure-html/unnamed-chunk-24-1.png 576x768 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 29362 bytes Input file size = 30256 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 27518 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 = 27518 Output IDAT size = 27518 bytes (1844 bytes decrease) Output file size = 27596 bytes (2660 bytes = 8.79% decrease) Quitting from lines at lines 226-234 [unnamed-chunk-25] (selected_features.Rmd) Error: processing vignette 'selected_features.Rmd' failed with diagnostics: there is no package called 'scagnostics' --- failed re-building ‘selected_features.Rmd’ SUMMARY: processing the following files failed: ‘intro.Rmd’ ‘selected_features.Rmd’ Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... [10s/10s] 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 See ‘/data/gannet/ripley/R/packages/tests-Suggests/zenplots.Rcheck/00check.log’ for details. Command exited with non-zero status 1 Time 2:21.94, 118.63 + 16.20