• using R Under development (unstable) (2025-02-20 r87772)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     gcc-14 (Debian 14.2.0-16) 14.2.0     GNU Fortran (Debian 14.2.0-16) 14.2.0
• running under: Debian GNU/Linux trixie/sid
• using session charset: UTF-8
• 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 ... INFO Package suggested but not available for checking: ‘Rgraphviz’
• 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 ‘zenplots’ can be installed ... OK See the install log for details.
• used C compiler: ‘gcc-14 (Debian 14.2.0-16) 14.2.0’
• 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 ... [1s/1s] OK
• checking whether the package can be loaded with stated dependencies ... [1s/1s] OK
• checking whether the package can be unloaded cleanly ... [1s/1s] OK
• checking whether the namespace can be loaded with stated dependencies ... [1s/2s] OK
• checking whether the namespace can be unloaded cleanly ... [1s/1s] OK
• checking loading without being on the library search path ... [1s/1s] 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 ... [15s/18s] OK
• checking Rd files ... [1s/1s] OK
• checking Rd metadata ... OK
• checking Rd line widths ... OK
• checking Rd cross-references ... NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors:   graph_pairs.Rd: graphNEL Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages.
• 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/0s] 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 ... [2s/2s] ERROR Running examples in ‘zenplots-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### 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 Loading required package: generics Attaching package: ‘generics’ The following objects are masked from ‘package:base’:     as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,     setequal, union 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, is.unsorted, lapply,     mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,     rank, rbind, rownames, sapply, saveRDS, table, tapply, 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 ‘demo’ ... NOTE 'library' or 'require' calls not declared from:   ‘crop’ ‘mvtnorm’
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [8s/8s] OK   Running ‘testthat.R’ [8s/8s]
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [12s/11s] ERROR Error(s) in re-building vignettes:   ... --- re-building ‘intro.Rmd’ using rmarkdown Quitting from 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: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/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: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/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: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/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: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/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: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/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: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/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: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/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: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/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: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/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 = 104172 bytes Input file size = 105174 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 100235   zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 100150   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 = 100150 Output IDAT size = 100150 bytes (4022 bytes decrease) Output file size = 100228 bytes (4946 bytes = 4.70% decrease) ** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/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: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/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 249-252 [unnamed-chunk-28] (selected_features.Rmd) Error: processing vignette 'selected_features.Rmd' failed with diagnostics: there is no package called 'Rgraphviz' --- 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 ... [6s/6s] OK
• checking HTML version of manual ... [3s/3s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 2 ERRORs, 2 NOTEs