• 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 ‘RSDA/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘RSDA’ version ‘3.2.1’
• package encoding: UTF-8
• checking package namespace information ... OK
• checking package dependencies ... INFO Imports includes 31 non-default packages. Importing from so many packages makes the package vulnerable to any of them becoming unavailable. Move as many as possible to Suggests and use conditionally.
• 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 ‘RSDA’ can be installed ... [38s/55s] OK See the install log for details.
• checking installed package size ... INFO   installed size is 5.2Mb   sub-directories of 1Mb or more:     doc 4.2Mb
• 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 ... [7s/10s] OK
• checking whether startup messages can be suppressed ... 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 ... [66s/89s] 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 installed files from ‘inst/doc’ ... OK
• checking files in ‘vignettes’ ... OK
• checking examples ... [26s/36s] OK
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [9s/11s] OK   Running ‘testthat.R’ [8s/11s]
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [31m/40m] ERROR Error(s) in re-building vignettes: --- re-building ‘introduction.Rmd’ using rmarkdown ** Processing: /data/gannet/ripley/R/packages/tests-clang/RSDA.Rcheck/vign_test/RSDA/vignettes/introduction_files/figure-html/unnamed-chunk-28-1.png 576x480 pixels, 3x8 bits/pixel, RGB Input IDAT size = 36617 bytes Input file size = 36743 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 26166   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 = 26166 Output IDAT size = 26166 bytes (10451 bytes decrease) Output file size = 26244 bytes (10499 bytes = 28.57% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-clang/RSDA.Rcheck/vign_test/RSDA/vignettes/introduction_files/figure-html/unnamed-chunk-28-2.png 576x480 pixels, 3x8 bits/pixel, RGB Input IDAT size = 38887 bytes Input file size = 39013 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 27823   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 = 27823 Output IDAT size = 27823 bytes (11064 bytes decrease) Output file size = 27901 bytes (11112 bytes = 28.48% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-clang/RSDA.Rcheck/vign_test/RSDA/vignettes/introduction_files/figure-html/unnamed-chunk-28-3.png 576x480 pixels, 3x8 bits/pixel, RGB Input IDAT size = 8914 bytes Input file size = 9004 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 8136   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 IDAT size = 7598   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 = 5 IDAT size = 7598 Output IDAT size = 7598 bytes (1316 bytes decrease) Output file size = 7676 bytes (1328 bytes = 14.75% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-clang/RSDA.Rcheck/vign_test/RSDA/vignettes/introduction_files/figure-html/unnamed-chunk-28-4.png 576x480 pixels, 3x8 bits/pixel, RGB Input IDAT size = 11328 bytes Input file size = 11418 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 9791   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 IDAT size = 9777   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 = 5 IDAT size = 9777 Output IDAT size = 9777 bytes (1551 bytes decrease) Output file size = 9855 bytes (1563 bytes = 13.69% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-clang/RSDA.Rcheck/vign_test/RSDA/vignettes/introduction_files/figure-html/unnamed-chunk-29-1.png 576x480 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 7076 bytes Input file size = 7934 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 6165   zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 6165   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 = 6165 Output IDAT size = 6165 bytes (911 bytes decrease) Output file size = 6243 bytes (1691 bytes = 21.31% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-clang/RSDA.Rcheck/vign_test/RSDA/vignettes/introduction_files/figure-html/unnamed-chunk-30-1.png 576x480 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 7750 bytes Input file size = 8608 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 6714   zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 6699   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 = 6699 Output IDAT size = 6699 bytes (1051 bytes decrease) Output file size = 6777 bytes (1831 bytes = 21.27% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-clang/RSDA.Rcheck/vign_test/RSDA/vignettes/introduction_files/figure-html/unnamed-chunk-31-1.png 576x480 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 7391 bytes Input file size = 8249 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 6110   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 = 6110 Output IDAT size = 6110 bytes (1281 bytes decrease) Output file size = 6188 bytes (2061 bytes = 24.98% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-clang/RSDA.Rcheck/vign_test/RSDA/vignettes/introduction_files/figure-html/unnamed-chunk-38-1.png 576x480 pixels, 3x8 bits/pixel, RGB Input IDAT size = 29484 bytes Input file size = 29598 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 21370   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 = 21370 Output IDAT size = 21370 bytes (8114 bytes decrease) Output file size = 21448 bytes (8150 bytes = 27.54% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-clang/RSDA.Rcheck/vign_test/RSDA/vignettes/introduction_files/figure-html/unnamed-chunk-38-2.png 576x480 pixels, 3x8 bits/pixel, RGB Input IDAT size = 31562 bytes Input file size = 31676 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 24683   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 = 24683 Output IDAT size = 24683 bytes (6879 bytes decrease) Output file size = 24761 bytes (6915 bytes = 21.83% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-clang/RSDA.Rcheck/vign_test/RSDA/vignettes/introduction_files/figure-html/unnamed-chunk-42-1.png 576x480 pixels, 3x8 bits/pixel, RGB Input IDAT size = 31444 bytes Input file size = 31558 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 22932   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 = 22932 Output IDAT size = 22932 bytes (8512 bytes decrease) Output file size = 23010 bytes (8548 bytes = 27.09% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-clang/RSDA.Rcheck/vign_test/RSDA/vignettes/introduction_files/figure-html/unnamed-chunk-42-2.png 576x480 pixels, 3x8 bits/pixel, RGB Input IDAT size = 32103 bytes Input file size = 32217 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 25854   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 = 25854 Output IDAT size = 25854 bytes (6249 bytes decrease) Output file size = 25932 bytes (6285 bytes = 19.51% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-clang/RSDA.Rcheck/vign_test/RSDA/vignettes/introduction_files/figure-html/unnamed-chunk-43-1.png 576x480 pixels, 3x8 bits/pixel, RGB Input IDAT size = 10465 bytes Input file size = 10555 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 8652   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 = 8652 Output IDAT size = 8652 bytes (1813 bytes decrease) Output file size = 8730 bytes (1825 bytes = 17.29% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-clang/RSDA.Rcheck/vign_test/RSDA/vignettes/introduction_files/figure-html/unnamed-chunk-43-2.png 576x480 pixels, 3x8 bits/pixel, RGB Input IDAT size = 27297 bytes Input file size = 27411 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 21070   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 = 21070 Output IDAT size = 21070 bytes (6227 bytes decrease) Output file size = 21148 bytes (6263 bytes = 22.85% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-clang/RSDA.Rcheck/vign_test/RSDA/vignettes/introduction_files/figure-html/unnamed-chunk-44-1.png 576x480 pixels, 3x8 bits/pixel, RGB Input IDAT size = 11365 bytes Input file size = 11455 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 9410   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 = 9410 Output IDAT size = 9410 bytes (1955 bytes decrease) Output file size = 9488 bytes (1967 bytes = 17.17% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-clang/RSDA.Rcheck/vign_test/RSDA/vignettes/introduction_files/figure-html/unnamed-chunk-45-1.png 576x480 pixels, 3x8 bits/pixel, RGB Input IDAT size = 15761 bytes Input file size = 15851 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 12690   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 = 12690 Output IDAT size = 12690 bytes (3071 bytes decrease) Output file size = 12768 bytes (3083 bytes = 19.45% decrease)
• checking PDF version of manual ... [13s/17s] OK
• checking HTML version of manual ... [7s/13s] OK
• checking for non-standard things in the check directory ... OK
• checking for detritus in the temp directory ... OK
• DONE

Status: 1 ERROR