* using log directory ‘/srv/hornik/tmp/CRAN_pretest/evolved.Rcheck’ * using R Under development (unstable) (2024-11-15 r87338) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 19.1.1 (1) Debian flang-new version 19.1.1 (1) * running under: Debian GNU/Linux trixie/sid * using session charset: UTF-8 * checking for file ‘evolved/DESCRIPTION’ ... OK * this is package ‘evolved’ version ‘1.0.0’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [4s/8s] NOTE Maintainer: ‘Matheus Januario ’ New submission Possibly misspelled words in DESCRIPTION: EvoLutionary (12:15) The Title field starts with the package name. Size of tarball: 7071631 bytes * 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 serialization versions ... OK * checking whether package ‘evolved’ can be installed ... [3s/3s] OK * 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 ... [0s/0s] OK * checking whether the package can be loaded with stated dependencies ... [0s/0s] OK * checking whether the package can be unloaded cleanly ... [0s/0s] OK * checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK * checking whether the namespace can be unloaded cleanly ... [0s/0s] OK * checking loading without being on the library search path ... [0s/0s] 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 ... [3s/3s] OK * checking Rd files ... [0s/0s] 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 ... [1s/1s] 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 ... [4s/11s] NOTE Examples with CPU (user + system) or elapsed time > 5s user system elapsed WFDriftSim 0.042 0 7.554 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... [1s/1s] OK Running ‘testthat.R’ [1s/1s] * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [178s/181s] ERROR Error(s) in re-building vignettes: ... --- re-building ‘birthdeath_deeptime.Rmd’ using rmarkdown ** Processing: /srv/hornik/tmp/CRAN_pretest/evolved.Rcheck/vign_test/evolved/vignettes/birthdeath_deeptime_files/figure-html/unnamed-chunk-7-1.png 288x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 16457 bytes Input file size = 16559 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 12456 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 = 12456 Output IDAT size = 12456 bytes (4001 bytes decrease) Output file size = 12534 bytes (4025 bytes = 24.31% decrease) ** Processing: /srv/hornik/tmp/CRAN_pretest/evolved.Rcheck/vign_test/evolved/vignettes/birthdeath_deeptime_files/figure-html/unnamed-chunk-8-1.png 288x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 17055 bytes Input file size = 17157 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 13490 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 = 13490 Output IDAT size = 13490 bytes (3565 bytes decrease) Output file size = 13568 bytes (3589 bytes = 20.92% decrease) ** Processing: /srv/hornik/tmp/CRAN_pretest/evolved.Rcheck/vign_test/evolved/vignettes/birthdeath_deeptime_files/figure-html/unnamed-chunk-9-1.png 288x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 13808 bytes Input file size = 13898 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 10886 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 = 10886 Output IDAT size = 10886 bytes (2922 bytes decrease) Output file size = 10964 bytes (2934 bytes = 21.11% decrease) ** Processing: /srv/hornik/tmp/CRAN_pretest/evolved.Rcheck/vign_test/evolved/vignettes/birthdeath_deeptime_files/figure-html/unnamed-chunk-10-1.png 288x288 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 5055 bytes Input file size = 5913 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 4631 zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 4612 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 = 4612 Output IDAT size = 4612 bytes (443 bytes decrease) Output file size = 4690 bytes (1223 bytes = 20.68% decrease) --- finished re-building ‘birthdeath_deeptime.Rmd’ --- re-building ‘birthdeath_phylogenies.Rmd’ using rmarkdown ** Processing: /srv/hornik/tmp/CRAN_pretest/evolved.Rcheck/vign_test/evolved/vignettes/birthdeath_phylogenies_files/figure-html/unnamed-chunk-4-1.png 288x288 pixels, 8 bits/pixel, 219 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 1749 bytes Input file size = 2496 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 1438 zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 1431 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 = 1431 Output IDAT size = 1431 bytes (318 bytes decrease) Output file size = 1509 bytes (987 bytes = 39.54% decrease) ** Processing: /srv/hornik/tmp/CRAN_pretest/evolved.Rcheck/vign_test/evolved/vignettes/birthdeath_phylogenies_files/figure-html/unnamed-chunk-6-1.png 288x288 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 6962 bytes Input file size = 7820 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 6242 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 = 6242 Output IDAT size = 6242 bytes (720 bytes decrease) Output file size = 6320 bytes (1500 bytes = 19.18% decrease) ** Processing: /srv/hornik/tmp/CRAN_pretest/evolved.Rcheck/vign_test/evolved/vignettes/birthdeath_phylogenies_files/figure-html/unnamed-chunk-7-1.png 288x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 10006 bytes Input file size = 10096 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 8084 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 = 8084 Output IDAT size = 8084 bytes (1922 bytes decrease) Output file size = 8162 bytes (1934 bytes = 19.16% decrease) ** Processing: /srv/hornik/tmp/CRAN_pretest/evolved.Rcheck/vign_test/evolved/vignettes/birthdeath_phylogenies_files/figure-html/unnamed-chunk-7-2.png 288x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 10653 bytes Input file size = 10743 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 8368 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 = 8368 Output IDAT size = 8368 bytes (2285 bytes decrease) Output file size = 8446 bytes (2297 bytes = 21.38% decrease) ** Processing: /srv/hornik/tmp/CRAN_pretest/evolved.Rcheck/vign_test/evolved/vignettes/birthdeath_phylogenies_files/figure-html/unnamed-chunk-7-3.png 288x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 12562 bytes Input file size = 12652 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 10166 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 = 10166 Output IDAT size = 10166 bytes (2396 bytes decrease) Output file size = 10244 bytes (2408 bytes = 19.03% decrease) ** Processing: /srv/hornik/tmp/CRAN_pretest/evolved.Rcheck/vign_test/evolved/vignettes/birthdeath_phylogenies_files/figure-html/unnamed-chunk-10-1.png 288x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 22680 bytes Input file size = 22782 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 18379 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 = 18379 Output IDAT size = 18379 bytes (4301 bytes decrease) Output file size = 18457 bytes (4325 bytes = 18.98% decrease) ** Processing: /srv/hornik/tmp/CRAN_pretest/evolved.Rcheck/vign_test/evolved/vignettes/birthdeath_phylogenies_files/figure-html/unnamed-chunk-12-1.png 288x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 25143 bytes Input file size = 25257 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 20321 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 = 20321 Output IDAT size = 20321 bytes (4822 bytes decrease) Output file size = 20399 bytes (4858 bytes = 19.23% decrease) Quitting from lines 289-317 [unnamed-chunk-14] (birthdeath_phylogenies.Rmd) Error: processing vignette 'birthdeath_phylogenies.Rmd' failed with diagnostics: Too many trees going extinct --- failed re-building ‘birthdeath_phylogenies.Rmd’ --- re-building ‘deeptime_clocks.Rmd’ using rmarkdown ** Processing: /srv/hornik/tmp/CRAN_pretest/evolved.Rcheck/vign_test/evolved/vignettes/deeptime_clocks_files/figure-html/unnamed-chunk-15-1.png 288x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 21191 bytes Input file size = 21293 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 15586 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 = 15586 Output IDAT size = 15586 bytes (5605 bytes decrease) Output file size = 15664 bytes (5629 bytes = 26.44% decrease) --- finished re-building ‘deeptime_clocks.Rmd’ --- re-building ‘deeptime_rocks.Rmd’ using rmarkdown ** Processing: /srv/hornik/tmp/CRAN_pretest/evolved.Rcheck/vign_test/evolved/vignettes/deeptime_rocks_files/figure-html/unnamed-chunk-10-1.png 288x288 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 5233 bytes Input file size = 6091 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 4759 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 = 4759 Output IDAT size = 4759 bytes (474 bytes decrease) Output file size = 4837 bytes (1254 bytes = 20.59% decrease) ** Processing: /srv/hornik/tmp/CRAN_pretest/evolved.Rcheck/vign_test/evolved/vignettes/deeptime_rocks_files/figure-html/unnamed-chunk-11-1.png 288x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 12259 bytes Input file size = 12349 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 9210 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 = 9210 Output IDAT size = 9210 bytes (3049 bytes decrease) Output file size = 9288 bytes (3061 bytes = 24.79% decrease) ** Processing: /srv/hornik/tmp/CRAN_pretest/evolved.Rcheck/vign_test/evolved/vignettes/deeptime_rocks_files/figure-html/unnamed-chunk-12-1.png 288x288 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 6080 bytes Input file size = 6938 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 5623 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 = 5623 Output IDAT size = 5623 bytes (457 bytes decrease) Output file size = 5701 bytes (1237 bytes = 17.83% decrease) ** Processing: /srv/hornik/tmp/CRAN_pretest/evolved.Rcheck/vign_test/evolved/vignettes/deeptime_rocks_files/figure-html/unnamed-chunk-13-1.png 288x288 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 6127 bytes Input file size = 6985 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 5687 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 = 5687 Output IDAT size = 5687 bytes (440 bytes decrease) Output file size = 5765 bytes (1220 bytes = 17.47% decrease) ** Processing: /srv/hornik/tmp/CRAN_pretest/evolved.Rcheck/vign_test/evolved/vignettes/deeptime_rocks_files/figure-html/unnamed-chunk-14-1.png 288x288 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 5584 bytes Input file size = 6442 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 5118 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 = 5118 Output IDAT size = 5118 bytes (466 bytes decrease) Output file size = 5196 bytes (1246 bytes = 19.34% decrease) ** Processing: /srv/hornik/tmp/CRAN_pretest/evolved.Rcheck/vign_test/evolved/vignettes/deeptime_rocks_files/figure-html/unnamed-chunk-15-1.png 288x288 pixels, 8 bits/pixel, 255 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 5315 bytes Input file size = 6170 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 4891 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 = 4891 Output IDAT size = 4891 bytes (424 bytes decrease) Output file size = 4969 bytes (1201 bytes = 19.47% decrease) ** Processing: /srv/hornik/tmp/CRAN_pretest/evolved.Rcheck/vign_test/evolved/vignettes/deeptime_rocks_files/figure-html/unnamed-chunk-17-1.png 288x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 12407 bytes Input file size = 12497 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 10420 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 = 10420 Output IDAT size = 10420 bytes (1987 bytes decrease) Output file size = 10498 bytes (1999 bytes = 16.00% decrease) ** Processing: /srv/hornik/tmp/CRAN_pretest/evolved.Rcheck/vign_test/evolved/vignettes/deeptime_rocks_files/figure-html/unnamed-chunk-18-1.png 288x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 14185 bytes Input file size = 14275 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 12242 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 = 12242 Output IDAT size = 12242 bytes (1943 bytes decrease) Output file size = 12320 bytes (1955 bytes = 13.70% decrease) ** Processing: /srv/hornik/tmp/CRAN_pretest/evolved.Rcheck/vign_test/evolved/vignettes/deeptime_rocks_files/figure-html/unnamed-chunk-19-1.png 288x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 14838 bytes Input file size = 14928 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 13091 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 = 13091 Output IDAT size = 13091 bytes (1747 bytes decrease) Output file size = 13169 bytes (1759 bytes = 11.78% decrease) ** Processing: /srv/hornik/tmp/CRAN_pretest/evolved.Rcheck/vign_test/evolved/vignettes/deeptime_rocks_files/figure-html/unnamed-chunk-20-1.png 288x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 17080 bytes Input file size = 17182 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 12620 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 = 12620 Output IDAT size = 12620 bytes (4460 bytes decrease) Output file size = 12698 bytes (4484 bytes = 26.10% decrease) ** Processing: /srv/hornik/tmp/CRAN_pretest/evolved.Rcheck/vign_test/evolved/vignettes/deeptime_rocks_files/figure-html/unnamed-chunk-21-1.png 960x672 pixels, 3x8 bits/pixel, RGB Input IDAT size = 85738 bytes Input file size = 85936 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 71968 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 = 71968 Output IDAT size = 71968 bytes (13770 bytes decrease) Output file size = 72046 bytes (13890 bytes = 16.16% decrease) --- finished re-building ‘deeptime_rocks.Rmd’ --- re-building ‘intro_R.Rmd’ using rmarkdown ** Processing: /srv/hornik/tmp/CRAN_pretest/evolved.Rcheck/vign_test/evolved/vignettes/intro_R_files/figure-html/unnamed-chunk-43-1.png 288x288 pixels, 8 bits/pixel, 255 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 4908 bytes Input file size = 5763 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 4476 zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 4461 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 = 4461 Output IDAT size = 4461 bytes (447 bytes decrease) Output file size = 4539 bytes (1224 bytes = 21.24% decrease) ** Processing: /srv/hornik/tmp/CRAN_pretest/evolved.Rcheck/vign_test/evolved/vignettes/intro_R_files/figure-html/unnamed-chunk-44-1.png 288x288 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 9678 bytes Input file size = 10548 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 9081 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 = 9081 Output IDAT size = 9081 bytes (597 bytes decrease) Output file size = 9159 bytes (1389 bytes = 13.17% decrease) ** Processing: /srv/hornik/tmp/CRAN_pretest/evolved.Rcheck/vign_test/evolved/vignettes/intro_R_files/figure-html/unnamed-chunk-45-1.png 288x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 27224 bytes Input file size = 27338 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 21688 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 = 21688 Output IDAT size = 21688 bytes (5536 bytes decrease) Output file size = 21766 bytes (5572 bytes = 20.38% decrease) ** Processing: /srv/hornik/tmp/CRAN_pretest/evolved.Rcheck/vign_test/evolved/vignettes/intro_R_files/figure-html/unnamed-chunk-46-1.png 288x288 pixels, 8 bits/pixel, 246 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 3026 bytes Input file size = 3854 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 2535 zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 2530 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 = 2530 Output IDAT size = 2530 bytes (496 bytes decrease) Output file size = 2608 bytes (1246 bytes = 32.33% decrease) ** Processing: /srv/hornik/tmp/CRAN_pretest/evolved.Rcheck/vign_test/evolved/vignettes/intro_R_files/figure-html/unnamed-chunk-47-1.png 288x288 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 5590 bytes Input file size = 6448 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 5039 zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 5010 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 = 5010 Output IDAT size = 5010 bytes (580 bytes decrease) Output file size = 5088 bytes (1360 bytes = 21.09% decrease) ** Processing: /srv/hornik/tmp/CRAN_pretest/evolved.Rcheck/vign_test/evolved/vignettes/intro_R_files/figure-html/unnamed-chunk-48-1.png 288x288 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 9184 bytes Input file size = 10054 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 8680 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 = 8680 Output IDAT size = 8680 bytes (504 bytes decrease) Output file size = 8758 bytes (1296 bytes = 12.89% decrease) ** Processing: /srv/hornik/tmp/CRAN_pretest/evolved.Rcheck/vign_test/evolved/vignettes/intro_R_files/figure-html/unnamed-chunk-49-1.png 288x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 20021 bytes Input file size = 20123 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 14085 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 = 14085 Output IDAT size = 14085 bytes (5936 bytes decrease) Output file size = 14163 bytes (5960 bytes = 29.62% decrease) --- finished re-building ‘intro_R.Rmd’ --- re-building ‘phylogenies_and_diversification.Rmd’ using rmarkdown ** Processing: /srv/hornik/tmp/CRAN_pretest/evolved.Rcheck/vign_test/evolved/vignettes/phylogenies_and_diversification_files/figure-html/unnamed-chunk-6-1.png 576x1152 pixels, 3x8 bits/pixel, RGB Input IDAT size = 114574 bytes Input file size = 114808 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 90021 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 = 90021 Output IDAT size = 90021 bytes (24553 bytes decrease) Output file size = 90099 bytes (24709 bytes = 21.52% decrease) ** Processing: /srv/hornik/tmp/CRAN_pretest/evolved.Rcheck/vign_test/evolved/vignettes/phylogenies_and_diversification_files/figure-html/unnamed-chunk-7-1.png 576x480 pixels, 3x8 bits/pixel, RGB Input IDAT size = 16927 bytes Input file size = 17029 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 13983 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 = 13983 Output IDAT size = 13983 bytes (2944 bytes decrease) Output file size = 14061 bytes (2968 bytes = 17.43% decrease) ** Processing: /srv/hornik/tmp/CRAN_pretest/evolved.Rcheck/vign_test/evolved/vignettes/phylogenies_and_diversification_files/figure-html/unnamed-chunk-9-1.png 576x480 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 6968 bytes Input file size = 7826 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 6217 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 = 6217 Output IDAT size = 6217 bytes (751 bytes decrease) Output file size = 6295 bytes (1531 bytes = 19.56% decrease) ** Processing: /srv/hornik/tmp/CRAN_pretest/evolved.Rcheck/vign_test/evolved/vignettes/phylogenies_and_diversification_files/figure-html/unnamed-chunk-10-1.png 576x480 pixels, 3x8 bits/pixel, RGB Input IDAT size = 35665 bytes Input file size = 35791 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 33164 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 = 32586 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 = 32586 Output IDAT size = 32586 bytes (3079 bytes decrease) Output file size = 32664 bytes (3127 bytes = 8.74% decrease) --- finished re-building ‘phylogenies_and_diversification.Rmd’ --- re-building ‘popgen_drift.Rmd’ using rmarkdown ** Processing: /srv/hornik/tmp/CRAN_pretest/evolved.Rcheck/vign_test/evolved/vignettes/popgen_drift_files/figure-html/unnamed-chunk-7-1.png 288x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 9871 bytes Input file size = 9961 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7423 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 = 7423 Output IDAT size = 7423 bytes (2448 bytes decrease) Output file size = 7501 bytes (2460 bytes = 24.70% decrease) ** Processing: /srv/hornik/tmp/CRAN_pretest/evolved.Rcheck/vign_test/evolved/vignettes/popgen_drift_files/figure-html/unnamed-chunk-13-1.png 288x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 10834 bytes Input file size = 10924 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 8593 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 = 8593 Output IDAT size = 8593 bytes (2241 bytes decrease) Output file size = 8671 bytes (2253 bytes = 20.62% decrease) ** Processing: /srv/hornik/tmp/CRAN_pretest/evolved.Rcheck/vign_test/evolved/vignettes/popgen_drift_files/figure-html/unnamed-chunk-14-1.png 288x288 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 5488 bytes Input file size = 6346 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 4991 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 = 4991 Output IDAT size = 4991 bytes (497 bytes decrease) Output file size = 5069 bytes (1277 bytes = 20.12% decrease) ** Processing: /srv/hornik/tmp/CRAN_pretest/evolved.Rcheck/vign_test/evolved/vignettes/popgen_drift_files/figure-html/unnamed-chunk-17-1.png 288x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 17834 bytes Input file size = 17936 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 14373 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 = 14373 Output IDAT size = 14373 bytes (3461 bytes decrease) Output file size = 14451 bytes (3485 bytes = 19.43% decrease) ** Processing: /srv/hornik/tmp/CRAN_pretest/evolved.Rcheck/vign_test/evolved/vignettes/popgen_drift_files/figure-html/unnamed-chunk-17-2.png 288x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 25892 bytes Input file size = 26006 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 20693 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 = 20693 Output IDAT size = 20693 bytes (5199 bytes decrease) Output file size = 20771 bytes (5235 bytes = 20.13% decrease) --- finished re-building ‘popgen_drift.Rmd’ --- re-building ‘popgen_intro.Rmd’ using rmarkdown ** Processing: /srv/hornik/tmp/CRAN_pretest/evolved.Rcheck/vign_test/evolved/vignettes/popgen_intro_files/figure-html/unnamed-chunk-6-1.png 288x288 pixels, 8 bits/pixel, 255 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 3890 bytes Input file size = 4745 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 3412 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 = 3412 Output IDAT size = 3412 bytes (478 bytes decrease) Output file size = 3490 bytes (1255 bytes = 26.45% decrease) ** Processing: /srv/hornik/tmp/CRAN_pretest/evolved.Rcheck/vign_test/evolved/vignettes/popgen_intro_files/figure-html/unnamed-chunk-9-1.png 288x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 9013 bytes Input file size = 9103 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7086 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 = 7086 Output IDAT size = 7086 bytes (1927 bytes decrease) Output file size = 7164 bytes (1939 bytes = 21.30% decrease) ** Processing: /srv/hornik/tmp/CRAN_pretest/evolved.Rcheck/vign_test/evolved/vignettes/popgen_intro_files/figure-html/unnamed-chunk-16-1.png 288x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 12370 bytes Input file size = 12460 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 9913 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 = 9913 Output IDAT size = 9913 bytes (2457 bytes decrease) Output file size = 9991 bytes (2469 bytes = 19.82% decrease) --- finished re-building ‘popgen_intro.Rmd’ --- re-building ‘popgen_selection.Rmd’ using rmarkdown --- finished re-building ‘popgen_selection.Rmd’ --- re-building ‘population_genetics.Rmd’ using rmarkdown ** Processing: /srv/hornik/tmp/CRAN_pretest/evolved.Rcheck/vign_test/evolved/vignettes/population_genetics_files/figure-html/unnamed-chunk-3-1.png 576x480 pixels, 3x8 bits/pixel, RGB Input IDAT size = 38763 bytes Input file size = 38889 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 30156 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 = 30156 Output IDAT size = 30156 bytes (8607 bytes decrease) Output file size = 30234 bytes (8655 bytes = 22.26% decrease) ** Processing: /srv/hornik/tmp/CRAN_pretest/evolved.Rcheck/vign_test/evolved/vignettes/population_genetics_files/figure-html/unnamed-chunk-5-1.png 576x480 pixels, 3x8 bits/pixel, RGB Input IDAT size = 211863 bytes Input file size = 212241 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 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 IDAT size = 209847 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 = 5 IDAT size = 209847 Output IDAT size = 209847 bytes (2016 bytes decrease) Output file size = 209925 bytes (2316 bytes = 1.09% decrease) ** Processing: /srv/hornik/tmp/CRAN_pretest/evolved.Rcheck/vign_test/evolved/vignettes/population_genetics_files/figure-html/unnamed-chunk-6-1.png 576x480 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 6879 bytes Input file size = 7737 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 5952 zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 5944 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 = 5944 Output IDAT size = 5944 bytes (935 bytes decrease) Output file size = 6022 bytes (1715 bytes = 22.17% decrease) ** Processing: /srv/hornik/tmp/CRAN_pretest/evolved.Rcheck/vign_test/evolved/vignettes/population_genetics_files/figure-html/unnamed-chunk-7-1.png 576x480 pixels, 3x8 bits/pixel, RGB Input IDAT size = 42776 bytes Input file size = 42914 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 33074 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 = 33074 Output IDAT size = 33074 bytes (9702 bytes decrease) Output file size = 33152 bytes (9762 bytes = 22.75% decrease) --- finished re-building ‘population_genetics.Rmd’ --- re-building ‘rocks_and_clocks.Rmd’ using rmarkdown ** Processing: /srv/hornik/tmp/CRAN_pretest/evolved.Rcheck/vign_test/evolved/vignettes/rocks_and_clocks_files/figure-html/unnamed-chunk-4-1.png 576x480 pixels, 3x8 bits/pixel, RGB Input IDAT size = 34383 bytes Input file size = 34509 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 32742 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 = 31962 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 = 31962 Output IDAT size = 31962 bytes (2421 bytes decrease) Output file size = 32040 bytes (2469 bytes = 7.15% decrease) ** Processing: /srv/hornik/tmp/CRAN_pretest/evolved.Rcheck/vign_test/evolved/vignettes/rocks_and_clocks_files/figure-html/unnamed-chunk-5-1.png 576x480 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 10348 bytes Input file size = 11218 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 9341 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 = 9341 Output IDAT size = 9341 bytes (1007 bytes decrease) Output file size = 9419 bytes (1799 bytes = 16.04% decrease) ** Processing: /srv/hornik/tmp/CRAN_pretest/evolved.Rcheck/vign_test/evolved/vignettes/rocks_and_clocks_files/figure-html/unnamed-chunk-5-2.png 576x480 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 10382 bytes Input file size = 11252 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 9307 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 = 9307 Output IDAT size = 9307 bytes (1075 bytes decrease) Output file size = 9385 bytes (1867 bytes = 16.59% decrease) ** Processing: /srv/hornik/tmp/CRAN_pretest/evolved.Rcheck/vign_test/evolved/vignettes/rocks_and_clocks_files/figure-html/unnamed-chunk-5-3.png 576x480 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 9869 bytes Input file size = 10739 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 8790 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 = 8790 Output IDAT size = 8790 bytes (1079 bytes decrease) Output file size = 8868 bytes (1871 bytes = 17.42% decrease) ** Processing: /srv/hornik/tmp/CRAN_pretest/evolved.Rcheck/vign_test/evolved/vignettes/rocks_and_clocks_files/figure-html/unnamed-chunk-11-1.png 576x480 pixels, 3x8 bits/pixel, RGB Input IDAT size = 44449 bytes Input file size = 44587 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 35747 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 = 35747 Output IDAT size = 35747 bytes (8702 bytes decrease) Output file size = 35825 bytes (8762 bytes = 19.65% decrease) ** Processing: /srv/hornik/tmp/CRAN_pretest/evolved.Rcheck/vign_test/evolved/vignettes/rocks_and_clocks_files/figure-html/unnamed-chunk-15-1.png 576x480 pixels, 3x8 bits/pixel, RGB Input IDAT size = 11705 bytes Input file size = 11795 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 11037 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 = 10286 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 = 10286 Output IDAT size = 10286 bytes (1419 bytes decrease) Output file size = 10364 bytes (1431 bytes = 12.13% decrease) --- finished re-building ‘rocks_and_clocks.Rmd’ SUMMARY: processing the following file failed: ‘birthdeath_phylogenies.Rmd’ Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... [3s/3s] OK * checking HTML version of manual ... [0s/0s] OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 1 ERROR, 2 NOTEs