CRAN Package Check Results for Package liger

Last updated on 2024-06-14 06:53:38 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 2.0.1 38.88 60.45 99.33 ERROR
r-devel-linux-x86_64-debian-gcc 2.0.1 23.70 47.24 70.94 ERROR
r-devel-linux-x86_64-fedora-clang 2.0.1 141.96 ERROR
r-devel-linux-x86_64-fedora-gcc 2.0.1 152.38 ERROR
r-devel-windows-x86_64 2.0.1 32.00 79.00 111.00 ERROR
r-patched-linux-x86_64 2.0.1 33.05 58.95 92.00 ERROR
r-release-linux-x86_64 2.0.1 37.51 58.81 96.32 ERROR
r-release-macos-arm64 2.0.1 77.00 NOTE
r-release-macos-x86_64 2.0.1 107.00 NOTE
r-release-windows-x86_64 2.0.1 31.00 81.00 112.00 ERROR
r-oldrel-macos-arm64 2.0.1 81.00 NOTE
r-oldrel-macos-x86_64 2.0.1 139.00 NOTE
r-oldrel-windows-x86_64 2.0.1 40.00 91.00 131.00 ERROR

Check Details

Version: 2.0.1
Check: re-building of vignette outputs
Result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘gsea.Rmd’ using rmarkdown Error: processing vignette 'gsea.Rmd' failed with diagnostics: The closing fence on line 87 ("````") in gsea.Rmd does not match the opening fence "```" on line 85. You are recommended to fix either the opening or closing fence of the code chunk to use exactly the same numbers of backticks and same level of indentation (or blockquote). See https://yihui.org/en/2021/10/unbalanced-delimiters/ for more info. --- failed re-building ‘gsea.Rmd’ --- re-building ‘interpreting.Rmd’ using rmarkdown ** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/liger.Rcheck/vign_test/liger/vignettes/interpreting_files/figure-html/unnamed-chunk-2-1.png 1344x960 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 8741 bytes Input file size = 9611 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7175 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 = 7175 Output IDAT size = 7175 bytes (1566 bytes decrease) Output file size = 7253 bytes (2358 bytes = 24.53% decrease) ** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/liger.Rcheck/vign_test/liger/vignettes/interpreting_files/figure-html/unnamed-chunk-5-1.png 1344x960 pixels, 3x8 bits/pixel, RGB Input IDAT size = 65957 bytes Input file size = 66131 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 53106 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 = 53106 Output IDAT size = 53106 bytes (12851 bytes decrease) Output file size = 53184 bytes (12947 bytes = 19.58% decrease) ** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/liger.Rcheck/vign_test/liger/vignettes/interpreting_files/figure-html/unnamed-chunk-6-1.png 1344x960 pixels, 3x8 bits/pixel, RGB Input IDAT size = 64262 bytes Input file size = 64424 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 52688 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 = 52688 Output IDAT size = 52688 bytes (11574 bytes decrease) Output file size = 52766 bytes (11658 bytes = 18.10% decrease) ** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/liger.Rcheck/vign_test/liger/vignettes/interpreting_files/figure-html/unnamed-chunk-7-1.png 1344x960 pixels, 3x8 bits/pixel, RGB Input IDAT size = 73543 bytes Input file size = 73717 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 61626 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 = 61626 Output IDAT size = 61626 bytes (11917 bytes decrease) Output file size = 61704 bytes (12013 bytes = 16.30% decrease) ** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/liger.Rcheck/vign_test/liger/vignettes/interpreting_files/figure-html/unnamed-chunk-8-1.png 1344x960 pixels, 3x8 bits/pixel, RGB Input IDAT size = 74745 bytes Input file size = 74931 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 63424 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 = 63424 Output IDAT size = 63424 bytes (11321 bytes decrease) Output file size = 63502 bytes (11429 bytes = 15.25% decrease) --- finished re-building ‘interpreting.Rmd’ --- re-building ‘permpvals.Rmd’ using rmarkdown Error: processing vignette 'permpvals.Rmd' failed with diagnostics: The closing fence on line 69 ("````") in permpvals.Rmd does not match the opening fence "```" on line 67. You are recommended to fix either the opening or closing fence of the code chunk to use exactly the same numbers of backticks and same level of indentation (or blockquote). See https://yihui.org/en/2021/10/unbalanced-delimiters/ for more info. --- failed re-building ‘permpvals.Rmd’ --- re-building ‘simulation.Rmd’ using rmarkdown Error: processing vignette 'simulation.Rmd' failed with diagnostics: The closing fence on line 93 ("````") in simulation.Rmd does not match the opening fence "```" on line 91. You are recommended to fix either the opening or closing fence of the code chunk to use exactly the same numbers of backticks and same level of indentation (or blockquote). See https://yihui.org/en/2021/10/unbalanced-delimiters/ for more info. --- failed re-building ‘simulation.Rmd’ SUMMARY: processing the following files failed: ‘gsea.Rmd’ ‘permpvals.Rmd’ ‘simulation.Rmd’ Error: Vignette re-building failed. Execution halted Flavor: r-devel-linux-x86_64-debian-clang

Version: 2.0.1
Check: re-building of vignette outputs
Result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘gsea.Rmd’ using rmarkdown Error: processing vignette 'gsea.Rmd' failed with diagnostics: The closing fence on line 87 ("````") in gsea.Rmd does not match the opening fence "```" on line 85. You are recommended to fix either the opening or closing fence of the code chunk to use exactly the same numbers of backticks and same level of indentation (or blockquote). See https://yihui.org/en/2021/10/unbalanced-delimiters/ for more info. --- failed re-building ‘gsea.Rmd’ --- re-building ‘interpreting.Rmd’ using rmarkdown ** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/liger.Rcheck/vign_test/liger/vignettes/interpreting_files/figure-html/unnamed-chunk-2-1.png 1344x960 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 8741 bytes Input file size = 9611 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7175 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 = 7175 Output IDAT size = 7175 bytes (1566 bytes decrease) Output file size = 7253 bytes (2358 bytes = 24.53% decrease) ** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/liger.Rcheck/vign_test/liger/vignettes/interpreting_files/figure-html/unnamed-chunk-5-1.png 1344x960 pixels, 3x8 bits/pixel, RGB Input IDAT size = 65957 bytes Input file size = 66131 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 53106 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 = 53106 Output IDAT size = 53106 bytes (12851 bytes decrease) Output file size = 53184 bytes (12947 bytes = 19.58% decrease) ** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/liger.Rcheck/vign_test/liger/vignettes/interpreting_files/figure-html/unnamed-chunk-6-1.png 1344x960 pixels, 3x8 bits/pixel, RGB Input IDAT size = 64262 bytes Input file size = 64424 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 52688 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 = 52688 Output IDAT size = 52688 bytes (11574 bytes decrease) Output file size = 52766 bytes (11658 bytes = 18.10% decrease) ** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/liger.Rcheck/vign_test/liger/vignettes/interpreting_files/figure-html/unnamed-chunk-7-1.png 1344x960 pixels, 3x8 bits/pixel, RGB Input IDAT size = 73543 bytes Input file size = 73717 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 61626 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 = 61626 Output IDAT size = 61626 bytes (11917 bytes decrease) Output file size = 61704 bytes (12013 bytes = 16.30% decrease) ** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/liger.Rcheck/vign_test/liger/vignettes/interpreting_files/figure-html/unnamed-chunk-8-1.png 1344x960 pixels, 3x8 bits/pixel, RGB Input IDAT size = 74745 bytes Input file size = 74931 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 63424 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 = 63424 Output IDAT size = 63424 bytes (11321 bytes decrease) Output file size = 63502 bytes (11429 bytes = 15.25% decrease) --- finished re-building ‘interpreting.Rmd’ --- re-building ‘permpvals.Rmd’ using rmarkdown Error: processing vignette 'permpvals.Rmd' failed with diagnostics: The closing fence on line 69 ("````") in permpvals.Rmd does not match the opening fence "```" on line 67. You are recommended to fix either the opening or closing fence of the code chunk to use exactly the same numbers of backticks and same level of indentation (or blockquote). See https://yihui.org/en/2021/10/unbalanced-delimiters/ for more info. --- failed re-building ‘permpvals.Rmd’ --- re-building ‘simulation.Rmd’ using rmarkdown Error: processing vignette 'simulation.Rmd' failed with diagnostics: The closing fence on line 93 ("````") in simulation.Rmd does not match the opening fence "```" on line 91. You are recommended to fix either the opening or closing fence of the code chunk to use exactly the same numbers of backticks and same level of indentation (or blockquote). See https://yihui.org/en/2021/10/unbalanced-delimiters/ for more info. --- failed re-building ‘simulation.Rmd’ SUMMARY: processing the following files failed: ‘gsea.Rmd’ ‘permpvals.Rmd’ ‘simulation.Rmd’ Error: Vignette re-building failed. Execution halted Flavor: r-devel-linux-x86_64-debian-gcc

Version: 2.0.1
Check: installed package size
Result: NOTE installed size is 5.7Mb sub-directories of 1Mb or more: data 3.3Mb doc 2.1Mb Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-windows-x86_64, r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64

Version: 2.0.1
Check: re-building of vignette outputs
Result: ERROR Error(s) in re-building vignettes: --- re-building ‘gsea.Rmd’ using rmarkdown Error: processing vignette 'gsea.Rmd' failed with diagnostics: The closing fence on line 87 ("````") in gsea.Rmd does not match the opening fence "```" on line 85. You are recommended to fix either the opening or closing fence of the code chunk to use exactly the same numbers of backticks and same level of indentation (or blockquote). See https://yihui.org/en/2021/10/unbalanced-delimiters/ for more info. --- failed re-building ‘gsea.Rmd’ --- re-building ‘interpreting.Rmd’ using rmarkdown ** Processing: /data/gannet/ripley/R/packages/tests-clang/liger.Rcheck/vign_test/liger/vignettes/interpreting_files/figure-html/unnamed-chunk-2-1.png 1344x960 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 8741 bytes Input file size = 9611 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7175 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 = 7175 Output IDAT size = 7175 bytes (1566 bytes decrease) Output file size = 7253 bytes (2358 bytes = 24.53% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-clang/liger.Rcheck/vign_test/liger/vignettes/interpreting_files/figure-html/unnamed-chunk-5-1.png 1344x960 pixels, 3x8 bits/pixel, RGB Input IDAT size = 65958 bytes Input file size = 66132 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 53106 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 = 53106 Output IDAT size = 53106 bytes (12852 bytes decrease) Output file size = 53184 bytes (12948 bytes = 19.58% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-clang/liger.Rcheck/vign_test/liger/vignettes/interpreting_files/figure-html/unnamed-chunk-6-1.png 1344x960 pixels, 3x8 bits/pixel, RGB Input IDAT size = 64263 bytes Input file size = 64425 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 52689 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 = 52689 Output IDAT size = 52689 bytes (11574 bytes decrease) Output file size = 52767 bytes (11658 bytes = 18.10% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-clang/liger.Rcheck/vign_test/liger/vignettes/interpreting_files/figure-html/unnamed-chunk-7-1.png 1344x960 pixels, 3x8 bits/pixel, RGB Input IDAT size = 73537 bytes Input file size = 73711 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 61615 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 = 61615 Output IDAT size = 61615 bytes (11922 bytes decrease) Output file size = 61693 bytes (12018 bytes = 16.30% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-clang/liger.Rcheck/vign_test/liger/vignettes/interpreting_files/figure-html/unnamed-chunk-8-1.png 1344x960 pixels, 3x8 bits/pixel, RGB Input IDAT size = 74765 bytes Input file size = 74951 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 63428 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 = 63428 Output IDAT size = 63428 bytes (11337 bytes decrease) Output file size = 63506 bytes (11445 bytes = 15.27% decrease) --- finished re-building ‘interpreting.Rmd’ --- re-building ‘permpvals.Rmd’ using rmarkdown Error: processing vignette 'permpvals.Rmd' failed with diagnostics: The closing fence on line 69 ("````") in permpvals.Rmd does not match the opening fence "```" on line 67. You are recommended to fix either the opening or closing fence of the code chunk to use exactly the same numbers of backticks and same level of indentation (or blockquote). See https://yihui.org/en/2021/10/unbalanced-delimiters/ for more info. --- failed re-building ‘permpvals.Rmd’ --- re-building ‘simulation.Rmd’ using rmarkdown Error: processing vignette 'simulation.Rmd' failed with diagnostics: The closing fence on line 93 ("````") in simulation.Rmd does not match the opening fence "```" on line 91. You are recommended to fix either the opening or closing fence of the code chunk to use exactly the same numbers of backticks and same level of indentation (or blockquote). See https://yihui.org/en/2021/10/unbalanced-delimiters/ for more info. --- failed re-building ‘simulation.Rmd’ SUMMARY: processing the following files failed: ‘gsea.Rmd’ ‘permpvals.Rmd’ ‘simulation.Rmd’ Error: Vignette re-building failed. Execution halted Flavor: r-devel-linux-x86_64-fedora-clang

Version: 2.0.1
Check: re-building of vignette outputs
Result: ERROR Error(s) in re-building vignettes: --- re-building ‘gsea.Rmd’ using rmarkdown Error: processing vignette 'gsea.Rmd' failed with diagnostics: The closing fence on line 87 ("````") in gsea.Rmd does not match the opening fence "```" on line 85. You are recommended to fix either the opening or closing fence of the code chunk to use exactly the same numbers of backticks and same level of indentation (or blockquote). See https://yihui.org/en/2021/10/unbalanced-delimiters/ for more info. --- failed re-building ‘gsea.Rmd’ --- re-building ‘interpreting.Rmd’ using rmarkdown ** Processing: /data/gannet/ripley/R/packages/tests-devel/liger.Rcheck/vign_test/liger/vignettes/interpreting_files/figure-html/unnamed-chunk-2-1.png 1344x960 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 8741 bytes Input file size = 9611 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7175 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 = 7175 Output IDAT size = 7175 bytes (1566 bytes decrease) Output file size = 7253 bytes (2358 bytes = 24.53% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-devel/liger.Rcheck/vign_test/liger/vignettes/interpreting_files/figure-html/unnamed-chunk-5-1.png 1344x960 pixels, 3x8 bits/pixel, RGB Input IDAT size = 65958 bytes Input file size = 66132 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 53106 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 = 53106 Output IDAT size = 53106 bytes (12852 bytes decrease) Output file size = 53184 bytes (12948 bytes = 19.58% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-devel/liger.Rcheck/vign_test/liger/vignettes/interpreting_files/figure-html/unnamed-chunk-6-1.png 1344x960 pixels, 3x8 bits/pixel, RGB Input IDAT size = 64263 bytes Input file size = 64425 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 52689 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 = 52689 Output IDAT size = 52689 bytes (11574 bytes decrease) Output file size = 52767 bytes (11658 bytes = 18.10% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-devel/liger.Rcheck/vign_test/liger/vignettes/interpreting_files/figure-html/unnamed-chunk-7-1.png 1344x960 pixels, 3x8 bits/pixel, RGB Input IDAT size = 73537 bytes Input file size = 73711 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 61615 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 = 61615 Output IDAT size = 61615 bytes (11922 bytes decrease) Output file size = 61693 bytes (12018 bytes = 16.30% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-devel/liger.Rcheck/vign_test/liger/vignettes/interpreting_files/figure-html/unnamed-chunk-8-1.png 1344x960 pixels, 3x8 bits/pixel, RGB Input IDAT size = 74765 bytes Input file size = 74951 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 63428 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 = 63428 Output IDAT size = 63428 bytes (11337 bytes decrease) Output file size = 63506 bytes (11445 bytes = 15.27% decrease) --- finished re-building ‘interpreting.Rmd’ --- re-building ‘permpvals.Rmd’ using rmarkdown Error: processing vignette 'permpvals.Rmd' failed with diagnostics: The closing fence on line 69 ("````") in permpvals.Rmd does not match the opening fence "```" on line 67. You are recommended to fix either the opening or closing fence of the code chunk to use exactly the same numbers of backticks and same level of indentation (or blockquote). See https://yihui.org/en/2021/10/unbalanced-delimiters/ for more info. --- failed re-building ‘permpvals.Rmd’ --- re-building ‘simulation.Rmd’ using rmarkdown Error: processing vignette 'simulation.Rmd' failed with diagnostics: The closing fence on line 93 ("````") in simulation.Rmd does not match the opening fence "```" on line 91. You are recommended to fix either the opening or closing fence of the code chunk to use exactly the same numbers of backticks and same level of indentation (or blockquote). See https://yihui.org/en/2021/10/unbalanced-delimiters/ for more info. --- failed re-building ‘simulation.Rmd’ SUMMARY: processing the following files failed: ‘gsea.Rmd’ ‘permpvals.Rmd’ ‘simulation.Rmd’ Error: Vignette re-building failed. Execution halted Flavor: r-devel-linux-x86_64-fedora-gcc

Version: 2.0.1
Check: re-building of vignette outputs
Result: ERROR Error(s) in re-building vignettes: --- re-building 'gsea.Rmd' using rmarkdown Error: processing vignette 'gsea.Rmd' failed with diagnostics: The closing fence on line 87 ("````") in gsea.Rmd does not match the opening fence "```" on line 85. You are recommended to fix either the opening or closing fence of the code chunk to use exactly the same numbers of backticks and same level of indentation (or blockquote). See https://yihui.org/en/2021/10/unbalanced-delimiters/ for more info. --- failed re-building 'gsea.Rmd' --- re-building 'interpreting.Rmd' using rmarkdown --- finished re-building 'interpreting.Rmd' --- re-building 'permpvals.Rmd' using rmarkdown Error: processing vignette 'permpvals.Rmd' failed with diagnostics: The closing fence on line 69 ("````") in permpvals.Rmd does not match the opening fence "```" on line 67. You are recommended to fix either the opening or closing fence of the code chunk to use exactly the same numbers of backticks and same level of indentation (or blockquote). See https://yihui.org/en/2021/10/unbalanced-delimiters/ for more info. --- failed re-building 'permpvals.Rmd' --- re-building 'simulation.Rmd' using rmarkdown Error: processing vignette 'simulation.Rmd' failed with diagnostics: The closing fence on line 93 ("````") in simulation.Rmd does not match the opening fence "```" on line 91. You are recommended to fix either the opening or closing fence of the code chunk to use exactly the same numbers of backticks and same level of indentation (or blockquote). See https://yihui.org/en/2021/10/unbalanced-delimiters/ for more info. --- failed re-building 'simulation.Rmd' SUMMARY: processing the following files failed: 'gsea.Rmd' 'permpvals.Rmd' 'simulation.Rmd' Error: Vignette re-building failed. Execution halted Flavors: r-devel-windows-x86_64, r-release-windows-x86_64, r-oldrel-windows-x86_64

Version: 2.0.1
Check: re-building of vignette outputs
Result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘gsea.Rmd’ using rmarkdown Error: processing vignette 'gsea.Rmd' failed with diagnostics: The closing fence on line 87 ("````") in gsea.Rmd does not match the opening fence "```" on line 85. You are recommended to fix either the opening or closing fence of the code chunk to use exactly the same numbers of backticks and same level of indentation (or blockquote). See https://yihui.org/en/2021/10/unbalanced-delimiters/ for more info. --- failed re-building ‘gsea.Rmd’ --- re-building ‘interpreting.Rmd’ using rmarkdown ** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/liger.Rcheck/vign_test/liger/vignettes/interpreting_files/figure-html/unnamed-chunk-2-1.png 1344x960 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 8741 bytes Input file size = 9611 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7175 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 = 7175 Output IDAT size = 7175 bytes (1566 bytes decrease) Output file size = 7253 bytes (2358 bytes = 24.53% decrease) ** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/liger.Rcheck/vign_test/liger/vignettes/interpreting_files/figure-html/unnamed-chunk-5-1.png 1344x960 pixels, 3x8 bits/pixel, RGB Input IDAT size = 65957 bytes Input file size = 66131 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 53106 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 = 53106 Output IDAT size = 53106 bytes (12851 bytes decrease) Output file size = 53184 bytes (12947 bytes = 19.58% decrease) ** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/liger.Rcheck/vign_test/liger/vignettes/interpreting_files/figure-html/unnamed-chunk-6-1.png 1344x960 pixels, 3x8 bits/pixel, RGB Input IDAT size = 64262 bytes Input file size = 64424 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 52688 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 = 52688 Output IDAT size = 52688 bytes (11574 bytes decrease) Output file size = 52766 bytes (11658 bytes = 18.10% decrease) ** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/liger.Rcheck/vign_test/liger/vignettes/interpreting_files/figure-html/unnamed-chunk-7-1.png 1344x960 pixels, 3x8 bits/pixel, RGB Input IDAT size = 73543 bytes Input file size = 73717 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 61626 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 = 61626 Output IDAT size = 61626 bytes (11917 bytes decrease) Output file size = 61704 bytes (12013 bytes = 16.30% decrease) ** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/liger.Rcheck/vign_test/liger/vignettes/interpreting_files/figure-html/unnamed-chunk-8-1.png 1344x960 pixels, 3x8 bits/pixel, RGB Input IDAT size = 74745 bytes Input file size = 74931 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 63424 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 = 63424 Output IDAT size = 63424 bytes (11321 bytes decrease) Output file size = 63502 bytes (11429 bytes = 15.25% decrease) --- finished re-building ‘interpreting.Rmd’ --- re-building ‘permpvals.Rmd’ using rmarkdown Error: processing vignette 'permpvals.Rmd' failed with diagnostics: The closing fence on line 69 ("````") in permpvals.Rmd does not match the opening fence "```" on line 67. You are recommended to fix either the opening or closing fence of the code chunk to use exactly the same numbers of backticks and same level of indentation (or blockquote). See https://yihui.org/en/2021/10/unbalanced-delimiters/ for more info. --- failed re-building ‘permpvals.Rmd’ --- re-building ‘simulation.Rmd’ using rmarkdown Error: processing vignette 'simulation.Rmd' failed with diagnostics: The closing fence on line 93 ("````") in simulation.Rmd does not match the opening fence "```" on line 91. You are recommended to fix either the opening or closing fence of the code chunk to use exactly the same numbers of backticks and same level of indentation (or blockquote). See https://yihui.org/en/2021/10/unbalanced-delimiters/ for more info. --- failed re-building ‘simulation.Rmd’ SUMMARY: processing the following files failed: ‘gsea.Rmd’ ‘permpvals.Rmd’ ‘simulation.Rmd’ Error: Vignette re-building failed. Execution halted Flavor: r-patched-linux-x86_64

Version: 2.0.1
Check: re-building of vignette outputs
Result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘gsea.Rmd’ using rmarkdown Error: processing vignette 'gsea.Rmd' failed with diagnostics: The closing fence on line 87 ("````") in gsea.Rmd does not match the opening fence "```" on line 85. You are recommended to fix either the opening or closing fence of the code chunk to use exactly the same numbers of backticks and same level of indentation (or blockquote). See https://yihui.org/en/2021/10/unbalanced-delimiters/ for more info. --- failed re-building ‘gsea.Rmd’ --- re-building ‘interpreting.Rmd’ using rmarkdown ** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/liger.Rcheck/vign_test/liger/vignettes/interpreting_files/figure-html/unnamed-chunk-2-1.png 1344x960 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 8741 bytes Input file size = 9611 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7175 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 = 7175 Output IDAT size = 7175 bytes (1566 bytes decrease) Output file size = 7253 bytes (2358 bytes = 24.53% decrease) ** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/liger.Rcheck/vign_test/liger/vignettes/interpreting_files/figure-html/unnamed-chunk-5-1.png 1344x960 pixels, 3x8 bits/pixel, RGB Input IDAT size = 65957 bytes Input file size = 66131 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 53106 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 = 53106 Output IDAT size = 53106 bytes (12851 bytes decrease) Output file size = 53184 bytes (12947 bytes = 19.58% decrease) ** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/liger.Rcheck/vign_test/liger/vignettes/interpreting_files/figure-html/unnamed-chunk-6-1.png 1344x960 pixels, 3x8 bits/pixel, RGB Input IDAT size = 64262 bytes Input file size = 64424 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 52688 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 = 52688 Output IDAT size = 52688 bytes (11574 bytes decrease) Output file size = 52766 bytes (11658 bytes = 18.10% decrease) ** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/liger.Rcheck/vign_test/liger/vignettes/interpreting_files/figure-html/unnamed-chunk-7-1.png 1344x960 pixels, 3x8 bits/pixel, RGB Input IDAT size = 73543 bytes Input file size = 73717 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 61626 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 = 61626 Output IDAT size = 61626 bytes (11917 bytes decrease) Output file size = 61704 bytes (12013 bytes = 16.30% decrease) ** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/liger.Rcheck/vign_test/liger/vignettes/interpreting_files/figure-html/unnamed-chunk-8-1.png 1344x960 pixels, 3x8 bits/pixel, RGB Input IDAT size = 74745 bytes Input file size = 74931 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 63424 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 = 63424 Output IDAT size = 63424 bytes (11321 bytes decrease) Output file size = 63502 bytes (11429 bytes = 15.25% decrease) --- finished re-building ‘interpreting.Rmd’ --- re-building ‘permpvals.Rmd’ using rmarkdown Error: processing vignette 'permpvals.Rmd' failed with diagnostics: The closing fence on line 69 ("````") in permpvals.Rmd does not match the opening fence "```" on line 67. You are recommended to fix either the opening or closing fence of the code chunk to use exactly the same numbers of backticks and same level of indentation (or blockquote). See https://yihui.org/en/2021/10/unbalanced-delimiters/ for more info. --- failed re-building ‘permpvals.Rmd’ --- re-building ‘simulation.Rmd’ using rmarkdown Error: processing vignette 'simulation.Rmd' failed with diagnostics: The closing fence on line 93 ("````") in simulation.Rmd does not match the opening fence "```" on line 91. You are recommended to fix either the opening or closing fence of the code chunk to use exactly the same numbers of backticks and same level of indentation (or blockquote). See https://yihui.org/en/2021/10/unbalanced-delimiters/ for more info. --- failed re-building ‘simulation.Rmd’ SUMMARY: processing the following files failed: ‘gsea.Rmd’ ‘permpvals.Rmd’ ‘simulation.Rmd’ Error: Vignette re-building failed. Execution halted Flavor: r-release-linux-x86_64