CRAN Package Check Results for Package harmony

Last updated on 2024-09-12 09:50:34 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.2.1 50.10 167.80 217.90 OK
r-devel-linux-x86_64-debian-gcc 1.2.1 38.49 93.94 132.43 ERROR
r-devel-linux-x86_64-fedora-clang 1.2.1 392.88 NOTE
r-devel-linux-x86_64-fedora-gcc 1.2.1 385.75 OK
r-devel-windows-x86_64 1.2.1 56.00 262.00 318.00 NOTE
r-patched-linux-x86_64 1.2.1 52.26 161.64 213.90 OK
r-release-linux-x86_64 1.2.1 53.90 121.80 175.70 ERROR
r-release-macos-arm64 1.2.1 112.00 NOTE
r-release-macos-x86_64 1.2.1 232.00 NOTE
r-release-windows-x86_64 1.2.1 58.00 193.00 251.00 NOTE
r-oldrel-macos-arm64 1.2.1 162.00 NOTE
r-oldrel-macos-x86_64 1.2.1 223.00 NOTE
r-oldrel-windows-x86_64 1.2.1 70.00 291.00 361.00 NOTE

Check Details

Version: 1.2.1
Check: package dependencies
Result: NOTE Package suggested but not available for checking: ‘tidyverse’ Flavors: r-devel-linux-x86_64-debian-gcc, r-release-linux-x86_64

Version: 1.2.1
Check: re-building of vignette outputs
Result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘Seurat.Rmd’ using rmarkdown Calculating gene variances 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Calculating feature variances of standardized and clipped values 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Calculating gene variances 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Calculating feature variances of standardized and clipped values 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| ** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/harmony.Rcheck/vign_test/harmony/vignettes/Seurat_files/figure-html/unnamed-chunk-6-1.png 384x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 16524 bytes Input file size = 16626 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 12877 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 = 12877 Output IDAT size = 12877 bytes (3647 bytes decrease) Output file size = 12955 bytes (3671 bytes = 22.08% decrease) ** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/harmony.Rcheck/vign_test/harmony/vignettes/Seurat_files/figure-html/unnamed-chunk-8-1.png 480x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 44590 bytes Input file size = 44728 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 34692 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 = 34692 Output IDAT size = 34692 bytes (9898 bytes decrease) Output file size = 34770 bytes (9958 bytes = 22.26% decrease) ** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/harmony.Rcheck/vign_test/harmony/vignettes/Seurat_files/figure-html/unnamed-chunk-9-1.png 576x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 45257 bytes Input file size = 45395 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 32156 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 = 32156 Output IDAT size = 32156 bytes (13101 bytes decrease) Output file size = 32234 bytes (13161 bytes = 28.99% decrease) 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| ** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/harmony.Rcheck/vign_test/harmony/vignettes/Seurat_files/figure-html/unnamed-chunk-11-1.png 480x240 pixels, 3x8 bits/pixel, RGB Input IDAT size = 40279 bytes Input file size = 40405 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 32494 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 = 32494 Output IDAT size = 32494 bytes (7785 bytes decrease) Output file size = 32572 bytes (7833 bytes = 19.39% decrease) ** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/harmony.Rcheck/vign_test/harmony/vignettes/Seurat_files/figure-html/unnamed-chunk-12-1.png 672x672 pixels, 3x8 bits/pixel, RGB Input IDAT size = 121088 bytes Input file size = 121334 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 98136 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 = 98136 Output IDAT size = 98136 bytes (22952 bytes decrease) Output file size = 98214 bytes (23120 bytes = 19.05% decrease) Using method 'umap' 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| ** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/harmony.Rcheck/vign_test/harmony/vignettes/Seurat_files/figure-html/unnamed-chunk-13-1.png 480x240 pixels, 3x8 bits/pixel, RGB Input IDAT size = 22737 bytes Input file size = 22839 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 17928 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 = 17928 Output IDAT size = 17928 bytes (4809 bytes decrease) Output file size = 18006 bytes (4833 bytes = 21.16% decrease) --- finished re-building ‘Seurat.Rmd’ --- re-building ‘detailedWalkthrough.Rmd’ using rmarkdown Quitting from lines 27-106 [unnamed-chunk-1] (detailedWalkthrough.Rmd) Error: processing vignette 'detailedWalkthrough.Rmd' failed with diagnostics: there is no package called 'tidyverse' --- failed re-building ‘detailedWalkthrough.Rmd’ --- re-building ‘quickstart.Rmd’ using rmarkdown ** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/harmony.Rcheck/vign_test/harmony/vignettes/quickstart_files/figure-html/unnamed-chunk-5-1.png 480x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 21567 bytes Input file size = 21669 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 16185 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 = 16185 Output IDAT size = 16185 bytes (5382 bytes decrease) Output file size = 16263 bytes (5406 bytes = 24.95% decrease) ** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/harmony.Rcheck/vign_test/harmony/vignettes/quickstart_files/figure-html/unnamed-chunk-7-1.png 480x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 20549 bytes Input file size = 20651 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 15546 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 = 15546 Output IDAT size = 15546 bytes (5003 bytes decrease) Output file size = 15624 bytes (5027 bytes = 24.34% decrease) --- finished re-building ‘quickstart.Rmd’ SUMMARY: processing the following file failed: ‘detailedWalkthrough.Rmd’ Error: Vignette re-building failed. Execution halted Flavor: r-devel-linux-x86_64-debian-gcc

Version: 1.2.1
Check: installed package size
Result: NOTE installed size is 6.0Mb sub-directories of 1Mb or more: data 2.7Mb doc 2.4Mb 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: 1.2.1
Check: re-building of vignette outputs
Result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘Seurat.Rmd’ using rmarkdown Calculating gene variances 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Calculating feature variances of standardized and clipped values 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Calculating gene variances 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Calculating feature variances of standardized and clipped values 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| ** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/harmony.Rcheck/vign_test/harmony/vignettes/Seurat_files/figure-html/unnamed-chunk-6-1.png 384x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 16524 bytes Input file size = 16626 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 12877 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 = 12877 Output IDAT size = 12877 bytes (3647 bytes decrease) Output file size = 12955 bytes (3671 bytes = 22.08% decrease) ** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/harmony.Rcheck/vign_test/harmony/vignettes/Seurat_files/figure-html/unnamed-chunk-8-1.png 480x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 44590 bytes Input file size = 44728 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 34692 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 = 34692 Output IDAT size = 34692 bytes (9898 bytes decrease) Output file size = 34770 bytes (9958 bytes = 22.26% decrease) ** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/harmony.Rcheck/vign_test/harmony/vignettes/Seurat_files/figure-html/unnamed-chunk-9-1.png 576x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 45257 bytes Input file size = 45395 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 32156 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 = 32156 Output IDAT size = 32156 bytes (13101 bytes decrease) Output file size = 32234 bytes (13161 bytes = 28.99% decrease) 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| ** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/harmony.Rcheck/vign_test/harmony/vignettes/Seurat_files/figure-html/unnamed-chunk-11-1.png 480x240 pixels, 3x8 bits/pixel, RGB Input IDAT size = 40279 bytes Input file size = 40405 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 32494 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 = 32494 Output IDAT size = 32494 bytes (7785 bytes decrease) Output file size = 32572 bytes (7833 bytes = 19.39% decrease) ** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/harmony.Rcheck/vign_test/harmony/vignettes/Seurat_files/figure-html/unnamed-chunk-12-1.png 672x672 pixels, 3x8 bits/pixel, RGB Input IDAT size = 121088 bytes Input file size = 121334 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 98136 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 = 98136 Output IDAT size = 98136 bytes (22952 bytes decrease) Output file size = 98214 bytes (23120 bytes = 19.05% decrease) Using method 'umap' 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| ** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/harmony.Rcheck/vign_test/harmony/vignettes/Seurat_files/figure-html/unnamed-chunk-13-1.png 480x240 pixels, 3x8 bits/pixel, RGB Input IDAT size = 22737 bytes Input file size = 22839 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 17928 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 = 17928 Output IDAT size = 17928 bytes (4809 bytes decrease) Output file size = 18006 bytes (4833 bytes = 21.16% decrease) --- finished re-building ‘Seurat.Rmd’ --- re-building ‘detailedWalkthrough.Rmd’ using rmarkdown Quitting from lines 27-106 [unnamed-chunk-1] (detailedWalkthrough.Rmd) Error: processing vignette 'detailedWalkthrough.Rmd' failed with diagnostics: there is no package called 'tidyverse' --- failed re-building ‘detailedWalkthrough.Rmd’ --- re-building ‘quickstart.Rmd’ using rmarkdown ** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/harmony.Rcheck/vign_test/harmony/vignettes/quickstart_files/figure-html/unnamed-chunk-5-1.png 480x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 21608 bytes Input file size = 21710 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 16189 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 = 16189 Output IDAT size = 16189 bytes (5419 bytes decrease) Output file size = 16267 bytes (5443 bytes = 25.07% decrease) ** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/harmony.Rcheck/vign_test/harmony/vignettes/quickstart_files/figure-html/unnamed-chunk-7-1.png 480x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 20213 bytes Input file size = 20315 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 15360 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 = 15360 Output IDAT size = 15360 bytes (4853 bytes decrease) Output file size = 15438 bytes (4877 bytes = 24.01% decrease) --- finished re-building ‘quickstart.Rmd’ SUMMARY: processing the following file failed: ‘detailedWalkthrough.Rmd’ Error: Vignette re-building failed. Execution halted Flavor: r-release-linux-x86_64