Last updated on 2024-10-31 10:50:12 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 2.0.0 | 35.55 | 425.89 | 461.44 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 2.0.0 | 25.40 | 306.09 | 331.49 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 2.0.0 | 835.63 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 2.0.0 | 795.85 | ERROR | |||
| r-devel-windows-x86_64 | 2.0.0 | 42.00 | 440.00 | 482.00 | OK | |
| r-patched-linux-x86_64 | 2.0.0 | 37.90 | 402.28 | 440.18 | ERROR | |
| r-release-linux-x86_64 | 2.0.0 | 36.89 | 400.32 | 437.21 | ERROR | |
| r-release-macos-arm64 | 2.0.0 | 296.00 | NOTE | |||
| r-release-macos-x86_64 | 2.0.0 | 314.00 | NOTE | |||
| r-release-windows-x86_64 | 2.0.0 | 41.00 | 438.00 | 479.00 | NOTE | |
| r-oldrel-macos-arm64 | 2.0.0 | 13.00 | ERROR | |||
| r-oldrel-macos-x86_64 | 2.0.0 | 11.00 | ERROR | |||
| r-oldrel-windows-x86_64 | 2.0.0 | 55.00 | 814.00 | 869.00 | NOTE |
Version: 2.0.0
Check: examples
Result: ERROR
Running examples in ‘TOmicsVis-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: go_enrich_net
> ### Title: GO enrichment analysis and net plot (None/Exist Reference
> ### Genome).
> ### Aliases: go_enrich_net
>
> ### ** Examples
>
> # 1. Library TOmicsVis package
> library(TOmicsVis)
>
> # 2. Use example dataset
> data(gene_go_kegg)
> head(gene_go_kegg)
Genes
1 FN1
2 14-3-3ZETA
3 A1I3
4 A2M
5 AARS
6 ABAT
biological_process
1 GO:0003181(atrioventricular valve morphogenesis);GO:0003128(heart field specification);GO:0001756(somitogenesis)
2 <NA>
3 <NA>
4 <NA>
5 GO:0006419(alanyl-tRNA aminoacylation)
6 GO:0009448(gamma-aminobutyric acid metabolic process)
cellular_component
1 GO:0005576(extracellular region)
2 <NA>
3 GO:0005615(extracellular space)
4 GO:0005615(extracellular space)
5 GO:0005737(cytoplasm)
6 <NA>
molecular_function
1 <NA>
2 GO:0019904(protein domain specific binding)
3 GO:0004866(endopeptidase inhibitor activity)
4 GO:0004866(endopeptidase inhibitor activity)
5 GO:0004813(alanine-tRNA ligase activity);GO:0005524(ATP binding);GO:0000049(tRNA binding);GO:0008270(zinc ion binding)
6 GO:0003867(4-aminobutyrate transaminase activity);GO:0030170(pyridoxal phosphate binding)
kegg_pathway
1 ko04810(Regulation of actin cytoskeleton);ko04510(Focal adhesion);ko04151(PI3K-Akt signaling pathway);ko04512(ECM-receptor interaction)
2 ko04110(Cell cycle);ko04114(Oocyte meiosis);ko04390(Hippo signaling pathway);ko04391(Hippo signaling pathway -fly);ko04013(MAPK signaling pathway - fly);ko04151(PI3K-Akt signaling pathway);ko04212(Longevity regulating pathway - worm)
3 ko04610(Complement and coagulation cascades)
4 ko04610(Complement and coagulation cascades)
5 ko00970(Aminoacyl-tRNA biosynthesis)
6 ko00250(Alanine, aspartate and glutamate metabolism);ko00280(Valine, leucine and isoleucine degradation);ko00650(Butanoate metabolism);ko00640(Propanoate metabolism);ko00410(beta-Alanine metabolism);ko04727(GABAergic synapse)
>
> # 3. Default parameters
> go_enrich_net(gene_go_kegg[,-5], gene_go_kegg[100:200,1])
Warning: Expected 2 pieces. Additional pieces discarded in 82 rows [714, 928, 1523,
1543, 2042, 2191, 2192, 2193, 2194, 2195, 2197, 2198, 2200, 2202, 2203, 2205,
2206, 2207, 2208, 2552, ...].
Error in storage.mode(mat) <- "integer" :
'list' object cannot be coerced to type 'integer'
Calls: go_enrich_net ... ggplot.igraph -> setNames -> as.data.frame -> layout
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
chord_plot 11.558 0.996 16.033
circos_heatmap 6.687 0.478 8.652
box_plot 4.046 0.329 5.843
go_enrich_bar 2.888 0.122 5.468
Flavor: r-devel-linux-x86_64-debian-clang
Version: 2.0.0
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘Tutorials.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/quantile_plot-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 41924 bytes
Input file size = 42062 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 38517
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 = 38517
Output IDAT size = 38517 bytes (3407 bytes decrease)
Output file size = 38595 bytes (3467 bytes = 8.24% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/box_plot-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 56909 bytes
Input file size = 57059 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 46779
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 = 46779
Output IDAT size = 46779 bytes (10130 bytes decrease)
Output file size = 46857 bytes (10202 bytes = 17.88% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/violin_plot-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 45016 bytes
Input file size = 45154 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 42388
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 = 41850
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 = 41850
Output IDAT size = 41850 bytes (3166 bytes decrease)
Output file size = 41928 bytes (3226 bytes = 7.14% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/survival_plot-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 58889 bytes
Input file size = 59051 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 48780
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 = 48780
Output IDAT size = 48780 bytes (10109 bytes decrease)
Output file size = 48858 bytes (10193 bytes = 17.26% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/corr_heatmap-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 153101 bytes
Input file size = 153395 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 129350
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 = 129350
Output IDAT size = 129350 bytes (23751 bytes decrease)
Output file size = 129428 bytes (23967 bytes = 15.62% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/pca_plot-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 49834 bytes
Input file size = 49984 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 44377
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 = 44377
Output IDAT size = 44377 bytes (5457 bytes decrease)
Output file size = 44455 bytes (5529 bytes = 11.06% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/tsne_plot-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 46427 bytes
Input file size = 46565 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 41438
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 = 41438
Output IDAT size = 41438 bytes (4989 bytes decrease)
Output file size = 41516 bytes (5049 bytes = 10.84% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/umap_plot-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 32927 bytes
Input file size = 33053 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 30617
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 = 30617
Output IDAT size = 30617 bytes (2310 bytes decrease)
Output file size = 30695 bytes (2358 bytes = 7.13% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/dendro_plot-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 28540 bytes
Input file size = 28654 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 27759
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 = 27030
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 = 27030
Output IDAT size = 27030 bytes (1510 bytes decrease)
Output file size = 27108 bytes (1546 bytes = 5.40% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/venn_plot-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 48285 bytes
Input file size = 48423 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 35466
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 = 35466
Output IDAT size = 35466 bytes (12819 bytes decrease)
Output file size = 35544 bytes (12879 bytes = 26.60% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/upsetr_plot-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 23163 bytes
Input file size = 23265 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 19383
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 = 19383
Output IDAT size = 19383 bytes (3780 bytes decrease)
Output file size = 19461 bytes (3804 bytes = 16.35% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/flower_plot-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 23216 bytes
Input file size = 23318 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 18323
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 = 18323
Output IDAT size = 18323 bytes (4893 bytes decrease)
Output file size = 18401 bytes (4917 bytes = 21.09% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/volcano_plot-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 80024 bytes
Input file size = 80210 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 67402
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 = 67402
Output IDAT size = 67402 bytes (12622 bytes decrease)
Output file size = 67480 bytes (12730 bytes = 15.87% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/ma_plot-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 123201 bytes
Input file size = 123459 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 103207
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 = 103207
Output IDAT size = 103207 bytes (19994 bytes decrease)
Output file size = 103285 bytes (20174 bytes = 16.34% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/heatmap_group-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 132718 bytes
Input file size = 132988 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 110862
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 = 110862
Output IDAT size = 110862 bytes (21856 bytes decrease)
Output file size = 110940 bytes (22048 bytes = 16.58% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/circos_heatmap-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 124880 bytes
Input file size = 125138 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 104038
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 = 104038
Output IDAT size = 104038 bytes (20842 bytes decrease)
Output file size = 104116 bytes (21022 bytes = 16.80% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/chord_plot-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 160476 bytes
Input file size = 160782 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 110265
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 = 110265
Output IDAT size = 110265 bytes (50211 bytes decrease)
Output file size = 110343 bytes (50439 bytes = 31.37% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/gene_rank_plot-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 69962 bytes
Input file size = 70136 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 60362
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 = 60362
Output IDAT size = 60362 bytes (9600 bytes decrease)
Output file size = 60440 bytes (9696 bytes = 13.82% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/gene_cluster_trend-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 129384 bytes
Input file size = 129642 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 122749
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 = 122749
Output IDAT size = 122749 bytes (6635 bytes decrease)
Output file size = 122827 bytes (6815 bytes = 5.26% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/trend_plot-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 76572 bytes
Input file size = 76758 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 70463
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 = 70463
Output IDAT size = 70463 bytes (6109 bytes decrease)
Output file size = 70541 bytes (6217 bytes = 8.10% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/network_plot-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 141415 bytes
Input file size = 141697 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 96058
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 = 96058
Output IDAT size = 96058 bytes (45357 bytes decrease)
Output file size = 96136 bytes (45561 bytes = 32.15% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/heatmap_cluster-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 83800 bytes
Input file size = 83998 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 66636
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 = 66636
Output IDAT size = 66636 bytes (17164 bytes decrease)
Output file size = 66714 bytes (17284 bytes = 20.58% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/heatmap_cluster-2.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 37464 bytes
Input file size = 37590 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 30711
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 = 30711
Output IDAT size = 30711 bytes (6753 bytes decrease)
Output file size = 30789 bytes (6801 bytes = 18.09% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/heatmap_cluster-3.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 114394 bytes
Input file size = 114628 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 94726
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 = 94726
Output IDAT size = 94726 bytes (19668 bytes decrease)
Output file size = 94804 bytes (19824 bytes = 17.29% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/go_enrich_stat-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 122817 bytes
Input file size = 123063 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 99181
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 = 99181
Output IDAT size = 99181 bytes (23636 bytes decrease)
Output file size = 99259 bytes (23804 bytes = 19.34% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/go_enrich_bar-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 81382 bytes
Input file size = 81568 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 67225
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 = 67225
Output IDAT size = 67225 bytes (14157 bytes decrease)
Output file size = 67303 bytes (14265 bytes = 17.49% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/go_enrich_dot-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 90067 bytes
Input file size = 90265 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 74766
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 = 74766
Output IDAT size = 74766 bytes (15301 bytes decrease)
Output file size = 74844 bytes (15421 bytes = 17.08% decrease)
Quitting from lines 1146-1162 [go_enrich_net] (Tutorials.Rmd)
Error: processing vignette 'Tutorials.Rmd' failed with diagnostics:
'list' object cannot be coerced to type 'integer'
--- failed re-building ‘Tutorials.Rmd’
SUMMARY: processing the following file failed:
‘Tutorials.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 2.0.0
Check: examples
Result: ERROR
Running examples in ‘TOmicsVis-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: go_enrich_net
> ### Title: GO enrichment analysis and net plot (None/Exist Reference
> ### Genome).
> ### Aliases: go_enrich_net
>
> ### ** Examples
>
> # 1. Library TOmicsVis package
> library(TOmicsVis)
>
> # 2. Use example dataset
> data(gene_go_kegg)
> head(gene_go_kegg)
Genes
1 FN1
2 14-3-3ZETA
3 A1I3
4 A2M
5 AARS
6 ABAT
biological_process
1 GO:0003181(atrioventricular valve morphogenesis);GO:0003128(heart field specification);GO:0001756(somitogenesis)
2 <NA>
3 <NA>
4 <NA>
5 GO:0006419(alanyl-tRNA aminoacylation)
6 GO:0009448(gamma-aminobutyric acid metabolic process)
cellular_component
1 GO:0005576(extracellular region)
2 <NA>
3 GO:0005615(extracellular space)
4 GO:0005615(extracellular space)
5 GO:0005737(cytoplasm)
6 <NA>
molecular_function
1 <NA>
2 GO:0019904(protein domain specific binding)
3 GO:0004866(endopeptidase inhibitor activity)
4 GO:0004866(endopeptidase inhibitor activity)
5 GO:0004813(alanine-tRNA ligase activity);GO:0005524(ATP binding);GO:0000049(tRNA binding);GO:0008270(zinc ion binding)
6 GO:0003867(4-aminobutyrate transaminase activity);GO:0030170(pyridoxal phosphate binding)
kegg_pathway
1 ko04810(Regulation of actin cytoskeleton);ko04510(Focal adhesion);ko04151(PI3K-Akt signaling pathway);ko04512(ECM-receptor interaction)
2 ko04110(Cell cycle);ko04114(Oocyte meiosis);ko04390(Hippo signaling pathway);ko04391(Hippo signaling pathway -fly);ko04013(MAPK signaling pathway - fly);ko04151(PI3K-Akt signaling pathway);ko04212(Longevity regulating pathway - worm)
3 ko04610(Complement and coagulation cascades)
4 ko04610(Complement and coagulation cascades)
5 ko00970(Aminoacyl-tRNA biosynthesis)
6 ko00250(Alanine, aspartate and glutamate metabolism);ko00280(Valine, leucine and isoleucine degradation);ko00650(Butanoate metabolism);ko00640(Propanoate metabolism);ko00410(beta-Alanine metabolism);ko04727(GABAergic synapse)
>
> # 3. Default parameters
> go_enrich_net(gene_go_kegg[,-5], gene_go_kegg[100:200,1])
Warning: Expected 2 pieces. Additional pieces discarded in 82 rows [714, 928, 1523,
1543, 2042, 2191, 2192, 2193, 2194, 2195, 2197, 2198, 2200, 2202, 2203, 2205,
2206, 2207, 2208, 2552, ...].
Error in storage.mode(mat) <- "integer" :
'list' object cannot be coerced to type 'integer'
Calls: go_enrich_net ... ggplot.igraph -> setNames -> as.data.frame -> layout
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
chord_plot 6.503 1.320 9.925
circos_heatmap 3.707 0.775 6.062
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 2.0.0
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘Tutorials.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/quantile_plot-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 41924 bytes
Input file size = 42062 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 38517
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 = 38517
Output IDAT size = 38517 bytes (3407 bytes decrease)
Output file size = 38595 bytes (3467 bytes = 8.24% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/box_plot-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 56909 bytes
Input file size = 57059 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 46779
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 = 46779
Output IDAT size = 46779 bytes (10130 bytes decrease)
Output file size = 46857 bytes (10202 bytes = 17.88% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/violin_plot-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 45016 bytes
Input file size = 45154 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 42388
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 = 41850
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 = 41850
Output IDAT size = 41850 bytes (3166 bytes decrease)
Output file size = 41928 bytes (3226 bytes = 7.14% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/survival_plot-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 58889 bytes
Input file size = 59051 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 48780
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 = 48780
Output IDAT size = 48780 bytes (10109 bytes decrease)
Output file size = 48858 bytes (10193 bytes = 17.26% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/corr_heatmap-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 153101 bytes
Input file size = 153395 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 129350
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 = 129350
Output IDAT size = 129350 bytes (23751 bytes decrease)
Output file size = 129428 bytes (23967 bytes = 15.62% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/pca_plot-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 49834 bytes
Input file size = 49984 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 44377
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 = 44377
Output IDAT size = 44377 bytes (5457 bytes decrease)
Output file size = 44455 bytes (5529 bytes = 11.06% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/tsne_plot-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 46427 bytes
Input file size = 46565 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 41438
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 = 41438
Output IDAT size = 41438 bytes (4989 bytes decrease)
Output file size = 41516 bytes (5049 bytes = 10.84% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/umap_plot-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 32927 bytes
Input file size = 33053 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 30617
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 = 30617
Output IDAT size = 30617 bytes (2310 bytes decrease)
Output file size = 30695 bytes (2358 bytes = 7.13% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/dendro_plot-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 28540 bytes
Input file size = 28654 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 27759
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 = 27030
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 = 27030
Output IDAT size = 27030 bytes (1510 bytes decrease)
Output file size = 27108 bytes (1546 bytes = 5.40% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/venn_plot-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 48285 bytes
Input file size = 48423 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 35466
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 = 35466
Output IDAT size = 35466 bytes (12819 bytes decrease)
Output file size = 35544 bytes (12879 bytes = 26.60% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/upsetr_plot-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 23163 bytes
Input file size = 23265 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 19383
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 = 19383
Output IDAT size = 19383 bytes (3780 bytes decrease)
Output file size = 19461 bytes (3804 bytes = 16.35% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/flower_plot-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 23216 bytes
Input file size = 23318 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 18323
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 = 18323
Output IDAT size = 18323 bytes (4893 bytes decrease)
Output file size = 18401 bytes (4917 bytes = 21.09% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/volcano_plot-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 80024 bytes
Input file size = 80210 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 67402
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 = 67402
Output IDAT size = 67402 bytes (12622 bytes decrease)
Output file size = 67480 bytes (12730 bytes = 15.87% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/ma_plot-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 123201 bytes
Input file size = 123459 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 103207
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 = 103207
Output IDAT size = 103207 bytes (19994 bytes decrease)
Output file size = 103285 bytes (20174 bytes = 16.34% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/heatmap_group-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 132718 bytes
Input file size = 132988 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 110862
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 = 110862
Output IDAT size = 110862 bytes (21856 bytes decrease)
Output file size = 110940 bytes (22048 bytes = 16.58% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/circos_heatmap-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 124880 bytes
Input file size = 125138 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 104038
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 = 104038
Output IDAT size = 104038 bytes (20842 bytes decrease)
Output file size = 104116 bytes (21022 bytes = 16.80% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/chord_plot-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 159288 bytes
Input file size = 159594 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 110212
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 = 110212
Output IDAT size = 110212 bytes (49076 bytes decrease)
Output file size = 110290 bytes (49304 bytes = 30.89% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/gene_rank_plot-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 69962 bytes
Input file size = 70136 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 60362
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 = 60362
Output IDAT size = 60362 bytes (9600 bytes decrease)
Output file size = 60440 bytes (9696 bytes = 13.82% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/gene_cluster_trend-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 129384 bytes
Input file size = 129642 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 122749
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 = 122749
Output IDAT size = 122749 bytes (6635 bytes decrease)
Output file size = 122827 bytes (6815 bytes = 5.26% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/trend_plot-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 76572 bytes
Input file size = 76758 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 70463
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 = 70463
Output IDAT size = 70463 bytes (6109 bytes decrease)
Output file size = 70541 bytes (6217 bytes = 8.10% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/network_plot-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 141415 bytes
Input file size = 141697 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 96058
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 = 96058
Output IDAT size = 96058 bytes (45357 bytes decrease)
Output file size = 96136 bytes (45561 bytes = 32.15% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/heatmap_cluster-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 83800 bytes
Input file size = 83998 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 66636
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 = 66636
Output IDAT size = 66636 bytes (17164 bytes decrease)
Output file size = 66714 bytes (17284 bytes = 20.58% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/heatmap_cluster-2.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 37464 bytes
Input file size = 37590 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 30711
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 = 30711
Output IDAT size = 30711 bytes (6753 bytes decrease)
Output file size = 30789 bytes (6801 bytes = 18.09% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/heatmap_cluster-3.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 114394 bytes
Input file size = 114628 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 94726
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 = 94726
Output IDAT size = 94726 bytes (19668 bytes decrease)
Output file size = 94804 bytes (19824 bytes = 17.29% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/go_enrich_stat-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 122817 bytes
Input file size = 123063 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 99181
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 = 99181
Output IDAT size = 99181 bytes (23636 bytes decrease)
Output file size = 99259 bytes (23804 bytes = 19.34% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/go_enrich_bar-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 81382 bytes
Input file size = 81568 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 67225
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 = 67225
Output IDAT size = 67225 bytes (14157 bytes decrease)
Output file size = 67303 bytes (14265 bytes = 17.49% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/go_enrich_dot-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 90067 bytes
Input file size = 90265 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 74766
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 = 74766
Output IDAT size = 74766 bytes (15301 bytes decrease)
Output file size = 74844 bytes (15421 bytes = 17.08% decrease)
Quitting from lines 1146-1162 [go_enrich_net] (Tutorials.Rmd)
Error: processing vignette 'Tutorials.Rmd' failed with diagnostics:
'list' object cannot be coerced to type 'integer'
--- failed re-building ‘Tutorials.Rmd’
SUMMARY: processing the following file failed:
‘Tutorials.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 2.0.0
Check: examples
Result: ERROR
Running examples in ‘TOmicsVis-Ex.R’ failed
The error most likely occurred in:
> ### Name: go_enrich_net
> ### Title: GO enrichment analysis and net plot (None/Exist Reference
> ### Genome).
> ### Aliases: go_enrich_net
>
> ### ** Examples
>
> # 1. Library TOmicsVis package
> library(TOmicsVis)
>
> # 2. Use example dataset
> data(gene_go_kegg)
> head(gene_go_kegg)
Genes
1 FN1
2 14-3-3ZETA
3 A1I3
4 A2M
5 AARS
6 ABAT
biological_process
1 GO:0003181(atrioventricular valve morphogenesis);GO:0003128(heart field specification);GO:0001756(somitogenesis)
2 <NA>
3 <NA>
4 <NA>
5 GO:0006419(alanyl-tRNA aminoacylation)
6 GO:0009448(gamma-aminobutyric acid metabolic process)
cellular_component
1 GO:0005576(extracellular region)
2 <NA>
3 GO:0005615(extracellular space)
4 GO:0005615(extracellular space)
5 GO:0005737(cytoplasm)
6 <NA>
molecular_function
1 <NA>
2 GO:0019904(protein domain specific binding)
3 GO:0004866(endopeptidase inhibitor activity)
4 GO:0004866(endopeptidase inhibitor activity)
5 GO:0004813(alanine-tRNA ligase activity);GO:0005524(ATP binding);GO:0000049(tRNA binding);GO:0008270(zinc ion binding)
6 GO:0003867(4-aminobutyrate transaminase activity);GO:0030170(pyridoxal phosphate binding)
kegg_pathway
1 ko04810(Regulation of actin cytoskeleton);ko04510(Focal adhesion);ko04151(PI3K-Akt signaling pathway);ko04512(ECM-receptor interaction)
2 ko04110(Cell cycle);ko04114(Oocyte meiosis);ko04390(Hippo signaling pathway);ko04391(Hippo signaling pathway -fly);ko04013(MAPK signaling pathway - fly);ko04151(PI3K-Akt signaling pathway);ko04212(Longevity regulating pathway - worm)
3 ko04610(Complement and coagulation cascades)
4 ko04610(Complement and coagulation cascades)
5 ko00970(Aminoacyl-tRNA biosynthesis)
6 ko00250(Alanine, aspartate and glutamate metabolism);ko00280(Valine, leucine and isoleucine degradation);ko00650(Butanoate metabolism);ko00640(Propanoate metabolism);ko00410(beta-Alanine metabolism);ko04727(GABAergic synapse)
>
> # 3. Default parameters
> go_enrich_net(gene_go_kegg[,-5], gene_go_kegg[100:200,1])
Warning: Expected 2 pieces. Additional pieces discarded in 82 rows [714, 928, 1523,
1543, 2042, 2191, 2192, 2193, 2194, 2195, 2197, 2198, 2200, 2202, 2203, 2205,
2206, 2207, 2208, 2552, ...].
Error in storage.mode(mat) <- "integer" :
'list' object cannot be coerced to type 'integer'
Calls: go_enrich_net ... cnetplot -> cnetplot.list -> ggplot -> ggplot.igraph -> layout
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Version: 2.0.0
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘Tutorials.Rmd’ using rmarkdown
** Processing: /data/gannet/ripley/R/packages/tests-clang/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/quantile_plot-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 41924 bytes
Input file size = 42062 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 38517
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 = 38517
Output IDAT size = 38517 bytes (3407 bytes decrease)
Output file size = 38595 bytes (3467 bytes = 8.24% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/box_plot-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 56909 bytes
Input file size = 57059 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 46779
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 = 46779
Output IDAT size = 46779 bytes (10130 bytes decrease)
Output file size = 46857 bytes (10202 bytes = 17.88% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/violin_plot-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 45027 bytes
Input file size = 45165 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 42401
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 = 41855
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 = 41855
Output IDAT size = 41855 bytes (3172 bytes decrease)
Output file size = 41933 bytes (3232 bytes = 7.16% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/survival_plot-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 58889 bytes
Input file size = 59051 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 48780
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 = 48780
Output IDAT size = 48780 bytes (10109 bytes decrease)
Output file size = 48858 bytes (10193 bytes = 17.26% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/corr_heatmap-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 153101 bytes
Input file size = 153395 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 129350
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 = 129350
Output IDAT size = 129350 bytes (23751 bytes decrease)
Output file size = 129428 bytes (23967 bytes = 15.62% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/pca_plot-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 49856 bytes
Input file size = 50006 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 44423
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 = 44423
Output IDAT size = 44423 bytes (5433 bytes decrease)
Output file size = 44501 bytes (5505 bytes = 11.01% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/tsne_plot-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 46458 bytes
Input file size = 46596 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 41388
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 = 41388
Output IDAT size = 41388 bytes (5070 bytes decrease)
Output file size = 41466 bytes (5130 bytes = 11.01% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/umap_plot-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 34023 bytes
Input file size = 34149 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 30907
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 = 30907
Output IDAT size = 30907 bytes (3116 bytes decrease)
Output file size = 30985 bytes (3164 bytes = 9.27% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/dendro_plot-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 28540 bytes
Input file size = 28654 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 27759
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 = 27030
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 = 27030
Output IDAT size = 27030 bytes (1510 bytes decrease)
Output file size = 27108 bytes (1546 bytes = 5.40% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/venn_plot-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 48285 bytes
Input file size = 48423 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 35466
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 = 35466
Output IDAT size = 35466 bytes (12819 bytes decrease)
Output file size = 35544 bytes (12879 bytes = 26.60% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/upsetr_plot-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 23163 bytes
Input file size = 23265 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 19383
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 = 19383
Output IDAT size = 19383 bytes (3780 bytes decrease)
Output file size = 19461 bytes (3804 bytes = 16.35% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/flower_plot-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 23203 bytes
Input file size = 23305 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 18304
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 = 18304
Output IDAT size = 18304 bytes (4899 bytes decrease)
Output file size = 18382 bytes (4923 bytes = 21.12% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/volcano_plot-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 80024 bytes
Input file size = 80210 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 67402
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 = 67402
Output IDAT size = 67402 bytes (12622 bytes decrease)
Output file size = 67480 bytes (12730 bytes = 15.87% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/ma_plot-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 123184 bytes
Input file size = 123442 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 103213
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 = 103213
Output IDAT size = 103213 bytes (19971 bytes decrease)
Output file size = 103291 bytes (20151 bytes = 16.32% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/heatmap_group-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 132718 bytes
Input file size = 132988 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 110862
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 = 110862
Output IDAT size = 110862 bytes (21856 bytes decrease)
Output file size = 110940 bytes (22048 bytes = 16.58% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/circos_heatmap-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 124879 bytes
Input file size = 125137 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 104047
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 = 104047
Output IDAT size = 104047 bytes (20832 bytes decrease)
Output file size = 104125 bytes (21012 bytes = 16.79% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/chord_plot-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 162113 bytes
Input file size = 162419 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 110245
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 = 110245
Output IDAT size = 110245 bytes (51868 bytes decrease)
Output file size = 110323 bytes (52096 bytes = 32.08% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/gene_rank_plot-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 69962 bytes
Input file size = 70136 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 60362
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 = 60362
Output IDAT size = 60362 bytes (9600 bytes decrease)
Output file size = 60440 bytes (9696 bytes = 13.82% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/gene_cluster_trend-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 129393 bytes
Input file size = 129651 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 122773
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 = 122773
Output IDAT size = 122773 bytes (6620 bytes decrease)
Output file size = 122851 bytes (6800 bytes = 5.24% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/trend_plot-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 76574 bytes
Input file size = 76760 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 70464
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 = 70464
Output IDAT size = 70464 bytes (6110 bytes decrease)
Output file size = 70542 bytes (6218 bytes = 8.10% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/network_plot-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 141417 bytes
Input file size = 141699 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 96058
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 = 96058
Output IDAT size = 96058 bytes (45359 bytes decrease)
Output file size = 96136 bytes (45563 bytes = 32.15% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/heatmap_cluster-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 83800 bytes
Input file size = 83998 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 66636
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 = 66636
Output IDAT size = 66636 bytes (17164 bytes decrease)
Output file size = 66714 bytes (17284 bytes = 20.58% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/heatmap_cluster-2.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 37464 bytes
Input file size = 37590 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 30711
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 = 30711
Output IDAT size = 30711 bytes (6753 bytes decrease)
Output file size = 30789 bytes (6801 bytes = 18.09% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/heatmap_cluster-3.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 114382 bytes
Input file size = 114616 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 94722
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 = 94722
Output IDAT size = 94722 bytes (19660 bytes decrease)
Output file size = 94800 bytes (19816 bytes = 17.29% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/go_enrich_stat-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 122817 bytes
Input file size = 123063 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 99181
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 = 99181
Output IDAT size = 99181 bytes (23636 bytes decrease)
Output file size = 99259 bytes (23804 bytes = 19.34% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/go_enrich_bar-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 81382 bytes
Input file size = 81568 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 67225
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 = 67225
Output IDAT size = 67225 bytes (14157 bytes decrease)
Output file size = 67303 bytes (14265 bytes = 17.49% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/go_enrich_dot-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 90067 bytes
Input file size = 90265 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 74766
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 = 74766
Output IDAT size = 74766 bytes (15301 bytes decrease)
Output file size = 74844 bytes (15421 bytes = 17.08% decrease)
Quitting from lines 1146-1162 [go_enrich_net] (Tutorials.Rmd)
Error: processing vignette 'Tutorials.Rmd' failed with diagnostics:
'list' object cannot be coerced to type 'integer'
--- failed re-building ‘Tutorials.Rmd’
SUMMARY: processing the following file failed:
‘Tutorials.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 2.0.0
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘Tutorials.Rmd’ using rmarkdown
** Processing: /data/gannet/ripley/R/packages/tests-devel/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/quantile_plot-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 41924 bytes
Input file size = 42062 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 38517
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 = 38517
Output IDAT size = 38517 bytes (3407 bytes decrease)
Output file size = 38595 bytes (3467 bytes = 8.24% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/box_plot-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 56909 bytes
Input file size = 57059 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 46779
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 = 46779
Output IDAT size = 46779 bytes (10130 bytes decrease)
Output file size = 46857 bytes (10202 bytes = 17.88% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/violin_plot-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 45027 bytes
Input file size = 45165 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 42401
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 = 41855
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 = 41855
Output IDAT size = 41855 bytes (3172 bytes decrease)
Output file size = 41933 bytes (3232 bytes = 7.16% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/survival_plot-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 58889 bytes
Input file size = 59051 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 48780
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 = 48780
Output IDAT size = 48780 bytes (10109 bytes decrease)
Output file size = 48858 bytes (10193 bytes = 17.26% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/corr_heatmap-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 153101 bytes
Input file size = 153395 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 129350
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 = 129350
Output IDAT size = 129350 bytes (23751 bytes decrease)
Output file size = 129428 bytes (23967 bytes = 15.62% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/pca_plot-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 49856 bytes
Input file size = 50006 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 44423
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 = 44423
Output IDAT size = 44423 bytes (5433 bytes decrease)
Output file size = 44501 bytes (5505 bytes = 11.01% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/tsne_plot-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 51499 bytes
Input file size = 51649 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 46730
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 = 46730
Output IDAT size = 46730 bytes (4769 bytes decrease)
Output file size = 46808 bytes (4841 bytes = 9.37% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/umap_plot-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 34023 bytes
Input file size = 34149 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 30907
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 = 30907
Output IDAT size = 30907 bytes (3116 bytes decrease)
Output file size = 30985 bytes (3164 bytes = 9.27% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/dendro_plot-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 28540 bytes
Input file size = 28654 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 27759
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 = 27030
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 = 27030
Output IDAT size = 27030 bytes (1510 bytes decrease)
Output file size = 27108 bytes (1546 bytes = 5.40% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/venn_plot-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 48285 bytes
Input file size = 48423 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 35466
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 = 35466
Output IDAT size = 35466 bytes (12819 bytes decrease)
Output file size = 35544 bytes (12879 bytes = 26.60% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/upsetr_plot-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 23163 bytes
Input file size = 23265 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 19383
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 = 19383
Output IDAT size = 19383 bytes (3780 bytes decrease)
Output file size = 19461 bytes (3804 bytes = 16.35% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/flower_plot-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 23203 bytes
Input file size = 23305 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 18304
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 = 18304
Output IDAT size = 18304 bytes (4899 bytes decrease)
Output file size = 18382 bytes (4923 bytes = 21.12% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/volcano_plot-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 80024 bytes
Input file size = 80210 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 67402
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 = 67402
Output IDAT size = 67402 bytes (12622 bytes decrease)
Output file size = 67480 bytes (12730 bytes = 15.87% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/ma_plot-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 123284 bytes
Input file size = 123542 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 103467
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 = 103467
Output IDAT size = 103467 bytes (19817 bytes decrease)
Output file size = 103545 bytes (19997 bytes = 16.19% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/heatmap_group-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 132718 bytes
Input file size = 132988 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 110862
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 = 110862
Output IDAT size = 110862 bytes (21856 bytes decrease)
Output file size = 110940 bytes (22048 bytes = 16.58% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/circos_heatmap-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 124879 bytes
Input file size = 125137 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 104047
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 = 104047
Output IDAT size = 104047 bytes (20832 bytes decrease)
Output file size = 104125 bytes (21012 bytes = 16.79% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/chord_plot-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 159450 bytes
Input file size = 159756 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 110334
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 = 110334
Output IDAT size = 110334 bytes (49116 bytes decrease)
Output file size = 110412 bytes (49344 bytes = 30.89% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/gene_rank_plot-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 69962 bytes
Input file size = 70136 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 60362
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 = 60362
Output IDAT size = 60362 bytes (9600 bytes decrease)
Output file size = 60440 bytes (9696 bytes = 13.82% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/gene_cluster_trend-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 129393 bytes
Input file size = 129651 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 122773
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 = 122773
Output IDAT size = 122773 bytes (6620 bytes decrease)
Output file size = 122851 bytes (6800 bytes = 5.24% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/trend_plot-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 76574 bytes
Input file size = 76760 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 70464
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 = 70464
Output IDAT size = 70464 bytes (6110 bytes decrease)
Output file size = 70542 bytes (6218 bytes = 8.10% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/network_plot-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 141417 bytes
Input file size = 141699 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 96058
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 = 96058
Output IDAT size = 96058 bytes (45359 bytes decrease)
Output file size = 96136 bytes (45563 bytes = 32.15% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/heatmap_cluster-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 83800 bytes
Input file size = 83998 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 66636
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 = 66636
Output IDAT size = 66636 bytes (17164 bytes decrease)
Output file size = 66714 bytes (17284 bytes = 20.58% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/heatmap_cluster-2.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 37464 bytes
Input file size = 37590 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 30711
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 = 30711
Output IDAT size = 30711 bytes (6753 bytes decrease)
Output file size = 30789 bytes (6801 bytes = 18.09% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/heatmap_cluster-3.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 114382 bytes
Input file size = 114616 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 94722
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 = 94722
Output IDAT size = 94722 bytes (19660 bytes decrease)
Output file size = 94800 bytes (19816 bytes = 17.29% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/go_enrich_stat-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 122817 bytes
Input file size = 123063 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 99181
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 = 99181
Output IDAT size = 99181 bytes (23636 bytes decrease)
Output file size = 99259 bytes (23804 bytes = 19.34% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/go_enrich_bar-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 81382 bytes
Input file size = 81568 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 67225
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 = 67225
Output IDAT size = 67225 bytes (14157 bytes decrease)
Output file size = 67303 bytes (14265 bytes = 17.49% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/go_enrich_dot-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 90067 bytes
Input file size = 90265 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 74766
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 = 74766
Output IDAT size = 74766 bytes (15301 bytes decrease)
Output file size = 74844 bytes (15421 bytes = 17.08% decrease)
Quitting from lines 1146-1162 [go_enrich_net] (Tutorials.Rmd)
Error: processing vignette 'Tutorials.Rmd' failed with diagnostics:
'list' object cannot be coerced to type 'integer'
--- failed re-building ‘Tutorials.Rmd’
SUMMARY: processing the following file failed:
‘Tutorials.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 2.0.0
Check: examples
Result: ERROR
Running examples in ‘TOmicsVis-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: go_enrich_net
> ### Title: GO enrichment analysis and net plot (None/Exist Reference
> ### Genome).
> ### Aliases: go_enrich_net
>
> ### ** Examples
>
> # 1. Library TOmicsVis package
> library(TOmicsVis)
>
> # 2. Use example dataset
> data(gene_go_kegg)
> head(gene_go_kegg)
Genes
1 FN1
2 14-3-3ZETA
3 A1I3
4 A2M
5 AARS
6 ABAT
biological_process
1 GO:0003181(atrioventricular valve morphogenesis);GO:0003128(heart field specification);GO:0001756(somitogenesis)
2 <NA>
3 <NA>
4 <NA>
5 GO:0006419(alanyl-tRNA aminoacylation)
6 GO:0009448(gamma-aminobutyric acid metabolic process)
cellular_component
1 GO:0005576(extracellular region)
2 <NA>
3 GO:0005615(extracellular space)
4 GO:0005615(extracellular space)
5 GO:0005737(cytoplasm)
6 <NA>
molecular_function
1 <NA>
2 GO:0019904(protein domain specific binding)
3 GO:0004866(endopeptidase inhibitor activity)
4 GO:0004866(endopeptidase inhibitor activity)
5 GO:0004813(alanine-tRNA ligase activity);GO:0005524(ATP binding);GO:0000049(tRNA binding);GO:0008270(zinc ion binding)
6 GO:0003867(4-aminobutyrate transaminase activity);GO:0030170(pyridoxal phosphate binding)
kegg_pathway
1 ko04810(Regulation of actin cytoskeleton);ko04510(Focal adhesion);ko04151(PI3K-Akt signaling pathway);ko04512(ECM-receptor interaction)
2 ko04110(Cell cycle);ko04114(Oocyte meiosis);ko04390(Hippo signaling pathway);ko04391(Hippo signaling pathway -fly);ko04013(MAPK signaling pathway - fly);ko04151(PI3K-Akt signaling pathway);ko04212(Longevity regulating pathway - worm)
3 ko04610(Complement and coagulation cascades)
4 ko04610(Complement and coagulation cascades)
5 ko00970(Aminoacyl-tRNA biosynthesis)
6 ko00250(Alanine, aspartate and glutamate metabolism);ko00280(Valine, leucine and isoleucine degradation);ko00650(Butanoate metabolism);ko00640(Propanoate metabolism);ko00410(beta-Alanine metabolism);ko04727(GABAergic synapse)
>
> # 3. Default parameters
> go_enrich_net(gene_go_kegg[,-5], gene_go_kegg[100:200,1])
Warning: Expected 2 pieces. Additional pieces discarded in 82 rows [714, 928, 1523,
1543, 2042, 2191, 2192, 2193, 2194, 2195, 2197, 2198, 2200, 2202, 2203, 2205,
2206, 2207, 2208, 2552, ...].
Error in storage.mode(mat) <- "integer" :
'list' object cannot be coerced to type 'integer'
Calls: go_enrich_net ... ggplot.igraph -> setNames -> as.data.frame -> layout
Execution halted
Flavors: r-patched-linux-x86_64, r-release-linux-x86_64
Version: 2.0.0
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘Tutorials.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/quantile_plot-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 41924 bytes
Input file size = 42062 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 38517
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 = 38517
Output IDAT size = 38517 bytes (3407 bytes decrease)
Output file size = 38595 bytes (3467 bytes = 8.24% decrease)
** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/box_plot-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 56909 bytes
Input file size = 57059 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 46779
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 = 46779
Output IDAT size = 46779 bytes (10130 bytes decrease)
Output file size = 46857 bytes (10202 bytes = 17.88% decrease)
** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/violin_plot-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 45016 bytes
Input file size = 45154 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 42388
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 = 41850
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 = 41850
Output IDAT size = 41850 bytes (3166 bytes decrease)
Output file size = 41928 bytes (3226 bytes = 7.14% decrease)
** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/survival_plot-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 58889 bytes
Input file size = 59051 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 48780
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 = 48780
Output IDAT size = 48780 bytes (10109 bytes decrease)
Output file size = 48858 bytes (10193 bytes = 17.26% decrease)
** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/corr_heatmap-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 153101 bytes
Input file size = 153395 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 129350
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 = 129350
Output IDAT size = 129350 bytes (23751 bytes decrease)
Output file size = 129428 bytes (23967 bytes = 15.62% decrease)
** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/pca_plot-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 49834 bytes
Input file size = 49984 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 44377
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 = 44377
Output IDAT size = 44377 bytes (5457 bytes decrease)
Output file size = 44455 bytes (5529 bytes = 11.06% decrease)
** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/tsne_plot-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 46427 bytes
Input file size = 46565 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 41438
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 = 41438
Output IDAT size = 41438 bytes (4989 bytes decrease)
Output file size = 41516 bytes (5049 bytes = 10.84% decrease)
** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/umap_plot-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 32927 bytes
Input file size = 33053 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 30617
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 = 30617
Output IDAT size = 30617 bytes (2310 bytes decrease)
Output file size = 30695 bytes (2358 bytes = 7.13% decrease)
** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/dendro_plot-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 28540 bytes
Input file size = 28654 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 27759
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 = 27030
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 = 27030
Output IDAT size = 27030 bytes (1510 bytes decrease)
Output file size = 27108 bytes (1546 bytes = 5.40% decrease)
** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/venn_plot-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 48285 bytes
Input file size = 48423 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 35466
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 = 35466
Output IDAT size = 35466 bytes (12819 bytes decrease)
Output file size = 35544 bytes (12879 bytes = 26.60% decrease)
** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/upsetr_plot-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 23163 bytes
Input file size = 23265 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 19383
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 = 19383
Output IDAT size = 19383 bytes (3780 bytes decrease)
Output file size = 19461 bytes (3804 bytes = 16.35% decrease)
** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/flower_plot-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 23216 bytes
Input file size = 23318 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 18323
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 = 18323
Output IDAT size = 18323 bytes (4893 bytes decrease)
Output file size = 18401 bytes (4917 bytes = 21.09% decrease)
** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/volcano_plot-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 80024 bytes
Input file size = 80210 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 67402
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 = 67402
Output IDAT size = 67402 bytes (12622 bytes decrease)
Output file size = 67480 bytes (12730 bytes = 15.87% decrease)
** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/ma_plot-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 123201 bytes
Input file size = 123459 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 103207
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 = 103207
Output IDAT size = 103207 bytes (19994 bytes decrease)
Output file size = 103285 bytes (20174 bytes = 16.34% decrease)
** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/heatmap_group-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 132718 bytes
Input file size = 132988 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 110862
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 = 110862
Output IDAT size = 110862 bytes (21856 bytes decrease)
Output file size = 110940 bytes (22048 bytes = 16.58% decrease)
** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/circos_heatmap-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 124880 bytes
Input file size = 125138 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 104038
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 = 104038
Output IDAT size = 104038 bytes (20842 bytes decrease)
Output file size = 104116 bytes (21022 bytes = 16.80% decrease)
** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/chord_plot-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 159861 bytes
Input file size = 160167 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 110336
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 = 110336
Output IDAT size = 110336 bytes (49525 bytes decrease)
Output file size = 110414 bytes (49753 bytes = 31.06% decrease)
** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/gene_rank_plot-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 69962 bytes
Input file size = 70136 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 60362
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 = 60362
Output IDAT size = 60362 bytes (9600 bytes decrease)
Output file size = 60440 bytes (9696 bytes = 13.82% decrease)
** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/gene_cluster_trend-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 129384 bytes
Input file size = 129642 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 122749
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 = 122749
Output IDAT size = 122749 bytes (6635 bytes decrease)
Output file size = 122827 bytes (6815 bytes = 5.26% decrease)
** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/trend_plot-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 76572 bytes
Input file size = 76758 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 70463
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 = 70463
Output IDAT size = 70463 bytes (6109 bytes decrease)
Output file size = 70541 bytes (6217 bytes = 8.10% decrease)
** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/network_plot-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 141415 bytes
Input file size = 141697 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 96058
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 = 96058
Output IDAT size = 96058 bytes (45357 bytes decrease)
Output file size = 96136 bytes (45561 bytes = 32.15% decrease)
** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/heatmap_cluster-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 83800 bytes
Input file size = 83998 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 66636
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 = 66636
Output IDAT size = 66636 bytes (17164 bytes decrease)
Output file size = 66714 bytes (17284 bytes = 20.58% decrease)
** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/heatmap_cluster-2.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 37464 bytes
Input file size = 37590 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 30711
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 = 30711
Output IDAT size = 30711 bytes (6753 bytes decrease)
Output file size = 30789 bytes (6801 bytes = 18.09% decrease)
** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/heatmap_cluster-3.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 114394 bytes
Input file size = 114628 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 94726
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 = 94726
Output IDAT size = 94726 bytes (19668 bytes decrease)
Output file size = 94804 bytes (19824 bytes = 17.29% decrease)
** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/go_enrich_stat-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 122817 bytes
Input file size = 123063 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 99181
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 = 99181
Output IDAT size = 99181 bytes (23636 bytes decrease)
Output file size = 99259 bytes (23804 bytes = 19.34% decrease)
** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/go_enrich_bar-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 81382 bytes
Input file size = 81568 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 67225
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 = 67225
Output IDAT size = 67225 bytes (14157 bytes decrease)
Output file size = 67303 bytes (14265 bytes = 17.49% decrease)
** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/go_enrich_dot-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 90067 bytes
Input file size = 90265 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 74766
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 = 74766
Output IDAT size = 74766 bytes (15301 bytes decrease)
Output file size = 74844 bytes (15421 bytes = 17.08% decrease)
Quitting from lines 1146-1162 [go_enrich_net] (Tutorials.Rmd)
Error: processing vignette 'Tutorials.Rmd' failed with diagnostics:
'list' object cannot be coerced to type 'integer'
--- failed re-building ‘Tutorials.Rmd’
SUMMARY: processing the following file failed:
‘Tutorials.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-patched-linux-x86_64
Version: 2.0.0
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘Tutorials.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/quantile_plot-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 41924 bytes
Input file size = 42062 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 38517
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 = 38517
Output IDAT size = 38517 bytes (3407 bytes decrease)
Output file size = 38595 bytes (3467 bytes = 8.24% decrease)
** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/box_plot-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 56909 bytes
Input file size = 57059 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 46779
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 = 46779
Output IDAT size = 46779 bytes (10130 bytes decrease)
Output file size = 46857 bytes (10202 bytes = 17.88% decrease)
** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/violin_plot-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 45016 bytes
Input file size = 45154 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 42388
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 = 41850
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 = 41850
Output IDAT size = 41850 bytes (3166 bytes decrease)
Output file size = 41928 bytes (3226 bytes = 7.14% decrease)
** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/survival_plot-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 58889 bytes
Input file size = 59051 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 48780
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 = 48780
Output IDAT size = 48780 bytes (10109 bytes decrease)
Output file size = 48858 bytes (10193 bytes = 17.26% decrease)
** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/corr_heatmap-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 153101 bytes
Input file size = 153395 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 129350
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 = 129350
Output IDAT size = 129350 bytes (23751 bytes decrease)
Output file size = 129428 bytes (23967 bytes = 15.62% decrease)
** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/pca_plot-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 49834 bytes
Input file size = 49984 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 44377
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 = 44377
Output IDAT size = 44377 bytes (5457 bytes decrease)
Output file size = 44455 bytes (5529 bytes = 11.06% decrease)
** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/tsne_plot-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 46427 bytes
Input file size = 46565 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 41438
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 = 41438
Output IDAT size = 41438 bytes (4989 bytes decrease)
Output file size = 41516 bytes (5049 bytes = 10.84% decrease)
** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/umap_plot-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 32927 bytes
Input file size = 33053 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 30617
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 = 30617
Output IDAT size = 30617 bytes (2310 bytes decrease)
Output file size = 30695 bytes (2358 bytes = 7.13% decrease)
** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/dendro_plot-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 28540 bytes
Input file size = 28654 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 27759
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 = 27030
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 = 27030
Output IDAT size = 27030 bytes (1510 bytes decrease)
Output file size = 27108 bytes (1546 bytes = 5.40% decrease)
** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/venn_plot-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 48285 bytes
Input file size = 48423 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 35466
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 = 35466
Output IDAT size = 35466 bytes (12819 bytes decrease)
Output file size = 35544 bytes (12879 bytes = 26.60% decrease)
** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/upsetr_plot-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 23163 bytes
Input file size = 23265 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 19383
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 = 19383
Output IDAT size = 19383 bytes (3780 bytes decrease)
Output file size = 19461 bytes (3804 bytes = 16.35% decrease)
** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/flower_plot-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 23216 bytes
Input file size = 23318 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 18323
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 = 18323
Output IDAT size = 18323 bytes (4893 bytes decrease)
Output file size = 18401 bytes (4917 bytes = 21.09% decrease)
** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/volcano_plot-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 80024 bytes
Input file size = 80210 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 67402
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 = 67402
Output IDAT size = 67402 bytes (12622 bytes decrease)
Output file size = 67480 bytes (12730 bytes = 15.87% decrease)
** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/ma_plot-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 123201 bytes
Input file size = 123459 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 103207
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 = 103207
Output IDAT size = 103207 bytes (19994 bytes decrease)
Output file size = 103285 bytes (20174 bytes = 16.34% decrease)
** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/heatmap_group-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 132718 bytes
Input file size = 132988 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 110862
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 = 110862
Output IDAT size = 110862 bytes (21856 bytes decrease)
Output file size = 110940 bytes (22048 bytes = 16.58% decrease)
** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/circos_heatmap-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 124880 bytes
Input file size = 125138 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 104038
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 = 104038
Output IDAT size = 104038 bytes (20842 bytes decrease)
Output file size = 104116 bytes (21022 bytes = 16.80% decrease)
** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/chord_plot-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 161097 bytes
Input file size = 161403 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 110398
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 = 110398
Output IDAT size = 110398 bytes (50699 bytes decrease)
Output file size = 110476 bytes (50927 bytes = 31.55% decrease)
** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/gene_rank_plot-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 69962 bytes
Input file size = 70136 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 60362
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 = 60362
Output IDAT size = 60362 bytes (9600 bytes decrease)
Output file size = 60440 bytes (9696 bytes = 13.82% decrease)
** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/gene_cluster_trend-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 129384 bytes
Input file size = 129642 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 122749
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 = 122749
Output IDAT size = 122749 bytes (6635 bytes decrease)
Output file size = 122827 bytes (6815 bytes = 5.26% decrease)
** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/trend_plot-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 76572 bytes
Input file size = 76758 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 70463
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 = 70463
Output IDAT size = 70463 bytes (6109 bytes decrease)
Output file size = 70541 bytes (6217 bytes = 8.10% decrease)
** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/network_plot-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 141415 bytes
Input file size = 141697 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 96058
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 = 96058
Output IDAT size = 96058 bytes (45357 bytes decrease)
Output file size = 96136 bytes (45561 bytes = 32.15% decrease)
** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/heatmap_cluster-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 83800 bytes
Input file size = 83998 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 66636
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 = 66636
Output IDAT size = 66636 bytes (17164 bytes decrease)
Output file size = 66714 bytes (17284 bytes = 20.58% decrease)
** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/heatmap_cluster-2.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 37464 bytes
Input file size = 37590 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 30711
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 = 30711
Output IDAT size = 30711 bytes (6753 bytes decrease)
Output file size = 30789 bytes (6801 bytes = 18.09% decrease)
** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/heatmap_cluster-3.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 114394 bytes
Input file size = 114628 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 94726
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 = 94726
Output IDAT size = 94726 bytes (19668 bytes decrease)
Output file size = 94804 bytes (19824 bytes = 17.29% decrease)
** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/go_enrich_stat-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 122817 bytes
Input file size = 123063 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 99181
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 = 99181
Output IDAT size = 99181 bytes (23636 bytes decrease)
Output file size = 99259 bytes (23804 bytes = 19.34% decrease)
** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/go_enrich_bar-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 81382 bytes
Input file size = 81568 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 67225
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 = 67225
Output IDAT size = 67225 bytes (14157 bytes decrease)
Output file size = 67303 bytes (14265 bytes = 17.49% decrease)
** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/TOmicsVis.Rcheck/vign_test/TOmicsVis/vignettes/Tutorials_files/figure-html/go_enrich_dot-1.png
960x593 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 90067 bytes
Input file size = 90265 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 74766
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 = 74766
Output IDAT size = 74766 bytes (15301 bytes decrease)
Output file size = 74844 bytes (15421 bytes = 17.08% decrease)
Quitting from lines 1146-1162 [go_enrich_net] (Tutorials.Rmd)
Error: processing vignette 'Tutorials.Rmd' failed with diagnostics:
'list' object cannot be coerced to type 'integer'
--- failed re-building ‘Tutorials.Rmd’
SUMMARY: processing the following file failed:
‘Tutorials.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-release-linux-x86_64
Version: 2.0.0
Check: installed package size
Result: NOTE
installed size is 6.4Mb
sub-directories of 1Mb or more:
data-tables 1.4Mb
doc 1.9Mb
help 1.2Mb
Flavors: r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64, r-oldrel-windows-x86_64
Version: 2.0.0
Check: package dependencies
Result: ERROR
Package required but not available: ‘EnhancedVolcano’
See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64