- using R Under development (unstable) (2024-11-06 r87293)
- using platform: x86_64-pc-linux-gnu
- R was compiled by
Debian clang version 19.1.2 (2)
Debian flang-new version 19.1.2 (2)
- running under: Debian GNU/Linux trixie/sid
- using session charset: UTF-8
- checking for file ‘TOmicsVis/DESCRIPTION’ ... OK
- checking extension type ... Package
- this is package ‘TOmicsVis’ version ‘2.0.0’
- package encoding: UTF-8
- checking package namespace information ... OK
- checking package dependencies ... OK
- checking if this is a source package ... OK
- checking if there is a namespace ... OK
- checking for executable files ... OK
- checking for hidden files and directories ... OK
- checking for portable file names ... OK
- checking for sufficient/correct file permissions ... OK
- checking whether package ‘TOmicsVis’ can be installed ... OK
See the install log for details.
- checking package directory ... OK
- checking for future file timestamps ... OK
- checking ‘build’ directory ... OK
- checking DESCRIPTION meta-information ... OK
- checking top-level files ... OK
- checking for left-over files ... OK
- checking index information ... OK
- checking package subdirectories ... OK
- checking code files for non-ASCII characters ... OK
- checking R files for syntax errors ... OK
- checking whether the package can be loaded ... [13s/17s] OK
- checking whether the package can be loaded with stated dependencies ... [12s/16s] OK
- checking whether the package can be unloaded cleanly ... [12s/16s] OK
- checking whether the namespace can be loaded with stated dependencies ... [11s/14s] OK
- checking whether the namespace can be unloaded cleanly ... [12s/16s] OK
- checking loading without being on the library search path ... [12s/16s] OK
- checking use of S3 registration ... OK
- checking dependencies in R code ... OK
- checking S3 generic/method consistency ... OK
- checking replacement functions ... OK
- checking foreign function calls ... OK
- checking R code for possible problems ... [60s/71s] OK
- checking Rd files ... [1s/1s] OK
- checking Rd metadata ... OK
- checking Rd line widths ... OK
- checking Rd cross-references ... OK
- checking for missing documentation entries ... OK
- checking for code/documentation mismatches ... OK
- checking Rd \usage sections ... OK
- checking Rd contents ... OK
- checking for unstated dependencies in examples ... OK
- checking contents of ‘data’ directory ... OK
- checking data for non-ASCII characters ... [0s/1s] OK
- checking LazyData ... OK
- checking data for ASCII and uncompressed saves ... OK
- checking installed files from ‘inst/doc’ ... OK
- checking files in ‘vignettes’ ... OK
- checking examples ... [52s/66s] 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 ... cnetplot -> cnetplot.list -> ggplot -> ggplot.igraph -> layout
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
chord_plot 11.629 0.942 17.426
circos_heatmap 6.983 0.618 8.777
- checking for unstated dependencies in vignettes ... OK
- checking package vignettes ... OK
- checking re-building of vignette outputs ... [90s/118s] 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 = 160781 bytes
Input file size = 161087 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 110318
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 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 = 110318
Output IDAT size = 110318 bytes (50463 bytes decrease)
Output file size = 110396 bytes (50691 bytes = 31.47% 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
- checking PDF version of manual ... [6s/9s] OK
- checking HTML version of manual ... [2s/4s] OK
- checking for non-standard things in the check directory ... OK
- DONE
Status: 2 ERRORs