pavian crash with example data

[ArmandBester]

Thanks again for this tool.

I am trying:

> shiny::runGitHub("fbreitwieser/pavian", subdir = "inst/shinyapp")
Downloading https://github.com/fbreitwieser/pavian/archive/HEAD.tar.gz

Listening on http://127.0.0.1:3018
The `name` provided ('sun-o') does not correspond to a known icon
[Jul04 12:20] Started new shiny session #3 ( session(s) running)
[Jul04 12:21] Reading files in /home/armand/R/x86_64-pc-linux-gnu-library/4.3/pavian/shinyapp/example-data
Warning: Error in &&: 'length = 43' in coercion to 'logical(1)'
  3: runApp
  2: runUrl
  1: shiny::runGitHub
[Jul04 12:21] Exiting session #3

I have also tried

 pavian::runApp(port=5000)

Listening on http://127.0.0.1:5000
The `name` provided ('sun-o') does not correspond to a known icon
[Jul04 12:30] Started new shiny session #1 (1 session(s) running)
[Jul04 12:31] Reading files in /home/armand/R/x86_64-pc-linux-gnu-library/4.3/pavian/shinyapp/example-data
Warning: Error in &&: 'length = 43' in coercion to 'logical(1)'
  3: runApp
  2: print.shiny.appobj
  1: <Anonymous>
[Jul04 12:31] Exiting session #1

I get the above when I load the example data on linux mint vera

Kind regards Armand

[lptolik]

I have exactly the same problem. My system is:

sessionInfo() R version 4.3.0 (2023-04-21) Platform: aarch64-apple-darwin20 (64-bit) Running under: macOS Monterey 12.5.1

Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0

locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: Asia/Tokyo tzcode source: internal

attached base packages: [1] stats graphics grDevices utils datasets methods base

other attached packages: [1] shiny_1.7.4.1 pavian_1.2.0

loaded via a namespace (and not attached): [1] sass_0.4.6 utf8_1.2.3 generics_0.1.3 shinyFileTree_0.0.0.9000 [5] digest_0.6.33 magrittr_2.0.3 rhandsontable_0.3.8 sankeyD3_0.3.2
[9] grid_4.3.0 fastmap_1.1.1 jsonlite_1.8.7 promises_1.2.0.1
[13] fansi_1.0.4 crosstalk_1.2.0 scales_1.2.1 jquerylib_0.1.4
[17] shinydashboard_0.7.2 cli_3.6.1 rlang_1.1.1 crayon_1.5.2
[21] ellipsis_0.3.2 munsell_0.5.0 cachem_1.0.8 yaml_2.3.7
[25] tools_4.3.0 memoise_2.0.1 dplyr_1.1.2 colorspace_2.1-0
[29] ggplot2_3.4.2 httpuv_1.6.11 DT_0.28 vctrs_0.6.3
[33] R6_2.5.1 mime_0.12 lifecycle_1.0.3 htmlwidgets_1.6.2
[37] fontawesome_0.5.1 shinyjs_2.1.0 pkgconfig_2.0.3 pillar_1.9.0
[41] bslib_0.5.0 later_1.3.1 gtable_0.3.3 glue_1.6.2
[45] Rcpp_1.0.11 tibble_3.2.1 tidyselect_1.2.0 rstudioapi_0.15.0
[49] xtable_1.8-4 htmltools_0.5.5 shinyWidgets_0.7.6 compiler_4.3.0

[nmflack]

Same issue!

R version 4.3.0 (2023-04-21)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Ventura 13.1

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib 
LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.11.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: Europe/Zurich
tzcode source: internal

attached base packages:
[1] stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] Rsamtools_2.16.0     Biostrings_2.68.1    XVector_0.40.0       GenomicRanges_1.52.0
 [5] GenomeInfoDb_1.36.1  IRanges_2.34.1       S4Vectors_0.38.1     BiocGenerics_0.46.0 
 [9] pavian_1.2.0         ggExtra_0.10.0       ggpubr_0.6.0         ggrepel_0.9.3       
[13] lubridate_1.9.2      forcats_1.0.0        stringr_1.5.0        dplyr_1.1.2         
[17] purrr_1.0.1          readr_2.1.4          tidyr_1.3.0          tibble_3.2.1        
[21] ggplot2_3.4.2        tidyverse_2.0.0     

loaded via a namespace (and not attached):
 [1] bitops_1.0-7             shinyFeedback_0.4.0      remotes_2.4.2           
 [4] rlang_1.1.1              magrittr_2.0.3           shinydashboard_0.7.2    
 [7] compiler_4.3.0           systemfonts_1.0.4        vctrs_0.6.3             
[10] pkgconfig_2.0.3          crayon_1.5.2             fastmap_1.1.1           
[13] backports_1.4.1          ellipsis_0.3.2           fontawesome_0.5.1       
[16] labeling_0.4.2           utf8_1.2.3               promises_1.2.0.1        
[19] shinyFileTree_0.0.0.9000 rmarkdown_2.23           tzdb_0.4.0              
[22] ragg_1.2.5               bit_4.0.5                sankeyD3_0.3.2          
[25] xfun_0.39                zlibbioc_1.46.0          cachem_1.0.8            
[28] jsonlite_1.8.7           later_1.3.1              BiocParallel_1.34.2     
[31] broom_1.0.5              parallel_4.3.0           R6_2.5.1                
[34] bslib_0.5.0              stringi_1.7.12           car_3.1-2               
[37] jquerylib_0.1.4          Rcpp_1.0.11              knitr_1.43              
[40] httpuv_1.6.11            timechange_0.2.0         tidyselect_1.2.0        
[43] rstudioapi_0.15.0        abind_1.4-5              yaml_2.3.7              
[46] codetools_0.2-19         miniUI_0.1.1.1           curl_5.0.1              
[49] shiny_1.7.4.1            withr_2.5.0              evaluate_0.21           
[52] pillar_1.9.0             BiocManager_1.30.21      carData_3.0-5           
[55] DT_0.28                  shinyjs_2.1.0            generics_0.1.3          
[58] vroom_1.6.3              RCurl_1.98-1.12          hms_1.1.3               
[61] munsell_0.5.0            scales_1.2.1             xtable_1.8-4            
[64] glue_1.6.2               tools_4.3.0              ggsignif_0.6.4          
[67] fs_1.6.2                 grid_4.3.0               crosstalk_1.2.0         
[70] colorspace_2.1-0         GenomeInfoDbData_1.2.10  cli_3.6.1               
[73] textshaping_0.3.6        rhandsontable_0.3.8      fansi_1.0.4             
[76] viridisLite_0.4.2        gtable_0.3.3             rstatix_0.7.2           
[79] sass_0.4.7               digest_0.6.33            htmlwidgets_1.6.2       
[82] farver_2.1.1             memoise_2.0.1            htmltools_0.5.5         
[85] lifecycle_1.0.3          shinyWidgets_0.7.6       mime_0.12               
[88] bit64_4.0.5             

[freixas84]

same issue, has it been fixed?

Loading required package: shiny

Listening on http://127.0.0.1:3469
The `name` provided ('sun-o') does not correspond to a known icon
[Jul17 15:29] Started new shiny session #1 (1 session(s) running)
Warning: Error in &&: 'length = 71' in coercion to 'logical(1)'
  3: runApp
  2: print.shiny.appobj
  1: <Anonymous>
[Jul17 15:30] Exiting session #1

[ilnamkang]

I'm experiencing the same issue.

https://github.com/fbreitwieser/pavian/issues/106 According to the above thread, using the Docker image may be a temporary solution. I analyzed my data successfully using the Docker image.

https://github.com/fbreitwieser/pavian#docker-image

[ArmandBester]

Thank you Ilnamkang

I tried that on an old laptop and it did not load the website. After your message I tried it on my desktop and the docker image on it works fine.

Kind regards Armand

[Neymiti]

Hi, same issue and same error code here:

Listening on http://127.0.0.1:5000 The name provided ('sun-o') does not correspond to a known icon [Sep06 10:46] Started new shiny session #1 (1 session(s) running) [Sep06 10:46] Reading files in C:/.../AppData/Local/R/win-library/4.3/pavian/shinyapp/example-data Warning: Error in &&: 'length = 43' in coercion to 'logical(1)' 3: runApp 2: print.shiny.appobj 1: [Sep06 10:46] Exiting session #1

Moreover, I get a similar error code when trying to load the example data: _Listening on http://127.0.0.1:5000 The name provided ('sun-o') does not correspond to a known icon [Sep06 10:53] Started new shiny session #1 (1 session(s) running) Loading required namespace: Rsamtools Warning: Error in read.table: more columns than column names 130: stop 129: read.table 128: utils::read.delim 127: download_assembly_info 123: 107: assembly_info 106: exprFunc 105: widgetFunc 104: :: htmlwidgets shinyRenderWidget 103: func 90: renderFunc 89: renderFunc 85: renderFunc 84: output$alignment-dt_assemblyinfo 3: runApp 2: print.shiny.appobj 1: [Sep06 11:01] Reading files in C:/.../AppData/Local/R/win-library/4.3/pavian/shinyapp/example-data Warning: Error in &&: 'length = 43' in coercion to 'logical(1)' 3: runApp 2: print.shiny.appobj 1: [Sep06 11:01] Exiting session #1

[gregorysprenger]

It appears using R version >=4.2.0 will make pavian unusable: R Warning 'length(x) = 2 > 1' in coercion to 'logical(1)'

[fbreitwieser]

Hi everyone, sorry for the late reply, this should be fixed now in version v1.2.1! Can you try again with the latest version and let me know the results? Thanks

[gregorysprenger]

Tested on Windows 10, RStudio 2022.07.02, and R 4.2.2 shiny::runGitHub("fbreitwieser/pavian", subdir = "inst/shinyapp") and pavian::runApp(port=5000) works without the loigcal(1) error.

Though, I do get the following warning with the example data (the sankey diagram renders fine for me): Warning: It looks like Source/Target is not zero-indexed. This is required in JavaScript and so your plot may not render.