Subscript out of bounds error when running library(MetaboShiny)

[BartHee]

running start.metshi(inBrowser = T) opens and closes with the following errors: start.metshi(inBrowser = T) [1] "Orca isn't working, please check your installation. If on Mac, please try starting Rstudio from the command line with the command 'open -a Rstudio'"

Listening on http://0.0.0.0:8080 Warning: Error in [[: subscript out of bounds 46: MetaboShiny::getOptions 45: [C:\Program Files\R\R-3.6.0\library\MetaboShiny/server.R#184] 2: shiny::runApp 1: start.metshi Warning: Error in [[: subscript out of bounds 75: MetaboShiny::getOptions 74: MetaboShiny::setOption 73: observeEventHandler [C:\Program Files\R\R-3.6.0\library\MetaboShiny/server.R#951] 2: shiny::runApp 1: start.metshi Warning: Error in [[: subscript out of bounds 75: MetaboShiny::getOptions 74: MetaboShiny::setOption 73: observeEventHandler [C:\Program Files\R\R-3.6.0\library\MetaboShiny/server.R#962] 2: shiny::runApp 1: start.metshi Warning: Error in [[: subscript out of bounds 75: MetaboShiny::getOptions 74: MetaboShiny::setOption 73: observeEventHandler [reactive/aesthetics.R#36] 2: shiny::runApp 1: start.metshi Warning in match(x, table, nomatch = 0L) : closing unused connection 8 (~/MetaboShiny/saves/admin/options.txt) Warning in match(x, table, nomatch = 0L) : closing unused connection 7 (~/MetaboShiny/saves/admin/options.txt) Warning in match(x, table, nomatch = 0L) : closing unused connection 6 (~/MetaboShiny/saves/admin/options.txt) Warning: The 'plotly_click' event tied a source ID of 'A' is not registered. In order to obtain this event data, please add event_register(p, 'plotly_click') to the plot (p) that you wish to obtain event data from. [1] "Closing metaboShiny ~ヾ(＾∇＾)"

[BartHee]

Running on Docker, this error persists. Perhaps it is something in the saves/admin/options.txt file (however, checking ls does not give odd rows). This is the options file content:

db_dir = ~/MetaboShiny/databases work_dir = ~/MetaboShiny/saves/admin proj_name = MY_METSHI ppm = 2 packages_installed = Y font1 = Pacifico font2 = Pacifico font3 = Open Sans font4 = Open Sans col1 = #000000 col2 = #DBDBDB col3 = #FFFFFF col4 = #FFFFFF size1 = 40 size2 = 20 size3 = 15 size4 = 11 taskbar_image = metshi_logo.png gtheme = classic gcols = #1C1400&#FFE552&#D49C1A&#EBC173&#8A00ED&#00E0C2&#95C200&#FF6BE4&#FFFFFF&#FFFFFF&#FFFFFF&#FFFFFF&#FFFFFF&#FFFFFF&#FFFFFF&#FFFFFF&#FFFFFF&#FFFFFF&#FFFFFF&#FFFFFF gspec = RdBu mode = complete cores = 1 apikey =

[joannawolthuis]

Thanks for putting it on Github Bart! Makes it a bit easier for me to keep a mental overview :D I will be rolling out a version today that should have this issue fixed. It was due to some new options being added that are not in the older options files - I will be merging with the DEV branch soon, if you want you can already switch to there:

devtools::install_github("UMCUGenetics/MetaboShiny", ref="dev")

to see if you still run into issues. I will be merging with Master at the end of the day too :)

[joannawolthuis]

Oh and also, if you want to export figures, orca is a bit necessary, it is easier to install through conda : O Once installed, it can be used(at least in my case) either through running metshi from the command line or opening rstudio through:

open -a rstudio

in the command line.

[BartHee]

RStudio: Thanks, the fix worked. I had to remove the previous folder tree ~/MetaboShiny/{databases,saves/admin} in order to have it work. The localhost 8080 now opens the app! So RStudio is covered.

Docker: Pulling the new docker image results in an updated image with a few new downloads. However, running the commands results in the out of bounds error again, so perhaps the docker image is not updated with the @dev yet?