Error - Something is wrong with your input data!

[gustavodscotrim]

The data provided as "examples" is showing the error message "Something is wrong with your input data!" when they are inserted.
Please, is it possible to provide an excel table containing the layout to be used?
Is it possible to use only the data collected in the negative ionization mode? Or does it necessarily have to be in both ionization modes (positive and negative)?

Thank you very much!

library(MetaboShiny)
Warning message:
replacing previous import ‘httr::config’ by ‘plotly::config’ when loading ‘MetaboShiny’
start.metshi(inBrowser=T)
Loading required package: shiny
data.table 1.12.8 using 4 threads (see ?getDTthreads). Latest news: r-datatable.com

Attaching package: ‘plotly’

The following object is masked from ‘package:ggplot2’:

last_plot

The following object is masked from ‘package:httr’:

config

The following object is masked from ‘package:ChemmineR’:

groups

The following object is masked from ‘package:stats’:

filter

The following object is masked from ‘package:graphics’:

layout

Stackoverflow is a great place to get help:
https://stackoverflow.com/tags/shinyjs

Attaching package: ‘shinyjs’

The following object is masked from ‘package:shiny’:

runExample

The following object is masked from ‘package:ChemmineR’:

show

The following objects are masked from ‘package:methods’:

removeClass, show

[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: Since v0.2.0, there is no need to call includeJqueryUI() before using other shinyjqui functions
Warning in if (getAttribs(panels[[i]])$value %in% open) { :
the condition has length > 1 and only the first element will be used
Loading required package: tidytext
Loading required package: classyfireR
Loading required package: magrittr
[1] TRUE
Warning: replacing previous import ‘XML::xml’ by ‘rvest::xml’ when loading ‘MetaDBparse’
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.
Warning in set(x, j = name, value = value) :
Column 'individual' does not exist to remove
[1] "Remaining m/z values for positive mode:21"
[1] "Remaining m/z values for negative mode:21"
Error in setnames(x, value) :
Passed a vector of type 'list'. Needs to be type 'character'.
Warning in set(x, j = name, value = value) :
Column 'individual' does not exist to remove
[1] "Remaining m/z values for positive mode:21"
[1] "Remaining m/z values for negative mode:21"
Error in setnames(x, value) :
Passed a vector of type 'list'. Needs to be type 'character'.

[joannawolthuis]

Hi there! Thank you for your interest and patience :) I have been on leave and am returning now. It is correct that the example files are outdated for the current version - thanks for catching that! I will upload the new format (two examples) ASAP.

[gustavodscotrim]

@joannawolthuis thanks for the reply, and also for sharing the platform. I await the update of the files! :)

[RuiNascimento]

Having the same problem in input data. Tried the docker version as well installing in R. Also tried to upload my on data, still no luck.

[joannawolthuis]

Hi both of you! Thank you for your patience :) The most recent master branch and docker update have new example files included! This is the dataset also included in the paper in 3 different formats (MetaboAnalyst, MetaboLights, MetaboShiny 'native'). We will be uploading a more extensive manual at the end of today.

[RuiNascimento]

@joannawolthuis thank you for the quick response and updates. Upload data seems to work fine now, thank you very much!
Just a heads up, in order to perform the normalization I needed to load the data.table package before launching MetaboShiny, otherwise and error would come up saying that the fread function could not be found.

[joannawolthuis]

Hi :) No problem! And thanks for catching that - I've been replacing all the library() commands with :: notations but I still manage to miss a few. Will fix in next push!

[RuiNascimento]

@joannawolthuis Input data is broken again, just updated MetaboShiny to latest commits and now I can't import datasets that worked before. My last update was from a month ago.
Tried the example datasets provided with the package and both the metabolights as well as metaboshiny example formats gives an error.

[joannawolthuis]

@RuiNascimento Whoops, good catch,thank you! Should be fixed now. Booting up docker to upload the new version there too. :)