Add optional Sirius job

[Saanaelle]

Dear Adafede,
I would like to add my Sirius results in the TimaR job with the optional input.
To do so, I followed the documentation you provide : I downloaded the Sirius results, named it [name of my job]_sirius, compressed it and put it in path Documents/data/interim/annotations.
But the job failed.
However, if I run the same job without the optional input, it works.
Do you notice something wrong what I am doing?
Best,

[Adafede]

Dear @Saanaelle,

Sorry to hear so!
Could you attach the error message, the sirius results and the version used, eventually with the command/parameters you used?
This will help me help you

Best

[Saanaelle]

Dear Adafede,

Thank you for your quick reply. I am using sirius 6.0.0. I used all default parameters in sirius, and used Predict and MSNovelist.
Here are the sirius results:
Kalanchoe3_sirius.zip

Here is the error message:
INFO [2025-10-06 11:41:12] Loading parameters for SIRIUS 613+, 0-]
TRACE [2025-10-06 11:41:12] Loading and formatting SIRIUS results...
✖ ann_sir_pre errored
✖ errored pipeline [18m 57.4s, 113 completed, 0 skipped]
Il y a eu 14 avis (utilisez warnings() pour les visionner)
Avis : Error in : Error in tar_make():
file must be a length one character vector or numeric
See https://books.ropensci.org/targets/debugging.html
92:
91: signalCondition
90: signal_abort
89: rlang::abort
88: tar_error
87: tar_throw_run
86: callr_error
84: callr_outer
83: targets::tar_make
82: observe [C:/Users/Maintenance/AppData/Local/R/win-library/4.4/tima/app.R#2649]
81: observer:observeEvent(input$launch)
2: shiny::runApp
1: tima::run_app

[Adafede]

Oh, this is the explanation.

As explained in https://taxonomicallyinformedannotation.github.io/tima/articles/II-preparing.html#sirius, you need to export ALL results, else it also makes no sense to re-rank them.

If you are using the CLI, please re-export using --full-summary
If you are using the GUI

This should fix the issue 😉

[Saanaelle]

Dear Adafede,

Thank you for your explanation. It worked!
I indeed saw this note in the documentation but I didn't understand what it was referring to. And because I am not use to CLI, I didn't get the command that is copied there.

Thanks a lot for you reactivity,
Best,