can't run SOI filtering - cleanup

[Emilyzwu]

Hi Roger,

I've manually installed miniconda and tensorflow, which I believed the installation has been successful:

reticulate::use_condaenv("newenv", required = TRUE)
tensorflow::tf_config()
Loaded Tensorflow version 2.1.0
TensorFlow v2.1.0 (D:\Miniconda3\envs\newenv\lib\site-packages\tensorflow_init_.p)
Python v3.6 (D:/Miniconda3/envs/newenv/python.exe)
model <- keras::load_model_hdf5(system.file("extdata", "ImprovedModel.h5",

•                                         package = "RHermes"))
  

2022-01-04 20:23:23.206567: I tensorflow/core/platform/cpu_feature_guard.cc:142] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX AVX2

is(model, "python.builtin.object")
[1] TRUE

I've downloaded the original data from ZENODO and attempted to go through all the process using RHermesGUI(). When I reached the step of SOI filtering - cleanup, the GUI turned grey and froze, and I got msg like this:

Listening on http://127.0.0.1:5091
Warning in readRDS(f) :
strings not representable in native encoding will be translated to UTF-8
Computing isotopic elution similarity:
Calculating isotope similarity:
Calculating isotopic fidelity metrics:
Removing confirmed isotope entries:
Recalculating peaklist for plotting:
Warning: Error in rep: invalid 'times' argument
2: shiny::runApp
1: RHermesGUI

Could you please let me know what's gone wrong and how to solve this issue?

Cheers,
Emily

[RogerGinBer]

Hi Emily,

I've tracked the error down and it's due to a problem with the GUI itself, not with the filterSOI function.
Thankfully, it was just a silly variable name mistake and I've fixed it in the next commit.

Cheers,
Roger

[Emilyzwu]

Hi Roger,

Have you already fixed the bug? Cuz I still got the same error msg when running the filterSOI in GUI:

Warning in readRDS(f) :
strings not representable in native encoding will be translated to UTF-8
Computing isotopic elution similarity:
Calculating isotope similarity:
Calculating isotopic fidelity metrics:
Removing confirmed isotope entries:
Recalculating peaklist for plotting:
Warning: Error in rep: invalid 'times' argument
2: shiny::runApp
1: RHermesGUI

Do I need to manually update anything to have it worked?

Cheers,
Em

[RogerGinBer]

Hi Emily,

Have you reinstalled/updated the package lately with devtools::install_github("RogerGinBer/RHermes") to apply the latest commit changes?

I've run some tests in the GUI and filterSOI() works with both the test dataset and the Zenodo files, so it's probably just a matter of updating. Let me know if it works 👍

Cheers,
Roger