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rickhelmus / patRoon

Workflow solutions for mass-spectrometry based non-target analysis.
https://rickhelmus.github.io/patRoon/
GNU General Public License v3.0
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findFeatures Error - Error in if (!recentFFM) settings <- c(settings, `-algorithm:epd:masstrace_snr_filtering` = boolToChr(traceSNRFiltering)) : missing value where TRUE/FALSE needed #112

Closed Theodoralee03 closed 5 months ago

Theodoralee03 commented 5 months ago

Dear Rick and Team,

I recently obtained a new workstation, and wish to run patRoon there instead of my original laptop. However, after setting up everything, i keep facing an error while trying to use the findFeatures() function. I even tried using the patRoon demo data, but i also got the same error

`> anaInfo <- patRoonData::exampleAnalysisInfo("positive")

fList <- findFeatures(anaInfo, "openms") Verifying if your data is centroided... Done! Finding features with OpenMS for 6 analyses ... Error in if (!recentFFM) settings <- c(settings, -algorithm:epd:masstrace_snr_filtering = boolToChr(traceSNRFiltering)) : missing value where TRUE/FALSE needed`

Here is a summary of what I have tried:

  1. Updating and reinstalling patRoon, all its dependencies, even external dependencies (These files are stored on my C Drive)
  2. Uninstalling R and R Studio
  3. Tried using similar R and R Studio versions as my old laptop, but some patRoon functions were not compatible with the older versions of R, even so, i still had the same error

I have been successful using patRoon before on my old laptop - R Version R-4.2.2 and R Studio 2022.12.0 Version. The current version of R on my new workstation is R-4.4.0 and R Studio 2024.04.2.

I have also tried looking for the log/openMS folder for more information, but somehow it doesn't exist in this new workstation. I have tried ways to create and redirect the error log by creating a new folder using sink(), but the log obtained was not very helpful. Example of the log output

Verifying if your data is centroided... Done! Finding features with OpenMS for 6 analyses ...

Do you have any advice on what else I can try to rectify this error?

Thank you so much!

Sincerely, Theo

rickhelmus commented 5 months ago

Hi Theo,

Strange...! It seems an internal function fails that is supposed to figure out your OpenMS version. Would you be able to run the following and tell me its output:

patRoon:::executeCommand(patRoon:::getExtDepPath("openms", "FeatureFinderMetabo"), stdout = TRUE, stderr = TRUE)

Thanks, Rick

Theodoralee03 commented 5 months ago

Hi Rick,

Here is the output

> patRoon:::executeCommand(patRoon:::getExtDepPath("openms", "FeatureFinderMetabo"), stdout = TRUE, stderr = TRUE) character(0) attr(,"status") [1] 309 Warning message: In system2(cmd, sapply(args, shQuote), ...) : running command '"C:/Users/arole/AppData/Local/R/win-library/4.4/patRoonExt/ext/openms/bin/FeatureFinderMetabo.exe"' had status 309

Thank you!

Theodoralee03 commented 5 months ago

Hi Rick,

I have found a solution. After what you've mentioned, I was wondering if it could be to do some dependency files that were missing and could not support OpenMS in patRoon

I downloaded OpenMS at https://abibuilder.cs.uni-tuebingen.de/archive/openms/OpenMSInstaller/release/latest/ That had managed to resolve my issue.

Thank you!

rickhelmus commented 4 months ago

Hi @Theodoralee03 ,

Sorry for the slow response. But I am happy to see you could fix the issue yourself! In the end it turned out that some DLLs were missing in the bundled OpenMS and OpenBabel files from patRoonExt. This should be fixed now.

Thanks, Rick