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optimHyperParams` function not found when running FRASER2 hyperparameter fitting #634
Description
When running the AberrantSplicing_pipeline_FRASER_04_fit_hyperparameters_FraseR_R step in the DROP pipeline with FRASER_version: "FRASER2",( packageVersion("FRASER") ‘2.4.3’) the pipeline fails because the optimHyperParams function is missing from the FRASER package.
Error:
Wed Aug 13 11:38:12 2025: jaccard
Error in optimHyperParams(fds, type = type, implementation = implementation, :
could not find function "optimHyperParams"
Execution halted
Full trace:
Error in rule AberrantSplicing_pipeline_FRASER_04_fit_hyperparameters_FraseR_R:
jobid: 130
input: /data/.../filter_FRASER2.done, Scripts/AberrantSplicing/pipeline/FRASER/04_fit_hyperparameters_FraseR.R
output: /data/.../hyper_FRASER2.done
log: /data/.../.drop/tmp/AS/fraser/04_hyper.Rds (check log file(s) for error details)
RuleException:
CalledProcessError in file /tmp/tmpeeeu7b3t, line 215:
Command 'Rscript --vanilla /data/.../04_fit_hyperparameters_FraseR.R' returned non-zero exit status 1.
Config.yaml snippet:
aberrantSplicing:
run: true
groups:
- fraser
recount: false
longRead: false
keepNonStandardChrs: false
filter: true
minExpressionInOneSample: 20
quantileMinExpression: 10
minDeltaPsi: 0
implementation: PCA
padjCutoff: 0.1
maxTestedDimensionProportion: 6
genesToTest: null
FRASER_version: "FRASER2"
deltaPsiCutoff : 0.1
quantileForFiltering: 0.75Investigation so far:
- Ran:
library(FRASER)
ls("package:FRASER", pattern = "optimHyperParams")Output:
character(0)
This confirms that optimHyperParams is not available in the installed FRASER2 version.
- This likely means the function was removed or renamed in newer FRASER2 versions.
- The DROP script
04_fit_hyperparameters_FraseR.Rstill calls it.
Environment:
- Memory: 251 GB RAM
- CPU: Intel(R) Xeon(R) Silver 4116 (48 cores)
- R version:"R version 4.4.3
- FRASER2 package version: 2.4.3
- DROP version: 1.4.0
Pipeline fails due to missing function optimHyperParams.
Questions for maintainers:
- Has
optimHyperParamsbeen removed or renamed in FRASER2? - If removed, what is the new recommended way to fit hyperparameters in FRASER2 for DROP?
- Is there a specific FRASER2 version that is compatible with the current DROP scripts?
Activity
vyepez88 commentedon Aug 13, 2025
Hi Anna, we have made lots of updates in FRASER2 and DROP. We made a new FRASER release 5 min ago (https://github.com/gagneurlab/FRASER/releases/tag/2.4.5). We plan to incorporate it into DROP and make a new DROP release. Most likely, this will be available on Monday. Do you mind waiting until then?
vyepez88 commentedon Aug 18, 2025
Hi @akosycarz, we ran into more issues than expected, so it will take some more days.
akosycarz commentedon Aug 25, 2025
ok, thank you please let me know when it will be ready :))
camisimoes44 commentedon Sep 9, 2025
Hi @vyepez88! I´m hitting the same issue. Are there any updates or reccomended workaround?
Thank you very much in advance!!
vyepez88 commentedon Mar 18, 2026
Hi @akosycarz and @camisimoes44, forgot about this, but this should be now fixed in v1.6.0