Gracefully handle pre-1.3.0 AQ XMLs when NULISAseqAQ unavailable#165
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Gracefully handle pre-1.3.0 AQ XMLs when NULISAseqAQ unavailable#165
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Changed behavior from throwing an error to issuing a warning and processing the file as RQ (relative quantification) when: - XML contains AQ metadata but version < 1.3.0 - NULISAseqAQ package is not installed Changes: - R/readNULISAseq.R: Replace stop() with warning() and set AbsAssay=FALSE - skeleton.Rmd: Use runs[[i]]$AbsAssay instead of checking ExecutionDetails - test-writeUpdatedXML.R: Update test to expect warning instead of error Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Skip NULISAseqAQ installation when building for NULISAseqR (public). Only install when repository contains '_internal' (NULISAseqR_internal). Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Skip NULISAseqAQ installation when NULISASEQAQ_BRANCH is empty. This works with the workflow change to only set NULISASEQAQ_BRANCH for internal repos. Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
jcbeer
requested changes
Jan 12, 2026
jcbeer
approved these changes
Jan 12, 2026
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Summary
AbsAssayflag fromloadNULISAseq()outputChanges
stop()withwarning()and setAbsAssay <- FALSEfor graceful degradationruns[[i]]$AbsAssayinstead of checkingExecutionDetailsdirectly🤖 Generated with Claude Code