[jonathangoeke]

Summary

• Fixes Trying to use bambu on an offline cluster  #339: bambu() failed on offline machines (e.g. an offline HPC cluster, or a self-contained biocontainers image with no internet egress — see comment) even when given a plain local FASTA file path for genome.
• Root cause: checkInputSequence() in R/bambu_utilityFunctions.R unconditionally called BSgenome::available.genomes() for any character genome argument, before ever checking whether the string was simply a local file path. That call reaches out to Bioconductor's package repository over the network, so it threw a raw Bioconductor/BiocManager error instead of just reading the FASTA.
• Fix: only attempt the BSgenome::available.genomes() / getBSgenome() lookup when the string is not an existing local file, and wrap that lookup in tryCatch so a blocked/failed network call falls through to the existing FASTA-read path (and its existing clear error message) instead of crashing.

Test plan

• devtools::load_all() + traced BSgenome::available.genomes() to confirm it is no longer called when checkInputSequence() is given the package's local test FASTA (inst/extdata/Homo_sapiens.GRCh38.dna_sm.primary_assembly_chr9_1_1000000.fa)
• Confirmed a nonexistent path still produces the original "Input genome file not readable." error
• testthat::test_file() passing locally for test_bambu_arguments.R, test_scoreRC.R, test_isore.R (all exercise checkInputSequence()/bambu() with a local FASTA path)
• test_setNDR.R fails identically before and after this change (missing fixture path in this environment) — confirmed unrelated to this fix

🤖 Generated with Claude Code

[cying111]

the change looks good to me and I have tested it offline where local fasta files are loaded, before the change there is an error similar like the one described in the issue, after the change it can run smoothly

[lingminhao]

same as community issue #581, can inform the user once it's approved.