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readXStringSet uses non-canonical warnings #120

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ahl27 opened this issue Dec 9, 2024 · 0 comments
Open

readXStringSet uses non-canonical warnings #120

ahl27 opened this issue Dec 9, 2024 · 0 comments

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@ahl27
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ahl27 commented Dec 9, 2024

Noting this for my own reference to fix in the (near) future:

readXStringSet internal methods do not use the correct method of throwing warnings. I'm assuming this is the case for both FASTA and FASTQ files. The error comes from read_fasta_files.c (and equivalent for fastq)--internal methods call snprintf rather than warning(). This means that warnings cannot be suppressed using R error handling (e.g., suppressWarnings) or elevated with options(warn=2). See for example read_fasta_files.c:326.

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