database disk image is malformed

[EperLuo]

Please ask questions about how to use recount3 on the
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appropriate tag(s) including the one for this package.

Note. Update the issue title to concisely describe the bug.

Hi! Thank you for this wonderful work. I was trying to download data via create_rse function, but encounter the following bug:

2024-07-03 17:09:59.968347 caching file sra.sra.SRP167804.MD.gz.
adding rname 'http://duffel.rail.bio/recount3/mouse/data_sources/sra/metadata/04/SRP167804/sra.sra.SRP167804.MD.gz'
Error in BiocFileCache::bfcrpath(bfc, url, exact = TRUE, verbose = verbose) : 
  not all 'rnames' found or unique.
Calls: create_rse ... file_retrieve -> vapply -> FUN -> <Anonymous> -> <Anonymous>
In addition: Warning message:
In value[[3L]](cond) : 
trying to add rname 'http://duffel.rail.bio/recount3/mouse/data_sources/sra/metadata/04/SRP167804/sra.sra.SRP167804.MD.gz' produced error:
  database disk image is malformed
Execution halted

Provide a minimally reproducible example (reprex)

This is my code. I can use it to download some of the datasets. But for most of the dataset, the above error occurred.

  proj_info <- subset(
    projects,
    project == SRA_Accession & project_type == "data_sources"
  )

  rse_gene <- create_rse(proj_info[1,])

I wonder if it is an internet connection problem. Can I manage to solve it? Any response would be much appreciated!

[lcolladotor]

Hi @EperLuo,

I believe that you are running into the issue described at Bioconductor/BiocFileCache#48 and curl/curl#13725.

What is the output of curl::curl_version() for you? Is it version 8.6.0?

best,
Leo