Problem related to `biomaRt::getBM()` during `R CMD check` execution
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Last seen 3 months ago

Hi I'm trying to develop a new package for Bioconductor, but I am experiencing an error when I run R CMD check, precisely when I call the biomaRt::getBM() command:

Warning in readChar(con, 5L, useBytes = TRUE) : truncating string with embedded nuls Warning: file ā€˜2a8c7fc7412c_file2a8c77d1db9cā€™ has magic number 'X' Use of save versions prior to 2 is deprecated Error in load(bfc[[rid]]) : bad restore file magic number (file may be corrupted) -- no data loaded Calls: getGenomicRegionsFromGeneSymbols -> <Anonymous> -> load Execution halted

And when I run the same command in a normal R setting, everything goes well:

probeset_array <- c("204347_at",   "202022_at",   "221497_x_at", "220942_x_at", "206686_at")
flank_len <- 25
flank_stream <- "downstream"
flank_type <- "gene"
flank_stream <- paste0(flank_stream, "_flank")                                                       
flank_type <- paste0(flank_type, "_flank")
currSpecieMart <- biomaRt::useMart(biomart = "ensembl",  dataset = 'hsapiens_gene_ensembl')
thisAnnotLookup <-  biomaRt::getBM(mart = currSpecieMart, 
          attributes = c( "affy_hg_u133a", "ensembl_gene_id", "gene_biotype", "external_gene_name", "chromosome_name", "start_position", "end_position", flank_type), 
          filter = c("affy_hg_u133a", flank_stream), 
          values = list(probeset_array, flank_len), 
          uniqueRows = TRUE, 
          checkFilters = FALSE, bmHeader = TRUE)

Apparently there is a problem with the call to biomaRt::getBM() that saves some data in a wrong way. Any idea on how to fix this issue?


biomaRt Bioconductor • 156 views
Entering edit mode
Last seen 5 hours ago
United States

Does the section in the biomaRt vignette that talks about caching (and using a temp dir) help?

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