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ebiederstedt
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@ebiederstedt-13718
Last seen 6.7 years ago
This is strange bug, even if the function isn't used correctly:
library(Biostrings) Warning messages: 1: package ‘BiocGenerics’ was built under R version 3.4.2 2: package ‘S4Vectors’ was built under R version 3.4.1 3: In eval(quote({ : bytecode version mismatch; using eval 4: package ‘IRanges’ was built under R version 3.4.1 5: undefined slot classes in definition of "XRaw": elementMetadata(class "DataTableORNULL") 6: undefined slot classes in definition of "XInteger": elementMetadata(class "DataTableORNULL") 7: undefined slot classes in definition of "XDouble": elementMetadata(class "DataTableORNULL") > DNAString("TTGAAA-CTC-N") 12-letter "DNAString" instance seq: TTGAAA-CTC-N > DNAString("TTGAAA-CTC-N", "A") Error in .normargSEW(start, "start") : 'start' must be a vector of integers > DNAString("TTGAAA-CTC-N", "A", "B") Error in .normargSEW(start, "start") : 'start' must be a vector of integers > DNA_BASES = c('A', 'G', 'C', 'T', 'N') > nnuc = 0 > mkAllStrings(DNA_BASES, nnuc*2 + 1) [1] "A" "G" "C" "T" "N" > typeof(mkAllStrings(DNA_BASES, nnuc*2 + 1)) [1] "character" > bases = mkAllStrings(DNA_BASES, nnuc*2 + 1) > DNAStringSet(bases) *** caught segfault *** address 0x1, cause 'memory not mapped' Traceback: 1: .Call(.NAME, ..., PACKAGE = PACKAGE) 2: .Call2("new_XStringSet_from_CHARACTER", ans_class, ans_elementType, x, start(solved_SEW), width(solved_SEW), get_seqtype_conversion_lookup("B", seqtype), PACKAGE = "Biostrings") 3: .charToXStringSet(seqtype, x, start, end, width, use.names) 4: XStringSet("DNA", x, start = start, end = end, width = width, use.names = use.names) 5: XStringSet("DNA", x, start = start, end = end, width = width, use.names = use.names) 6: DNAStringSet(bases) Possible actions: 1: abort (with core dump, if enabled) 2: normal R exit 3: exit R without saving workspace 4: exit R saving workspace
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The `undefined slot classes` implies that you have mis-matched package versions. What does `BiocInstaller::biocValid()` say?
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6.7 years ago
Martin Morgan
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