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I'm getting this type of error with some biomaRt queries:
library(biomaRt) mart <- useMart("ensembl", "hsapiens_gene_ensembl") chr <- c(1:22, "X", "Y", "MT") structures <- getBM( attributes=c("ensembl_gene_id", "interpro", "low_complexity", "transmembrane_domain", "signal_domain", "ncoils"), filters="chromosome_name", values=chr, mart=mart) Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings, : line 70966 did not have 6 elements functions <- getBM( attributes=c("ensembl_gene_id", "go_id", "reactome"), filters="chromosome_name", values=chr, mart=mart) Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings, : line 2021629 did not have 3 elements
Both examples should be reproducible.
Any idea what could cause this to fail?
Thank you,
> sessionInfo() R version 3.2.0 (2015-04-16) Platform: x86_64-unknown-linux-gnu (64-bit) Running under: Red Hat Enterprise Linux Server release 6.6 (Santiago) locale: [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C LC_TIME=en_GB.UTF-8 LC_COLLATE=C [5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=C LC_PAPER=en_GB.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] biomaRt_2.24.0 BiocInstaller_1.18.4 vimcom_1.2-6 colorout_1.0-2 setwidth_1.0-4 loaded via a namespace (and not attached): [1] IRanges_2.2.7 XML_3.98-1.3 bitops_1.0-6 GenomeInfoDb_1.4.1 DBI_0.3.1 stats4_3.2.0 [7] RSQLite_1.0.0 S4Vectors_0.6.3 tools_3.2.0 Biobase_2.28.0 RCurl_1.95-4.7 parallel_3.2.0 [13] BiocGenerics_0.14.0 AnnotationDbi_1.30.1