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lexitownley33
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@lexitownley33-10089
Last seen 8.0 years ago
I am learning the biomaRt packages by going through the vingette, and hit an error on task 4.8. When I type the command as shown in the example, I get the following result:
utr5=getSequence(chromosome=3,start=185514033,end=185535839,type="entrezgene",seqType="5utr",mart=ensembl)
V1
1 <!DOCTYPE HTML PUBLIC -//IETF//DTD HTML 2.0//EN>
2 <html><head>
3 <title>302 Found</title>
4 </head><body>
5 <h1>Found</h1>
6 <p>The document has moved <a href=//uswest.ensembl.org/biomart/martservice?;redirectsrc=//www.ensembl.org%2Fbiomart%2Fmartservice%3F>here</a>.</p>
Error in getBM(c(seqType, type), filters = c("chromosome_name", "start", :
The query to the BioMart webservice returned an invalid result: the number of columns in the result table does not equal the number of attributes in the query. Please report this to the mailing list.
Here is the output of the session Info (biomaRt 2.26.1)
R version 3.2.4 (2016-03-10) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows >= 8 x64 (build 9200) locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] biomaRt_2.26.1 loaded via a namespace (and not attached): [1] IRanges_2.4.8 XML_3.98-1.4 digest_0.6.9 crayon_1.3.1 bitops_1.0-6 [6] R6_2.1.2 DBI_0.3.1 stats4_3.2.4 magrittr_1.5 RSQLite_1.0.0 [11] swirl_2.4.0 httr_1.1.0 stringi_1.0-1 testthat_0.11.0 S4Vectors_0.8.11 [16] tools_3.2.4 stringr_1.0.0 Biobase_2.30.0 RCurl_1.95-4.8 parallel_3.2.4 [21] yaml_2.1.13 BiocGenerics_0.16.1 AnnotationDbi_1.32.3 memoise_1.0.0
Let me know if there is a way to work around this or if it is just a bug and we have to wait for the newest version to get around.
I could not reproduce this on windows or linux using the same version of biomaRt.
It could be some issue with networking at your location or it could be a transient hiccup on the biomaRt side, perhaps try again? Or try from another location/network.
I note that the code chunk you're having problems with is not actually evaluated in the vignette. I'm not sure why. But it does work for me to paste that code into an R session.
Also what do you get for
getOption("download.file.method")For me it's not set (NULL). I wonder if on your system it's set to something that is not smart enough to deal with redirects.
Also did you call
useMart()and change the default mart?