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g.hemani
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@ghemani-23533
Last seen 4.4 years ago
I think there is a server issue with some biomaRt datasets. Reproducible commands below and sessionInfo:
library(biomaRt)
mart36 <- useDataset(mart=useMart("ENSEMBL_MART_SNP", host="http://may2009.archive.ensembl.org"), dataset="hsapiens_snp")
getBM(attributes = c('refsnp_id','chr_name', 'chrom_start'), filters = c("refsnp"), values = c("rs234", "rs1205"), mart = mart36)
[1] non-BioMart die(): Cannot write to '/ensemblweb/tmp/archives/54/logs/biomart-log4perl.log': No space left on device at /localsw/perl-5.8.8/lib/site_perl/5.8.8/Log/Log4perl/Appender/File.pm line 225.
<0 rows> (or 0-length row.names)
Error in getBM(attributes = c("refsnp_id", "chr_name", "chrom_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 on the support site at http://support.bioconductor.org
sessionInfo()
R version 3.6.1 (2019-07-05)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Mojave 10.14.6
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib
locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] biomaRt_2.40.5
loaded via a namespace (and not attached):
[1] Rcpp_1.0.4 AnnotationDbi_1.46.1 magrittr_1.5
[4] BiocGenerics_0.32.0 hms_0.5.3 progress_1.2.2
[7] IRanges_2.18.3 bit_1.1-15.2 R6_2.4.1
[10] rlang_0.4.5 httr_1.4.1 stringr_1.4.0
[13] blob_1.2.1 tools_3.6.1 parallel_3.6.1
[16] Biobase_2.44.0 DBI_1.1.0 bit64_0.9-7
[19] digest_0.6.25 crayon_1.3.4 vctrs_0.2.4
[22] S4Vectors_0.24.4 bitops_1.0-6 curl_4.3
[25] RCurl_1.98-1.2 memoise_1.1.0 RSQLite_2.2.0
[28] stringi_1.4.6 compiler_3.6.1 prettyunits_1.1.1
[31] stats4_3.6.1 XML_3.99-0.3 pkgconfig_2.0.3
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