Server disk full for archived biomaRt database
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g.hemani • 0
@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
    >
software error • 407 views
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Entering edit mode
@james-w-macdonald-5106
Last seen 2 minutes ago
United States

There seem to be fundamental problems with the Ensembl servers right now. I can't get to ensembl.org, nor any of the mirrors.

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