Accessing to rat dataset is unstable during last few days. Sometimes it works, sometimes I get error like the following (R code):
library(biomaRt) human = useEnsembl("ENSEMBL_MART_ENSEMBL", dataset = "hsapiens_gene_ensembl") # works fine rat = useEnsembl("ENSEMBL_MART_ENSEMBL", dataset = "rnorvegicus_gene_ensembl") # Error! Error in checkDataset(dataset = dataset, mart = mart) : The given dataset: rnorvegicus_gene_ensembl , is not valid. Correct dataset names can be obtained with the listDatasets() function.
Update: Problem seems gone after I updated all bioconductor packages to 3.6. Will come back if it happens again.
Here is session info. I also tried yesterday with biomartian and faced the same problem.
sessionInfo() R version 3.4.4 (2018-03-15) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 16.04.4 LTS
Matrix products: default BLAS: /usr/lib/openblas-base/libblas.so.3 LAPACK: /usr/lib/libopenblasp-r0.2.18.so locale:  LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8 LC_MONETARY=en_GB.UTF-8  LC_MESSAGES=en_GB.UTF-8 LC_PAPER=en_GB.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C  LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C attached base packages:  parallel stats graphics grDevices utils datasets methods base other attached packages:  biomaRt_2.34.2 AnnotationHub_2.10.1 BiocGenerics_0.24.0 vimcom_1.2-5 setwidth_1.0-4 colorout_1.1-0 loaded via a namespace (and not attached):  SummarizedExperiment_1.8.1 progress_1.2.0 lattice_0.20-35 htmltools_0.3.6 stats4_3.4.4  rtracklayer_1.38.3 yaml_2.1.19 interactiveDisplayBase_1.16.0 blob_1.1.1 XML_3.98-1.11  rlang_0.2.1 later_0.7.3 DBI_1.0.0 BiocParallel_1.12.0 bit64_0.9-7  matrixStats_0.53.1 GenomeInfoDbData_1.0.0 stringr_1.3.1 zlibbioc_1.24.0 Biostrings_2.46.0  memoise_1.1.0 Biobase_2.38.0 IRanges_2.12.0 httpuv_126.96.36.199 GenomeInfoDb_1.14.0  BiocInstaller_1.28.0 AnnotationDbi_1.40.0 Rcpp_0.12.17 xtable_1.8-2 promises_1.0.1  DelayedArray_0.4.1 S4Vectors_0.16.0 XVector_0.18.0 mime_0.5 bit_1.1-14  Rsamtools_1.30.0 hms_0.4.2 digest_0.6.15 stringi_1.2.3 shiny_1.1.0  GenomicRanges_1.30.3 grid_3.4.4 tools_3.4.4 bitops_1.0-6 magrittr_1.5  RCurl_1.95-4.10 RSQLite_2.1.1 crayon_1.3.4 pkgconfig_2.0.1 Matrix_1.2-14  prettyunits_1.0.2 assertthat_0.2.0 httr_1.3.1 rstudioapi_0.7 R6_2.2.2  GenomicAlignments_1.14.2 compiler_3.4.4
Can you update your post to include the output of the command
sessionInfo()so we can see what version of R & biomaRt you are using?
Post that as an answer and then accept it to provide closure to this thread.
I will wait a few days to confirm. Not feel like to provide an uncertain answer with 'seems' :)
Reason @Mike Smith asked you that question was he would have asked you to upgrade to the latest. What version of biomaRt were you on before (just for the record).
I was using bioconductor version 3.5. I did not notice version of biomaRt.