I'm getting an error in makeTxDbFromBiomart.
> makeTxDbFromBiomart()

The full stacktrace is:

Download and preprocess the 'transcripts' data frame ... OK
Download and preprocess the 'chrominfo' data frame ... FAILED! (=>skipped)
Download and preprocess the 'splicings' data frame ... OK
Download and preprocess the 'genes' data frame ... OK
Prepare the 'metadata' data frame ... Error in .prepareBiomartMetadata
    (mart, is_full_dataset, host, port, taxonomyId,  :
          the BioMart database "ENSEMBL_MART_ENSEMBL" has no (or more than
    one)
          "hsapiens_gene_ensembl" datasets
        In addition: Warning messages:
        1: In scan(con, sep = "\t", blank.lines.skip = TRUE, what =
    "character",  :
          EOF within quoted string
        2: In scan(con, sep = "\t", blank.lines.skip = TRUE, what =
    "character",  :
          EOF within quoted string

I had used it in the last week or so, so I don't believe it is a
firewall/security issue on my end. Also, I tried the same command but for
the C. elegans dataset and that worked fine.

I have also contacted Ensembl and I have tried running the following:

library(biomaRt)
ensembl = useMart(biomart="ENSEMBL_MART_ENSEMBL", host="www.ensembl.org")
listDatasets(ensembl)

Which works, suggesting the problem is not on Ensembl's end.

Do you know whether the problem is on your end?

Best,

Katie

> sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.6

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/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] stats4    parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] AnnotationHub_2.12.1        biomaRt_2.36.1              GenomicAlignments_1.16.0    Rsamtools_1.32.3            Biostrings_2.48.0          
 [6] XVector_0.20.0              SummarizedExperiment_1.10.1 DelayedArray_0.6.6          BiocParallel_1.14.2         matrixStats_0.54.0         
[11] GenomicFeatures_1.32.3      AnnotationDbi_1.42.1        Biobase_2.40.0              GenomicRanges_1.32.7        GenomeInfoDb_1.16.0        
[16] IRanges_2.14.12             S4Vectors_0.18.3            BiocGenerics_0.26.0        

loaded via a namespace (and not attached):
 [1] progress_1.2.0                lattice_0.20-35               htmltools_0.3.6               rtracklayer_1.40.6            yaml_2.2.0                   
 [6] base64enc_0.1-3               interactiveDisplayBase_1.18.0 blob_1.1.1                    XML_3.98-1.16                 rlang_0.2.2                  
[11] later_0.7.5                   DBI_1.0.0                     bit64_0.9-7                   GenomeInfoDbData_1.1.0        stringr_1.3.1                
[16] zlibbioc_1.26.0               memoise_1.1.0                 evaluate_0.12                 knitr_1.20                    BiocInstaller_1.30.0         
[21] httpuv_1.4.5                  curl_3.2                      Rcpp_0.12.19                  xtable_1.8-3                  promises_1.0.1               
[26] backports_1.1.2               jsonlite_1.5                  mime_0.6                      bit_1.1-14                    hms_0.4.2                    
[31] digest_0.6.18                 stringi_1.2.4                 shiny_1.1.0                   grid_3.5.1                    rprojroot_1.3-2              
[36] tools_3.5.1                   bitops_1.0-6                  magrittr_1.5                  RCurl_1.95-4.11               RSQLite_2.1.1                
[41] crayon_1.3.4                  pkgconfig_2.0.2               Matrix_1.2-14                 prettyunits_1.0.2             assertthat_0.2.0             
[46] rmarkdown_1.10                httr_1.3.1                    rstudioapi_0.8                R6_2.3.0                      compiler_3.5.1