Entering edit mode
This suddenly stopped working after functioning for several weeks without issue:
ensemble = useMart("ENSEMBL_MART_ENSEMBL")
map_mart <- biomaRt::useEnsembl(biomart = "ENSEMBL_MART_ENSEMBL",
dataset = "dmelanogaster_gene_ensembl",
host = "www.ensembl.org")
t2g <- biomaRt::getBM(attributes=c("ensembl_transcript_id","external_gene_name"), mart = map_mart)
But, now throws the following error after running the last line:
Error in biomaRt::getBM(attributes = c("ensembl_transcript_id", "external_gene_name"), :
The query to the BioMart webservice returned an invalid result: biomaRt expected a character string of length 1.
Please report this on the support site at http://support.bioconductor.org
I'm not sure what the source of the problem is, any direction would be appreciated.
Versions: biomaRt: 2.4.3 R session info:
R version 3.6.2 (2019-12-12)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Mojave 10.14.6
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] preprocessCore_1.46.0 biomaRt_2.40.3 sleuth_0.30.0
[4] Rmisc_1.5 plyr_1.8.5 lattice_0.20-38
[7] forcats_0.4.0 stringr_1.4.0 dplyr_0.8.3
[10] purrr_0.3.3 readr_1.3.1 tidyr_1.0.0
[13] tibble_2.1.3 ggplot2_3.2.1 tidyverse_1.3.0
loaded via a namespace (and not attached):
[1] Rcpp_1.0.3 lubridate_1.7.4 prettyunits_1.0.2
[4] assertthat_0.2.1 zeallot_0.1.0 digest_0.6.23
[7] R6_2.4.1 cellranger_1.1.0 backports_1.1.5
[10] reprex_0.3.0 stats4_3.6.2 RSQLite_2.1.2
[13] httr_1.4.1 pillar_1.4.3 progress_1.2.2
[16] rlang_0.4.2 curl_4.3 lazyeval_0.2.2
[19] readxl_1.3.1 rstudioapi_0.10 data.table_1.12.2
[22] blob_1.2.0 S4Vectors_0.22.0 RCurl_1.95-4.12
[25] bit_1.1-14 munsell_0.5.0 broom_0.5.2
[28] compiler_3.6.2 modelr_0.1.5 pkgconfig_2.0.3
[31] BiocGenerics_0.30.0 tidyselect_0.2.5 IRanges_2.18.1
[34] XML_3.98-1.20 fansi_0.4.1 crayon_1.3.4
[37] dbplyr_1.4.2 withr_2.1.2 bitops_1.0-6
[40] grid_3.6.2 nlme_3.1-142 jsonlite_1.6
[43] gtable_0.3.0 lifecycle_0.1.0 DBI_1.1.0
[46] magrittr_1.5 scales_1.1.0 cli_2.0.1
[49] stringi_1.4.5 fs_1.3.1 xml2_1.2.2
[52] generics_0.0.2 vctrs_0.2.1 Rhdf5lib_1.6.0
[55] tools_3.6.2 bit64_0.9-7 Biobase_2.44.0
[58] glue_1.3.1 hms_0.5.3 parallel_3.6.2
[61] AnnotationDbi_1.46.0 colorspace_1.4-1 rhdf5_2.28.0
[64] rvest_0.3.5 memoise_1.1.0 haven_2.2.0
Thanks for the help. I figured that had to be what was going on. Both work this morning. I'll keep this in mind for the future!
Cheers, Elizabeth