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grimbough / biomaRt

R package providing query functionality to BioMart instances like Ensembl
https://bioconductor.org/packages/biomaRt/
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Error with biomaRt_2.46.0 #35

Open weijiaru opened 3 years ago

weijiaru commented 3 years ago

Hi, I am using biomaRt to transform geneID.

Here is my original code:

library("biomaRt") ensembl <- useMart("ensembl", dataset="mmusculus_gene_ensembl", host = "useast.ensembl.org")

I also tried the following code, but they did not work.

library("biomaRt") ensembl <- useEnsembl("ensembl", dataset="mmusculus_gene_ensembl", host = "useast.ensembl.org")

OR

library("biomaRt") library("curl") library(httr) set_config(config(ssl_verifypeer = 0L)) ensembl <- useEnsembl("ensembl", dataset="mmusculus_gene_ensembl", host = "useast.ensembl.org")

I got the similar problems: Ensembl site unresponsive, trying asia mirror. Ensembl site unresponsive, trying useast mirror. Ensembl site unresponsive, trying uswest mirror.

Here is my computer session information

sessionInfo() R version 4.0.3 (2020-10-10) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 18362)

Matrix products: default

locale: [1] LC_COLLATE=Chinese (Simplified)_China.936 LC_CTYPE=Chinese (Simplified)_China.936 LC_MONETARY=Chinese (Simplified)_China.936 LC_NUMERIC=C
[5] LC_TIME=Chinese (Simplified)_China.936

attached base packages: [1] stats graphics grDevices utils datasets methods base

other attached packages: [1] httr_1.4.2 curl_4.3 biomaRt_2.46.0 forcats_0.5.0 stringr_1.4.0 dplyr_1.0.2 purrr_0.3.4 readr_1.4.0 tidyr_1.1.2 tibble_3.0.4 ggplot2_3.3.2 tidyverse_1.3.0

loaded via a namespace (and not attached): [1] Rcpp_1.0.5 lubridate_1.7.9 prettyunits_1.1.1 assertthat_0.2.1 digest_0.6.27 BiocFileCache_1.14.0 R6_2.5.0 cellranger_1.1.0 backports_1.2.0
[10] reprex_0.3.0 stats4_4.0.3 RSQLite_2.2.1 pillar_1.4.6 rlang_0.4.8 progress_1.2.2 readxl_1.3.1 rstudioapi_0.11 blob_1.2.1
[19] S4Vectors_0.28.0 bit_4.0.4 munsell_0.5.0 tinytex_0.27 broom_0.7.2 compiler_4.0.3 modelr_0.1.8 xfun_0.19 askpass_1.1
[28] pkgconfig_2.0.3 BiocGenerics_0.36.0 openssl_1.4.3 tidyselect_1.1.0 IRanges_2.24.0 XML_3.99-0.5 fansi_0.4.1 crayon_1.3.4 dbplyr_2.0.0
[37] withr_2.3.0 rappdirs_0.3.1 grid_4.0.3 jsonlite_1.7.1 gtable_0.3.0 lifecycle_0.2.0 DBI_1.1.0 magrittr_1.5 scales_1.1.1
[46] cli_2.1.0 stringi_1.5.3 fs_1.5.0 xml2_1.3.2 ellipsis_0.3.1 generics_0.1.0 vctrs_0.3.4 tools_4.0.3 bit64_4.0.5
[55] Biobase_2.50.0 glue_1.4.2 hms_0.5.3 parallel_4.0.3 AnnotationDbi_1.52.0 colorspace_1.4-1 rvest_0.3.6 memoise_1.1.0 haven_2.3.1