Error: failed to load external

[BJWiley233]

Hi,

I am getting this error with R version 3.6.3, biomaRt version 2.45.6 as well as on R version 4.0.2 after install dev version of biomaRt 2.45.5.

From vignette:

library("biomaRt")

ensembl = useMart("ensembl",
                  dataset="hsapiens_gene_ensembl",
                  host = "useast.ensembl.org")

affyids=c("202763_at","209310_s_at","207500_at")
getBM(attributes=c('affy_hg_u133_plus_2', 'entrezgene_id'), 
      filters = 'affy_hg_u133_plus_2', 
      values = affyids, 
      mart = ensembl)

I get error:

Error: failed to load external entity "http://www.ensembl.org/info/website/archives/index.html?redirect=no"

I get error even when using useEnsembl as well.

[BJWiley233]

Update.

It worked in R 4.0.2 after restarting. In R 3.6.3 after install from github with install_github('grimbough/biomaRt') I get new error:

Error in curl::curl_fetch_memory(url, handle = handle) : 
  server certificate verification failed. CAfile: /etc/ssl/certs/ca-certificates.crt CRLfile: none

[grimbough]

Thanks for the report. This error is coming from the curl package, and I can't figure out why it would behave differently for two versions of R.

Are these running on the same computer? For both versions of R, can you give me the the output from the following code:

library(biomaRt)
sessionInfo()

[lldelisle]

Hi, I got the same error:

> library("biomaRt")
> ensembl = useMart("ensembl",dataset="hsapiens_gene_ensembl")
> affyids=c("202763_at","209310_s_at","207500_at")
> getBM(attributes=c('affy_hg_u133_plus_2', 'entrezgene_id'), 
+       filters = 'affy_hg_u133_plus_2', 
+       values = affyids, 
+       mart = ensembl)
Error: failed to load external entity "http://www.ensembl.org/info/website/archives/index.html?redirect=no"
> sessionInfo()
R version 4.0.3 (2020-10-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Arch Linux

Matrix products: default
BLAS:   /usr/lib/libblas.so.3.9.0
LAPACK: /usr/lib/liblapack.so.3.9.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8       
 [4] LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                  LC_ADDRESS=C              
[10] LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
[1] biomaRt_2.45.2

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.5              prettyunits_1.1.1       ps_1.3.4               
 [4] assertthat_0.2.1        rprojroot_1.3-2         digest_0.6.25          
 [7] BiocFileCache_1.13.1    R6_2.4.1                backports_1.1.9        
[10] stats4_4.0.3            RSQLite_2.2.0           evaluate_0.14          
[13] httr_1.4.2              ggplot2_3.3.2           pillar_1.4.6           
[16] rlang_0.4.7             progress_1.2.2          curl_4.3               
[19] rstudioapi_0.11         callr_3.4.3             blob_1.2.1             
[22] S4Vectors_0.27.12       rmarkdown_2.3           desc_1.2.0             
[25] devtools_2.3.1          stringr_1.4.0           bit_4.0.4              
[28] munsell_0.5.0           gridtext_0.1.1          compiler_4.0.3         
[31] xfun_0.16               pkgconfig_2.0.3         askpass_1.1            
[34] BiocGenerics_0.35.4     pkgbuild_1.1.0          htmltools_0.5.0        
[37] ggtext_0.1.0            openssl_1.4.2           tidyselect_1.1.0       
[40] tibble_3.0.3            IRanges_2.23.10         XML_3.99-0.5           
[43] fansi_0.4.1             dbplyr_1.4.4            crayon_1.3.4           
[46] dplyr_1.0.2             withr_2.2.0             rappdirs_0.3.1         
[49] grid_4.0.3              gtable_0.3.0            lifecycle_0.2.0        
[52] DBI_1.1.0               magrittr_1.5            scales_1.1.1           
[55] cli_2.0.2               stringi_1.4.6           fs_1.5.0               
[58] remotes_2.2.0           testthat_2.3.2          xml2_1.3.2             
[61] ellipsis_0.3.1          generics_0.0.2          vctrs_0.3.4            
[64] tools_4.0.3             usefulLDfunctions_0.1.4 bit64_4.0.5            
[67] Biobase_2.49.0          glue_1.4.2              purrr_0.3.4            
[70] hms_0.5.3               processx_3.4.3          pkgload_1.1.0          
[73] parallel_4.0.3          yaml_2.2.1              AnnotationDbi_1.51.3   
[76] colorspace_1.4-1        sessioninfo_1.1.1       memoise_1.1.0          
[79] knitr_1.29              usethis_1.6.1          

[BJWiley233]

I think we can close this. Last time I check in R 3.6.3 it was working after installing the dev version.

[lldelisle]

For me, doing

library(devtools)
install_github("grimbough/biomaRt")

Solved the issue.

[grimbough]

Great, glad it's working for you both.