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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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Proxy issue from version 2.48.0 #52

Open echarpentier opened 2 years ago

echarpentier commented 2 years ago

Hi, I work behind the anonymous (no login, no password) proxy of the university of Nantes, France. I'm having trouble with some functions of the biomaRt package for the latest versions. Since version 2.48.0, the functions "listEnsembl()", "useEnsembl", "getBM" (haven't tested much more) do not work behind my proxy. My proxy is correctly set and verified with 

> Sys.getenv("http_proxy")
[1] "http://<hidden>univ-nantes<hidden>:<hidden>"

The symptoms are that every time I use one of the functions above, nothing happens and the prompt never returns. I have to manually kill the linux process. I tried defining the RCurlOption (with my proxy settings) as below:

options(RCurlOptions = list(proxy="http://proxy.domain.com:800", proxyuserpwd="myuser:mypassword"))

without success.

All versions before 2.48.0 work properly behind the proxy and all versions also work properly with my code when I'm not behind the proxy. It is like biomaRt was not using the proxy settings when using the functions around ensembl.

Here's my sessionInfo():

> sessionInfo()
R version 4.1.1 (2021-08-10)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS/LAPACK: <hidden>

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=fr_FR.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=fr_FR.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=fr_FR.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=fr_FR.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
[1] biomaRt_2.50.0

loaded via a namespace (and not attached):
 [1] KEGGREST_1.34.0        progress_1.2.2         tidyselect_1.1.1      
 [4] purrr_0.3.4            vctrs_0.3.8            generics_0.1.1        
 [7] stats4_4.1.1           BiocFileCache_2.2.0    utf8_1.2.2            
[10] blob_1.2.2             XML_3.99-0.8           rlang_0.4.12          
[13] pillar_1.6.4           glue_1.4.2             DBI_1.1.1             
[16] rappdirs_0.3.3         BiocGenerics_0.40.0    bit64_4.0.5           
[19] dbplyr_2.1.1           GenomeInfoDbData_1.2.7 lifecycle_1.0.1       
[22] stringr_1.4.0          zlibbioc_1.40.0        Biostrings_2.62.0     
[25] memoise_2.0.0          Biobase_2.54.0         IRanges_2.28.0        
[28] fastmap_1.1.0          GenomeInfoDb_1.30.0    curl_4.3.2            
[31] AnnotationDbi_1.56.0   fansi_0.5.0            Rcpp_1.0.7            
[34] filelock_1.0.2         cachem_1.0.6           S4Vectors_0.32.0      
[37] XVector_0.34.0         bit_4.0.4              hms_1.1.1             
[40] png_0.1-7              digest_0.6.28          stringi_1.7.5         
[43] dplyr_1.0.7            tools_4.1.1            bitops_1.0-7          
[46] magrittr_2.0.1         RCurl_1.98-1.5         RSQLite_2.2.8         
[49] tibble_3.1.5           crayon_1.4.1           pkgconfig_2.0.3       
[52] ellipsis_0.3.2         xml2_1.3.2             prettyunits_1.1.1     
[55] assertthat_0.2.1       httr_1.4.2             rstudioapi_0.13       
[58] R6_2.5.1               compiler_4.1.1