biomaRt query interrupted "expected a character string of length 1."
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@3a93e3ab
Last seen 10 days ago
Portugal

first time this happened to me:

> Peaks_TSS_all_hgnc<- getBM(filters= "ensembl_transcript_id", attributes=c("ensembl_transcript_id","ensembl_gene_id","hgnc_symbol"),values=Peaks_TSS_all$ClosestTSS_ID,mart= mart)
Batch submitting query [=============================>-]  95% eta:  2mError in getBM(filters = "ensembl_transcript_id", attributes = c("ensembl_transcript_id",  : 
  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

> sessionInfo()
R version 3.6.3 (2020-02-29)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Mojave 10.14.6

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/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] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] gtools_3.9.2   biomaRt_2.40.5 grex_1.9       edgeR_3.26.8   limma_3.40.6  

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.7           compiler_3.6.3       prettyunits_1.1.1   
 [4] bitops_1.0-7         tools_3.6.3          progress_1.2.2      
 [7] bit_4.0.4            RSQLite_2.2.8        memoise_2.0.0       
[10] lifecycle_1.0.0      lattice_0.20-38      pkgconfig_2.0.3     
[13] rlang_0.4.11         DBI_1.1.1            curl_4.3.2          
[16] parallel_3.6.3       fastmap_1.1.0        xml2_1.3.2          
[19] httr_1.4.2           stringr_1.4.0        vctrs_0.3.8         
[22] S4Vectors_0.22.1     IRanges_2.18.3       hms_1.1.0           
[25] locfit_1.5-9.4       stats4_3.6.3         bit64_4.0.5         
[28] grid_3.6.3           Biobase_2.44.0       R6_2.5.1            
[31] AnnotationDbi_1.46.1 tcltk_3.6.3          XML_3.99-0.3        
[34] magrittr_2.0.1       blob_1.2.2           ellipsis_0.3.2      
[37] BiocGenerics_0.30.0  stringi_1.7.4        RCurl_1.98-1.4      
[40] cachem_1.0.6         crayon_1.4.1
biomaRt • 61 views
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@james-w-macdonald-5106
Last seen 22 hours ago
United States

The first thing you need to do is rectify this situation ----> R version 3.6.3 (2020-02-29)

You are 1.5 years out of date, and I believe Mike Smith has made many improvements in the intervening period. Plus, we don't support old versions (it's enough to support the current release), so unless you get the same error on the current release, nobody is going to provide help anyway, other than to say you should update. So you should update.

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