Dear BioC community,

I recently updated my R installation as well as all my BioC packages, including biomaRt.

While before updated, the code bellow (for microarray probe annotation, 40k probes) ran in less than one minutes, it now takes more than half an hour.

library(biomaRt)

probes <- row.names(data_rma_ets1_f)

# Connexion to BioMart hg19 (aka GRCh37)
ensembl <- useMart(biomart="ENSEMBL_MART_ENSEMBL",
                   host="grch37.ensembl.org",
                   path="/biomart/martservice",
                   dataset="hsapiens_gene_ensembl")

# Querying Biomart to map probe names to various features
annotation_ensembl <- getBM(attributes = c("affy_hta_2_0",
                                           "ensembl_gene_id",
                                           "chromosome_name",
                                           "start_position",
                                           "end_position",
                                           "strand",
                                           "entrezgene",
                                           "hgnc_symbol"),
                            filters = "affy_hta_2_0",
                            values = gsub("\\.1", "", probes),
                            mart = ensembl)
Batch submitting query [==-----------------------------------------------------------------------------------------------]   2% eta: 40m

> sessionInfo()
R version 3.4.4 (2018-03-15)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.5

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib

locale:
[1] fr_FR.UTF-8/fr_FR.UTF-8/fr_FR.UTF-8/C/fr_FR.UTF-8/fr_FR.UTF-8

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] rtracklayer_1.38.3                      EnsDb.Hsapiens.v75_2.99.0               ensembldb_2.2.2                        
 [4] AnnotationFilter_1.2.0                  TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2 GenomicFeatures_1.30.3                 
 [7] AnnotationDbi_1.40.0                    GenomicRanges_1.30.3                    GenomeInfoDb_1.14.0                    
[10] biomaRt_2.36.1                          pd.hta.2.0_3.12.2                       DBI_1.0.0                              
[13] RSQLite_2.1.1                           oligo_1.42.0                            Biostrings_2.46.0                      
[16] XVector_0.18.0                          IRanges_2.12.0                          S4Vectors_0.16.0                       
[19] Biobase_2.38.0                          oligoClasses_1.40.0                     BiocGenerics_0.24.0                    

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.17                  lattice_0.20-35               prettyunits_1.0.2             Rsamtools_1.30.0             
 [5] assertthat_0.2.0              digest_0.6.15                 foreach_1.4.4                 mime_0.5                     
 [9] R6_2.2.2                      httr_1.3.1                    BiocInstaller_1.28.0          zlibbioc_1.24.0              
[13] progress_1.1.2                curl_3.2                      lazyeval_0.2.1                blob_1.1.1                   
[17] Matrix_1.2-14                 preprocessCore_1.40.0         splines_3.4.4                 RMySQL_0.10.15               
[21] BiocParallel_1.12.0           AnnotationHub_2.10.1          stringr_1.3.1                 ProtGenerics_1.10.0          
[25] RCurl_1.95-4.10               bit_1.1-14                    shiny_1.1.0                   DelayedArray_0.4.1           
[29] compiler_3.4.4                httpuv_1.4.3                  pkgconfig_2.0.1               htmltools_0.3.6              
[33] SummarizedExperiment_1.8.1    GenomeInfoDbData_1.0.0        interactiveDisplayBase_1.16.0 ff_2.2-14                    
[37] codetools_0.2-15              matrixStats_0.53.1            XML_3.98-1.11                 later_0.7.2                  
[41] GenomicAlignments_1.14.2      bitops_1.0-6                  grid_3.4.4                    xtable_1.8-2                 
[45] magrittr_1.5                  stringi_1.2.2                 promises_1.0.1                affyio_1.48.0                
[49] iterators_1.0.9               tools_3.4.4                   bit64_0.9-7                   yaml_2.1.19                  
[53] memoise_1.1.0                 affxparser_1.50.0   

Is there anything I can do to make the annotation process faster with the last release of biomaRt ?

Many thanks for your advices !

Cheers ! 

-Pef-