Hello everyone!

so, I'm trying to retireve some information from biomaRt and just found this error:

   > library(biomaRt)
   > ensembl = useMart(host='http://sep2019.archive.ensembl.org', biomart='ENSEMBL_MART_ENSEMBL', dataset='hsapiens_gene_ensembl')

   > unique(ad.b.wb.a3.3$groupID)
     [1] "ENSG00000168280" "ENSG00000144867" "ENSG00000091513" "ENSG00000242337"
     [5] "ENSG00000197971" "ENSG00000279811" "ENSG00000106125" "ENSG00000241644"
     [9] "ENSG00000240583" "ENSG00000250424" "ENSG00000254959" "ENSG00000273269"
    [13] "ENSG00000143933" "ENSG00000239605" "ENSG00000173786" "ENSG00000007237"

    > et = getBM(attributes=c("ensembl_gene_id","external_gene_name","gene_biotype"),
                 filters = "ensembl_gene_id", 
                 values = unique(ad.b.wb.a3.3$groupID), 
                 mart = ensembl)
        Error in readChar(con, 5L, useBytes = TRUE) : cannot open the connection
        In addition: Warning message:
        In readChar(con, 5L, useBytes = TRUE) :
          cannot open compressed file '/tmp/biomaRt/5ea3405a17cc_file5ea353305cde', probable reason 'No such file or directory'

I don't know why this error is happening. The object exists and the vector had the ids. Most curious, if I remove one of the ids, it works:

> et = getBM(attributes=c("ensembl_gene_id","external_gene_name","gene_biotype"), 
             filters = "ensembl_gene_id", 
             values = unique(ad.b.wb.a3.3$groupID)[1:15], 
             mart = ensembl) # Minus the last element
> et = getBM(attributes=c("ensembl_gene_id","external_gene_name","gene_biotype"), 
             filters = "ensembl_gene_id", 
             values = unique(ad.b.wb.a3.3$groupID)[2:16], 
             mart = ensembl) # Minus the 1st element
> et = getBM(attributes=c("ensembl_gene_id","external_gene_name","gene_biotype"), 
             filters = "ensembl_gene_id", 
             values = unique(ad.b.wb.a3.3$groupID)[c(1:6,8:16)], 
             mart = ensembl) #Minus the 7th element

I also trying saving it in a different vetor, but the same error happened:

> aa=c("ENSG00000168280","ENSG00000144867","ENSG00000091513","ENSG00000242337","ENSG00000197971","ENSG00000279811","ENSG00000106125","ENSG00000241644","ENSG00000240583","ENSG00000250424","ENSG00000254959","ENSG00000273269","ENSG00000143933","ENSG00000239605","ENSG00000173786","ENSG00000007237")
> et = getBM(attributes=c("ensembl_gene_id","external_gene_name","gene_biotype"), filters = "ensembl_gene_id", values = aa, mart = ensembl)
Error in readChar(con, 5L, useBytes = TRUE) : cannot open the connection
In addition: Warning message:
In readChar(con, 5L, useBytes = TRUE) :
  cannot open compressed file '/tmp/biomaRt/5ea3405a17cc_file5ea353305cde', probable reason 'No such file or directory'

Here is the sessionInfo():

> sessionInfo()
R version 4.0.2 (2020-06-22)
Platform: x86_64-conda_cos6-linux-gnu (64-bit)
Running under: Fedora 30 (Workstation Edition)

Matrix products: default
BLAS/LAPACK: /homes/brauerei/natasha/miniconda2/envs/r4/lib/libopenblasp-r0.3.10.so

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

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

other attached packages:
 [1] GenomicAlignments_1.24.0    Rsamtools_2.4.0            
 [3] Biostrings_2.56.0           XVector_0.28.0             
 [5] SummarizedExperiment_1.18.2 DelayedArray_0.14.1        
 [7] matrixStats_0.57.0          GenomicFeatures_1.40.1     
 [9] AnnotationDbi_1.50.3        Biobase_2.48.0             
[11] GenomicRanges_1.40.0        GenomeInfoDb_1.24.2        
[13] IRanges_2.22.2              S4Vectors_0.26.1           
[15] BiocGenerics_0.34.0         ComplexUpset_0.5.17        
[17] ggplot2_3.3.2               pathview_1.28.1            
[19] gageData_2.26.0             gage_2.38.3                
[21] dplyr_1.0.2                 biomaRt_2.44.1             
[23] tidyr_1.1.2                

loaded via a namespace (and not attached):
 [1] httr_1.4.2             bit64_4.0.5            assertthat_0.2.1      
 [4] askpass_1.1            BiocManager_1.30.10    BiocFileCache_1.12.1  
 [7] blob_1.2.1             GenomeInfoDbData_1.2.3 progress_1.2.2        
[10] pillar_1.4.6           RSQLite_2.2.1          lattice_0.20-41       
[13] glue_1.4.2             digest_0.6.25          colorspace_1.4-1      
[16] Matrix_1.2-18          XML_3.99-0.5           pkgconfig_2.0.3       
[19] zlibbioc_1.34.0        purrr_0.3.4            GO.db_3.11.4          
[22] patchwork_1.0.1        scales_1.1.1           BiocParallel_1.22.0   
[25] tibble_3.0.3           openssl_1.4.3          KEGGREST_1.28.0       
[28] generics_0.0.2         farver_2.0.3           ellipsis_0.3.1        
[31] withr_2.3.0            cli_2.0.2              magrittr_1.5          
[34] crayon_1.3.4           memoise_1.1.0          KEGGgraph_1.48.0      
[37] fansi_0.4.1            graph_1.66.0           tools_4.0.2           
[40] prettyunits_1.1.1      hms_0.5.3              org.Hs.eg.db_3.11.4   
[43] lifecycle_0.2.0        stringr_1.4.0          munsell_0.5.0         
[46] compiler_4.0.2         rlang_0.4.7            grid_4.0.2            
[49] RCurl_1.98-1.2         rappdirs_0.3.1         bitops_1.0-6          
[52] labeling_0.3           gtable_0.3.0           DBI_1.1.0             
[55] curl_4.3               R6_2.4.1               rtracklayer_1.48.0    
[58] bit_4.0.4              Rgraphviz_2.32.0       stringi_1.5.3         
[61] Rcpp_1.0.5             vctrs_0.3.4            png_0.1-7             
[64] dbplyr_1.4.4           tidyselect_1.1.0

Can anyone help me? Thanks in advance

Natasha