biomaRt_getBM_Failed to collect lazy table
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Entering edit mode
ai.yaku • 0
@a31e9b58
Last seen 11 weeks ago
United States

I used the below command and got the error below. How can I solve it?

>agilent <- getBM(attributes = c("hgnc_symbol", "ensembl_gene_id", "agilent_wholegenome_4x44k_v1"), 
                 filters=c("agilent_wholegenome_4x44k_v1"),
                 values=probes, mart=ensembl)

Error in `collect()`:
Failed to collect lazy table.
Caused by error in `db_collect()`:
Arguments in `...` must be used.
Problematic argument:
 ..1 = Inf
Did you misspell an argument name?
Run `rlang::last_trace()` to see where the error occurred.

>sessionInfo( )
R version 4.3.1 (2023-06-16)
Platform: x86_64-apple-darwin20 (64-bit)
Running under: macOS Sonoma 14.1.2

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib 
LAPACK: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRlapack.dylib;  LAPACK version 3.11.0

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

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

other attached packages:
[1] dplyr_1.1.4         BiocManager_1.30.22 readxl_1.4.3        dbplyr_2.4.0        biomaRt_2.58.0     

loaded via a namespace (and not attached):
 [1] KEGGREST_1.42.0         remotes_2.4.2.1         htmlwidgets_1.6.3       devtools_2.4.5         
 [5] processx_3.8.2          Biobase_2.62.0          callr_3.7.3             ps_1.7.5               
 [9] vctrs_0.6.5             tools_4.3.1             bitops_1.0-7            generics_0.1.3         
[13] stats4_4.3.1            curl_5.1.0              tibble_3.2.1            fansi_1.0.5            
[17] AnnotationDbi_1.64.1    RSQLite_2.3.3           blob_1.2.4              pkgconfig_2.0.3        
[21] desc_1.4.2              S4Vectors_0.40.2        lifecycle_1.0.4         GenomeInfoDbData_1.2.11
[25] compiler_4.3.1          stringr_1.5.1           Biostrings_2.70.1       progress_1.2.2         
[29] httpuv_1.6.12           GenomeInfoDb_1.38.1     usethis_2.2.2           htmltools_0.5.7        
[33] RCurl_1.98-1.13         urlchecker_1.0.1        pillar_1.9.0            later_1.3.1            
[37] crayon_1.5.2            ellipsis_0.3.2          cachem_1.0.8            sessioninfo_1.2.2      
[41] mime_0.12               tidyselect_1.2.0        digest_0.6.33           stringi_1.8.2          
[45] purrr_1.0.2             rprojroot_2.0.4         fastmap_1.1.1           cli_3.6.1              
[49] magrittr_2.0.3          pkgbuild_1.4.2          XML_3.99-0.16           utf8_1.2.4             
[53] promises_1.2.1          prettyunits_1.2.0       filelock_1.0.2          rappdirs_0.3.3         
[57] bit64_4.0.5             XVector_0.42.0          httr_1.4.7              bit_4.0.5              
[61] cellranger_1.1.0        png_0.1-8               hms_1.1.3               memoise_2.0.1          
[65] shiny_1.8.0             IRanges_2.36.0          miniUI_0.1.1.1          BiocFileCache_2.11.1   
[69] profvis_0.3.8           rlang_1.1.2             Rcpp_1.0.11             xtable_1.8-4           
[73] glue_1.6.2              DBI_1.1.3               xml2_1.3.6              BiocGenerics_0.48.1    
[77] pkgload_1.3.3           rstudioapi_0.15.0       R6_2.5.1                fs_1.6.3               
[81] zlibbioc_1.48.0
getBM biomaRt • 400 views
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Entering edit mode
@james-w-macdonald-5106
Last seen 9 hours ago
United States

That's an old bug that you should be able to fix by updating. I can't remember what package, although db_collect comes from dbplyr (and we have the same version of that package).

library(BiocManager)
install(ask = FALSE)

I can get similar code to run:

> z <- head(getBM("agilent_wholegenome_4x44k_v1", mart = mart))
> z
  agilent_wholegenome_4x44k_v1
1                 A_24_P179339
2                  A_24_P42453
3                 A_24_P179336
4                 A_23_P331028
5                 A_24_P182122
6                 A_23_P431853

> getBM(c("hgnc_symbol","ensembl_gene_id","agilent_wholegenome_4x44k_v1"), "agilent_wholegenome_4x44k_v1", z[,1], mart)
   hgnc_symbol ensembl_gene_id
1      MT-RNR1 ENSG00000211459
2      MT-RNR1 ENSG00000211459
3        MT-TV ENSG00000210077
4        MT-TV ENSG00000210077
5      MT-RNR2 ENSG00000210082
6      MT-RNR2 ENSG00000210082
7      MT-RNR2 ENSG00000210082
8      MT-RNR2 ENSG00000210082
9      MT-RNR2 ENSG00000210082
10      MT-TL1 ENSG00000209082
11      MT-TL1 ENSG00000209082
12      MT-ND1 ENSG00000198888
13      MT-ND1 ENSG00000198888
14      MT-ND1 ENSG00000198888
15       MT-TI ENSG00000210100
16       MT-TI ENSG00000210100
17       MT-TM ENSG00000210112
18       MT-TM ENSG00000210112
19      MT-ND2 ENSG00000198763
20    MTND1P23 ENSG00000225972
   agilent_wholegenome_4x44k_v1
1                  A_24_P179339
2                   A_24_P42453
3                  A_24_P179339
4                   A_24_P42453
5                  A_24_P179336
6                  A_24_P179339
7                   A_24_P42453
8                  A_23_P331028
9                  A_24_P182122
10                 A_23_P331028
11                 A_24_P182122
12                 A_23_P431853
13                 A_23_P331028
14                 A_24_P182122
15                 A_23_P431853
16                 A_23_P331028
17                 A_23_P431853
18                 A_23_P331028
19                 A_23_P431853
20                 A_23_P331028
> sessionInfo()
R version 4.3.1 (2023-06-16 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 11 x64 (build 22621)

Matrix products: default


locale:
[1] LC_COLLATE=English_United States.utf8 
[2] LC_CTYPE=English_United States.utf8   
[3] LC_MONETARY=English_United States.utf8
[4] LC_NUMERIC=C                          
[5] LC_TIME=English_United States.utf8    

time zone: America/New_York
tzcode source: internal

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

other attached packages:
[1] biomaRt_2.58.0

loaded via a namespace (and not attached):
 [1] rappdirs_0.3.3         
 [2] utf8_1.2.4             
 [3] generics_0.1.3         
 [4] bitops_1.0-7           
 [5] xml2_1.3.5             
 [6] RSQLite_2.3.1          
 [7] stringi_1.7.12         
 [8] hms_1.1.3              
 [9] digest_0.6.33          
[10] magrittr_2.0.3         
[11] fastmap_1.1.1          
[12] blob_1.2.4             
[13] progress_1.2.2         
[14] AnnotationDbi_1.64.0   
[15] GenomeInfoDb_1.38.0    
[16] DBI_1.1.3              
[17] httr_1.4.7             
[18] purrr_1.0.2            
[19] fansi_1.0.5            
[20] XML_3.99-0.14          
[21] Biostrings_2.70.1      
[22] cli_3.6.1              
[23] rlang_1.1.1            
[24] crayon_1.5.2           
[25] dbplyr_2.4.0           
[26] XVector_0.42.0         
[27] Biobase_2.62.0         
[28] bit64_4.0.5            
[29] withr_2.5.1            
[30] cachem_1.0.8           
[31] tools_4.3.1            
[32] memoise_2.0.1          
[33] dplyr_1.1.3            
[34] GenomeInfoDbData_1.2.11
[35] filelock_1.0.2         
[36] BiocGenerics_0.48.0    
[37] curl_5.1.0             
[38] vctrs_0.6.4            
[39] R6_2.5.1               
[40] png_0.1-8              
[41] stats4_4.3.1           
[42] lifecycle_1.0.3        
[43] BiocFileCache_2.10.1   
[44] zlibbioc_1.48.0        
[45] KEGGREST_1.42.0        
[46] stringr_1.5.0          
[47] S4Vectors_0.40.1       
[48] IRanges_2.36.0         
[49] bit_4.0.5              
[50] pkgconfig_2.0.3        
[51] pillar_1.9.0           
[52] glue_1.6.2             
[53] tibble_3.2.1           
[54] tidyselect_1.2.0       
[55] compiler_4.3.1         
[56] prettyunits_1.2.0      
[57] RCurl_1.98-1.12        
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