Hello,

I'm trying to create a txDb object from biomart.

Below you can find the command and the error message. Any idea how I can fix this?

TxDb.SL_3.0.BioMart <- makeTxDbFromBiomart(biomart = "plants_mart", 
                                           dataset = "slycopersicum_eg_gene", 
                                           transcript_ids = NULL, 
                                           circ_seqs = DEFAULT_CIRC_SEQS, 
                                           filter = NULL, 
                                           id_prefix = "ensembl_", 
                                           host = "https://plants.ensembl.org", 
                                           port,
                                           taxonomyId = NA, 
                                           miRBaseBuild = NA)



Download and preprocess the 'transcripts' data frame ... OK

Download and preprocess the 'chrominfo' data frame ... FAILED! (=> skipped)

Download and preprocess the 'splicings' data frame ... OK

Download and preprocess the 'genes' data frame ... OK

Prepare the 'metadata' data frame ... Error in function (type, msg, asError = TRUE)  : 

  Failed to connect to ftp.ensemblgenomes.org port 21 after 21042 ms: Couldn't connect to server

In addition: Warning message:

In makeTxDbFromBiomart(biomart = "plants_mart", dataset = "slycopersicum_eg_gene",  :

  The 'port' argument is deprecated and will be ignored



sessionInfo( )

R version 4.3.0 (2023-04-21 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  LC_CTYPE=English_United States.utf8    LC_MONETARY=English_United States.utf8
[4] LC_NUMERIC=C                           LC_TIME=English_United States.utf8    

time zone: Europe/Berlin
tzcode source: internal

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

other attached packages:
[1] GenomicFeatures_1.52.1 AnnotationDbi_1.62.2   Biobase_2.60.0         GenomicRanges_1.52.0   GenomeInfoDb_1.36.1    IRanges_2.34.1        
[7] S4Vectors_0.38.1       BiocGenerics_0.46.0    biomaRt_2.56.1        

loaded via a namespace (and not attached):
 [1] SummarizedExperiment_1.30.2 KEGGREST_1.40.0             rjson_0.2.21                lattice_0.21-8              vctrs_0.6.3                
 [6] tools_4.3.0                 bitops_1.0-7                generics_0.1.3              curl_5.0.1                  parallel_4.3.0             
[11] tibble_3.2.1                fansi_1.0.4                 RSQLite_2.3.1               blob_1.2.4                  pkgconfig_2.0.3            
[16] Matrix_1.5-4                dbplyr_2.3.3                lifecycle_1.0.3             GenomeInfoDbData_1.2.10     compiler_4.3.0             
[21] stringr_1.5.0               Rsamtools_2.16.0            Biostrings_2.68.1           progress_1.2.2              codetools_0.2-19           
[26] RCurl_1.98-1.12             yaml_2.3.7                  pillar_1.9.0                crayon_1.5.2                BiocParallel_1.34.2        
[31] DelayedArray_0.26.7         cachem_1.0.8                abind_1.4-5                 tidyselect_1.2.0            digest_0.6.33              
[36] stringi_1.7.12              dplyr_1.1.2                 purrr_1.0.2                 restfulr_0.0.15             grid_4.3.0                 
[41] fastmap_1.1.1               cli_3.6.1                   magrittr_2.0.3              S4Arrays_1.0.5              XML_3.99-0.14              
[46] utf8_1.2.3                  withr_2.5.0                 prettyunits_1.1.1           filelock_1.0.2              rappdirs_0.3.3             
[51] bit64_4.0.5                 XVector_0.40.0              httr_1.4.6                  matrixStats_1.0.0           bit_4.0.5                  
[56] png_0.1-8                   hms_1.1.3                   memoise_2.0.1               BiocIO_1.10.0               BiocFileCache_2.8.0        
[61] rtracklayer_1.60.0          rlang_1.1.1                 glue_1.6.2                  DBI_1.1.3                   BiocManager_1.30.22        
[66] xml2_1.3.5                  rstudioapi_0.15.0           R6_2.5.1                    MatrixGenerics_1.12.3       GenomicAlignments_1.36.0   
[71] zlibbioc_1.46.0

Sometimes the Biomart server is flaky. It works for me right now, so you might try again.

See this discussion for 2 alternatives to makeTxDbFromBiomart().