identical(current_classes, .UCSC_TXCOL2CLASS) is not TRUE

@mikhail-dozmorov-23744

Last seen 1 day ago

United States

Hi,
The GenomicFeatures::makeTxDbFromUCSC function fails with:

library(GenomicFeatures)
> hg19.refseq.db <- makeTxDbFromUCSC(genome="hg19", table="refGene")
Download the refGene table ... Error in .fetch_UCSC_txtable(genome(session), tablename, transcript_ids = transcript_ids) : 
  identical(current_classes, .UCSC_TXCOL2CLASS) is not TRUE
OK

The same error breaks the package built on all platforms, e.g. here. Reproducible on multiple computers. Any suggestions how to solve?

> sessionInfo()
R version 4.1.0 (2021-05-18)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur 11.6.1

Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib

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] stats4    stats     graphics  grDevices datasets  utils     methods   base     

other attached packages:
[1] GenomicFeatures_1.46.1 AnnotationDbi_1.56.2   Biobase_2.54.0         GenomicRanges_1.46.1  
[5] GenomeInfoDb_1.30.0    IRanges_2.28.0         S4Vectors_0.32.3       BiocGenerics_0.40.0   

loaded via a namespace (and not attached):
 [1] MatrixGenerics_1.6.0        httr_1.4.2                  bit64_4.0.5                
 [4] assertthat_0.2.1            BiocFileCache_2.2.0         blob_1.2.2                 
 [7] GenomeInfoDbData_1.2.7      Rsamtools_2.10.0            yaml_2.2.1                 
[10] progress_1.2.2              pillar_1.6.4                RSQLite_2.2.8              
[13] lattice_0.20-45             glue_1.5.0                  digest_0.6.28              
[16] XVector_0.34.0              htmltools_0.5.2             Matrix_1.3-4               
[19] XML_3.99-0.8                pkgconfig_2.0.3             biomaRt_2.50.1             
[22] zlibbioc_1.40.0             purrr_0.3.4                 BiocParallel_1.28.2        
[25] tibble_3.1.6                KEGGREST_1.34.0             generics_0.1.1             
[28] ellipsis_0.3.2              cachem_1.0.6                SummarizedExperiment_1.24.0
[31] magrittr_2.0.1              crayon_1.4.2                memoise_2.0.1              
[34] evaluate_0.14               fansi_0.5.0                 xml2_1.3.2                 
[37] tools_4.1.0                 RMariaDB_1.2.1              prettyunits_1.1.1          
[40] hms_1.1.1                   BiocIO_1.4.0                lifecycle_1.0.1            
[43] matrixStats_0.61.0          stringr_1.4.0               DelayedArray_0.20.0        
[46] Biostrings_2.62.0           compiler_4.1.0              rlang_0.4.12               
[49] grid_4.1.0                  RCurl_1.98-1.5              rstudioapi_0.13            
[52] rjson_0.2.20                rappdirs_0.3.3              bitops_1.0-7               
[55] rmarkdown_2.11              restfulr_0.0.13             DBI_1.1.1                  
[58] curl_4.3.2                  R6_2.5.1                    GenomicAlignments_1.30.0   
[61] lubridate_1.8.0             knitr_1.36                  dplyr_1.0.7                
[64] rtracklayer_1.54.0          fastmap_1.1.0               bit_4.0.4                  
[67] utf8_1.2.2                  filelock_1.0.2              stringi_1.7.5              
[70] parallel_4.1.0              Rcpp_1.0.7                  vctrs_0.3.8                
[73] png_0.1-7                   dbplyr_2.1.1                tidyselect_1.1.1           
[76] xfun_0.28

Thanks,
Mikhail