Hi,

I am trying to generate at TxDb object using makeTxDbFromUCSC function from GenomicFeatures package for hg19 reference genome, and no matter which gene database I use, I always get the following error:

hg19.refseq.db <- makeTxDbFromUCSC(genome="hg19", table="knownGene", url="https://genome.ucsc.edu/cgi-bin/";)
Error in names(trackIds) <- sub("^ ", "", nms[nms != "new"]) :    'names' attribute [210] must be the same length as the vector [209]

Indeed if I tried to list the possible gene annotations for hg19 I got the same error message

supportedUCSCtables(genome="hg19", url="http://genome.ucsc.edu/cgi-bin/")
Error in names(trackIds) <- sub("^ ", "", nms[nms != "new"]) : 
  'names' attribute [210] must be the same length as the vector [209]

I guess this has to do with the recent update you did today on the package. I am not running the most updated version of the package nor of R/Bioconductor. But I would not like to have to update the entire R and installed packages just to make GenomicFeatures to run properly. Here is the info of my session:

R version 3.4.2 (2017-09-28)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.4

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] 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    parallel  grid      stats     graphics  grDevices utils     datasets  methods  
[10] base     

other attached packages:
 [1] GenomicFeatures_1.30.3 AnnotationDbi_1.40.0   Biobase_2.38.0        
 [4] data.table_1.10.4-3    ChIPpeakAnno_3.12.7    BiocInstaller_1.28.0  
 [7] VennDiagram_1.6.20     futile.logger_1.4.3    GenomicRanges_1.30.3  
[10] GenomeInfoDb_1.14.0    Biostrings_2.46.0      XVector_0.18.0        
[13] IRanges_2.12.0         S4Vectors_0.16.0       BiocGenerics_0.24.0   

loaded via a namespace (and not attached):
 [1] httr_1.3.1                    idr_1.2                       RMySQL_0.10.14               
 [4] regioneR_1.10.0               bit64_0.9-7                   AnnotationHub_2.10.1         
 [7] splines_3.4.2                 shiny_1.0.5                   assertthat_0.2.0             
[10] interactiveDisplayBase_1.16.0 RBGL_1.54.0                   blob_1.1.1                   
[13] BSgenome_1.46.0               GenomeInfoDbData_1.0.0        Rsamtools_1.30.0             
[16] yaml_2.1.19                   progress_1.1.2                RSQLite_2.1.0                
[19] lattice_0.20-35               limma_3.34.9                  digest_0.6.15                
[22] promises_1.0.1                htmltools_0.3.6               httpuv_1.4.1                 
[25] Matrix_1.2-14                 XML_3.98-1.11                 pkgconfig_2.0.1              
[28] biomaRt_2.34.2                zlibbioc_1.24.0               xtable_1.8-2                 
[31] GO.db_3.5.0                   later_0.7.2                   BiocParallel_1.12.0          
[34] AnnotationFilter_1.2.0        SummarizedExperiment_1.8.1    lazyeval_0.2.1               
[37] survival_2.42-3               magrittr_1.5                  mime_0.5                     
[40] memoise_1.1.0                 MASS_7.3-50                   graph_1.56.0                 
[43] tools_3.4.2                   prettyunits_1.0.2             formatR_1.5                  
[46] matrixStats_0.53.1            stringr_1.3.0                 DelayedArray_0.4.1           
[49] ensembldb_2.2.2               lambda.r_1.2.2                ade4_1.7-11                  
[52] compiler_3.4.2                RCurl_1.95-4.10               bitops_1.0-6                 
[55] multtest_2.34.0               DBI_1.0.0                     curl_3.2                     
[58] R6_2.2.2                      GenomicAlignments_1.14.2      rtracklayer_1.38.3           
[61] seqinr_3.4-5                  bit_1.1-12                    ProtGenerics_1.10.0          
[64] futile.options_1.0.1          stringi_1.2.2                 Rcpp_0.12.16                 

That error doesn't have anything to do with the version of Bioconductor you are using, or any recent changes on our end. It comes from an internal function in rtracklayer that is trying to get the track names from UCSC, and it appears they have made some changes at UCSC that are breaking the function. I'll put in a fix in a minute, but it will take a while to propagate.

And the fix will go into the release and devel versions. Unfortunately we don't update any old software, so you will have to not only wait to get the fixed version, but you will have to update your R/Bioconductor installation.

As an alternative, do note that the TxDb.Hsapiens.UCSC.hg19.knownGene is exactly the same thing you would get by building one yourself, and it's available using biocLite, so there is really no profit in re-doing something that has already been done.