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lawremi / rtracklayer

R interface to genome annotation files and the UCSC genome browser
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Error in ucscTables("hg19", "Assembly") : Invalid genome :'hg19' #91

Closed sakuramodokich closed 9 months ago

sakuramodokich commented 9 months ago 
> ucscTables("hg19", "Assembly")
Error in ucscTables("hg19", "Assembly") : Invalid genome :'hg19'

> sessionInfo()
R version 4.3.1 (2023-06-16)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.6 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0 
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0

...

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

other attached packages:
[1] rtracklayer_1.60.1   GenomicRanges_1.52.0 GenomeInfoDb_1.36.3  IRanges_2.34.1       S4Vectors_0.38.1     BiocGenerics_0.46.0 

loaded via a namespace (and not attached):
 [1] crayon_1.5.2                DelayedArray_0.26.7         SummarizedExperiment_1.30.2 GenomicAlignments_1.36.0   
 [5] rjson_0.2.21                RCurl_1.98-1.12             Biostrings_2.68.1           XML_3.99-0.14              
 [9] MatrixGenerics_1.12.3       Biobase_2.60.0              grid_4.3.1                  restfulr_0.0.15            
[13] abind_1.4-5                 bitops_1.0-7                yaml_2.3.7                  compiler_4.3.1             
[17] codetools_0.2-19            gwasglue_0.0.0.9000         XVector_0.40.0              BiocParallel_1.34.2        
[21] rstudioapi_0.15.0           lattice_0.21-8              BiocIO_1.10.0               parallel_4.3.1             
[25] GenomeInfoDbData_1.2.10     magrittr_2.0.3              Matrix_1.6-0                tools_4.3.1                
[29] matrixStats_1.0.0           Rsamtools_2.16.0            zlibbioc_1.46.0             S4Arrays_1.0.6
sanchit-saini commented 9 months ago

Hi @sakuramodokich

Thanks for reporting it. It seems UCSC is redirecting HTTP to HTTPS because of that, rtracklayer could not get the right HTML content. I have crated a PR to fix it.