Error in .local(.Object, ...) : Failed to obtain 'hguid' cookie even with local .ucscCache file

[sakuramodokich]

Error occurred:

library(Gviz)

saveRDS(Gviz:::.ucscCache, file=sprintf("ucscCache.%s.rds", "hg19"))
.ucscCache <- readRDS(sprintf("ucscCache.%s.rds", "hg19"))
assignInNamespace(".ucscCache", .ucscCache, ns="Gviz")

from <- 9217084
to <- 10698980

knownGenes <-UcscTrack(genome = "hg19", chromosome = "chr4", 
                       track = "knownGene", from = from, to = to,
                       trackType = "GeneRegionTrack", 
                       rstarts = "exonStarts", rends = "exonEnds", 
                       gene = "name", symbol = "name", 
                       transcript = "name", strand = "strand", 
                       fill = "#8282d2", name = "UCSC Genes")

Error in .local(.Object, ...) : Failed to obtain 'hguid' cookie

My session info:

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] grid      stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] Gviz_1.44.1          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] DBI_1.1.3                   bitops_1.0-7                deldir_1.0-9                gridExtra_2.3              
  [5] biomaRt_2.56.1              rlang_1.1.1                 magrittr_2.0.3              biovizBase_1.48.0          
  [9] matrixStats_1.0.0           compiler_4.3.1              RSQLite_2.3.1               GenomicFeatures_1.52.2     
 [13] png_0.1-8                   vctrs_0.6.3                 ProtGenerics_1.32.0         stringr_1.5.0              
 [17] pkgconfig_2.0.3             crayon_1.5.2                fastmap_1.1.1               backports_1.4.1            
 [21] dbplyr_2.3.3                XVector_0.40.0              utf8_1.2.3                  Rsamtools_2.16.0           
 [25] rmarkdown_2.24              bit_4.0.5                   xfun_0.40                   zlibbioc_1.46.0            
 [29] cachem_1.0.8                progress_1.2.2              blob_1.2.4                  DelayedArray_0.26.7        
 [33] BiocParallel_1.34.2         jpeg_0.1-10                 parallel_4.3.1              prettyunits_1.1.1          
 [37] cluster_2.1.4               VariantAnnotation_1.46.0    R6_2.5.1                    stringi_1.7.12             
 [41] RColorBrewer_1.1-3          rtracklayer_1.60.1          rpart_4.1.19                Rcpp_1.0.11                
 [45] SummarizedExperiment_1.30.2 knitr_1.44                  base64enc_0.1-3             Matrix_1.6-0               
 [49] nnet_7.3-19                 tidyselect_1.2.0            rstudioapi_0.15.0           dichromat_2.0-0.1          
 [53] abind_1.4-5                 yaml_2.3.7                  codetools_0.2-19            curl_5.0.2                 
 [57] lattice_0.21-8              tibble_3.2.1                Biobase_2.60.0              KEGGREST_1.40.0            
 [61] evaluate_0.21               foreign_0.8-82              BiocFileCache_2.8.0         xml2_1.3.5                 
 [65] Biostrings_2.68.1           pillar_1.9.0                filelock_1.0.2              MatrixGenerics_1.12.3      
 [69] checkmate_2.2.0             generics_0.1.3              RCurl_1.98-1.12             ensembldb_2.24.0           
 [73] hms_1.1.3                   ggplot2_3.4.3               munsell_0.5.0               scales_1.2.1               
 [77] glue_1.6.2                  Hmisc_5.1-0                 lazyeval_0.2.2              tools_4.3.1                
 [81] interp_1.1-4                BiocIO_1.10.0               data.table_1.14.8           BSgenome_1.68.0            
 [85] GenomicAlignments_1.36.0    XML_3.99-0.14               latticeExtra_0.6-30         AnnotationDbi_1.62.2       
 [89] colorspace_2.1-0            GenomeInfoDbData_1.2.10     htmlTable_2.4.1             restfulr_0.0.15            
 [93] Formula_1.2-5               cli_3.6.1                   rappdirs_0.3.3              gwasglue_0.0.0.9000        
 [97] fansi_1.0.4                 S4Arrays_1.0.6              dplyr_1.1.3                 AnnotationFilter_1.24.0    
[101] gtable_0.3.4                digest_0.6.33               rjson_0.2.21                htmlwidgets_1.6.2          
[105] memoise_2.0.1               htmltools_0.5.6             lifecycle_1.0.3             httr_1.4.7                 
[109] bit64_4.0.5      

[RinconFer]

Same problem here, Yesterday was working perfectly fine. I reboot the computer and now IdeogramTrack() and browserSession() functions, at least, are throwing the error: Error in .local(.Object, ...) : Failed to obtain 'hguid' cookie

[cristianrohr]

Related to this, when I try to use IdeogramTrack get this error:

Error in (function (classes, fdef, mtable) : unable to find an inherited method for function 'displayPars<-' for signature '"numeric", "list"'

This issue started two days ago

[ivanek]

Hi, I believe it is related to the issue of rtrackalyer package as they are suing http instead of https: https://github.com/lawremi/rtracklayer/pull/92

[sakuramodokich]

I updated the rtracklayer package, but the issue still persists. I also tried using options(Gviz.ucscUrl="http://genome-euro.ucsc.edu/cgi-bin/") but it didn't solve the problem.

[slsevilla]

Anyone have any fixes for this? Getting the same error and I can't find a workaround.

[RinconFer]

For me the error disappeared the same way it appeared, 2 days later it started to work fine again 🤷

[andrewgalbraith21]

Same error for me around. Please update with fix when available thanks!

[daswind]

I have same problem.

[FSCM-lab]

have the same problem

[tlaus]

I'm also having the same issue.

[ytwangZero]

The same problem. Please update with fix when available. Thanks!

[ivanek]

This has been fixed upstream in rtracklayer in both release (Bioc 3.18): 1.62.0 and devel (Bioc 3.19) version: 1.63.0.

If the issue persists with the versions above, it might be an connection issue (not available UCSC server).