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Question: Gviz IdeogramTrack fails with Error: failed to load HTTP resource
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gravatar for enricoferrero
4 months ago by
enricoferrero560
United Kingdom
enricoferrero560 wrote:

Hello,

I get an HTTP connection error when using Gviz::IdeogramTrack():

library(Gviz)
IdeogramTrack(genome="hg19", chromosome="chr7")
Error: failed to load HTTP resource

traceback()
18: stop(e)
17: (function (msg, code, domain, line, col, level, filename, class = "XMLError") 
    {
        e = makeXMLError(msg, code, domain, line, col, level, filename, 
            class)
        dom = names(e$domain)
        class(e) = c(names(e$code), sprintf("%s_Error", gsub("_FROM_", 
            "_", dom)), class(e))
        if (e$code == xmlParserErrors["XML_IO_LOAD_ERROR"]) 
            stop(e)
    })("failed to load HTTP resource\n", 1549L, 8L, 0L, 0L, 1L, character(0))
16: .Call("RS_XML_ParseTree", as.character(file), handlers, as.logical(ignoreBlanks), 
        as.logical(replaceEntities), as.logical(asText), as.logical(trim), 
        as.logical(validate), as.logical(getDTD), as.logical(isURL), 
        as.logical(addAttributeNamespaces), as.logical(useInternalNodes), 
        as.logical(isHTML), as.logical(isSchema), as.logical(fullNamespaceInfo), 
        as.character(encoding), as.logical(useDotNames), xinclude, 
        error, addFinalizer, as.integer(options), as.logical(parentFirst), 
        PACKAGE = "XML")
15: htmlParse(doc, encoding = encoding)
14: .local(doc, header, colClasses, skip.rows, trim, elFun, as.data.frame, 
        which, ...)
13: readHTMLTable(url)
12: readHTMLTable(url)
11: ucscGenomes()
10: eval(expression, envir = callEnv)
9: eval(expression, envir = callEnv)
8: eval(expression, envir = callEnv)
7: .doCache(availToken, expression(ucscGenomes()), env)
6: .cacheGenomes(genome = genome)
5: .local(.Object, ...)
4: initialize(value, ...)
3: initialize(value, ...)
2: new("IdeogramTrack", chromosome = chromosome, genome = genome, 
       name = name, bands = bands, ...)
1: IdeogramTrack(genome = "hg19", chromosome = "chr7")

 

The connection between rtracklayer and UCSC is working:

library(rtracklayer)
session <- browseSession()
track(session, "knownGene")
UCSC track 'knownGene'
UCSCData object with 197782 ranges and 5 metadata columns:
                          seqnames           ranges strand |        name     score     itemRgb            thick                                     blocks
                             <Rle>        <IRanges>  <Rle> | <character> <numeric> <character>        <IRanges>                              <IRangesList>
       [1]                    chr1   [17369, 17436]      - |  uc031tla.1         0        <NA>   [17369, 17368]                                    [1, 68]
       [2]                    chr1   [29554, 31097]      + |  uc057aty.1         0        <NA>   [29554, 29553]     [   1,  486] [1011, 1114] [1423, 1544]
       [3]                    chr1   [30267, 31109]      + |  uc057atz.1         0        <NA>   [30267, 30266]                      [  1, 401] [710, 843]
       [4]                    chr1   [30366, 30503]      + |  uc031tlb.1         0        <NA>   [30366, 30365]                                   [1, 138]
       [5]                    chr1   [34554, 36081]      - |  uc001aak.4         0        <NA>   [34554, 34553]     [   1,  621] [ 724,  928] [1168, 1528]
       ...                     ...              ...    ... .         ...       ...         ...              ...                                        ...
  [197778] chr22_KI270733v1_random [179370, 179418]      + |  uc062fri.1         0        <NA> [179370, 179369]                                    [1, 49]
  [197779] chr22_KI270734v1_random [ 72411,  74814]      + |  uc062frj.1         0        <NA> [ 72838,  74124]                                  [1, 2404]
  [197780] chr22_KI270734v1_random [131494, 137392]      + |  uc032quk.2         0        <NA> [131646, 136994] [   1,  262] [ 343,  503] [3950, 4050] ...
  [197781] chr22_KI270734v1_random [138082, 161750]      - |  uc032qun.2         0        <NA> [138480, 156446] [   1,  586] [ 662,  750] [4113, 4211] ...
  [197782] chr22_KI270734v1_random [138082, 161852]      - |  uc032qum.2         0        <NA> [138480, 161586] [   1,  586] [ 662,  750] [4113, 4211] ...
  -------
  seqinfo: 455 sequences from hg38 genome

 

I updated both rtracklayer and Gviz today. Any pointers on how to fix this would be much appreciated.

Thanks!
Enrico

 

sessionInfo()
R version 3.4.2 (2017-09-28)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

Matrix products: default

locale:
[1] LC_COLLATE=English_United Kingdom.1252  LC_CTYPE=English_United Kingdom.1252    LC_MONETARY=English_United Kingdom.1252 LC_NUMERIC=C                            LC_TIME=English_United Kingdom.1252    

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

other attached packages:
[1] rtracklayer_1.38.3   Gviz_1.22.2          GenomicRanges_1.30.0 GenomeInfoDb_1.14.0  IRanges_2.12.0       S4Vectors_0.16.0     BiocGenerics_0.24.0 

loaded via a namespace (and not attached):
[1] Biobase_2.38.0                httr_1.3.1                    RMySQL_0.10.13                AnnotationHub_2.10.1          bit64_0.9-7                   splines_3.4.2                 shiny_1.0.5                 
[8] Formula_1.2-2                 assertthat_0.2.0              interactiveDisplayBase_1.16.0 latticeExtra_0.6-28           blob_1.1.0                    BSgenome_1.46.0               GenomeInfoDbData_1.0.0      
[15] Rsamtools_1.30.0              yaml_2.1.16                   progress_1.1.2                pillar_1.1.0                  RSQLite_2.0                   backports_1.1.2               lattice_0.20-35             
[22] biovizBase_1.26.0             digest_0.6.15                 RColorBrewer_1.1-2            XVector_0.18.0                checkmate_1.8.5               colorspace_1.3-2              httpuv_1.3.5                
[29] htmltools_0.3.6               Matrix_1.2-12                 plyr_1.8.4                    XML_3.98-1.9                  biomaRt_2.34.2                zlibbioc_1.24.0               xtable_1.8-2                
[36] scales_0.5.0                  BiocParallel_1.12.0           htmlTable_1.11.2              tibble_1.4.2                  AnnotationFilter_1.2.0        ggplot2_2.2.1                 SummarizedExperiment_1.8.1  
[43] GenomicFeatures_1.30.1        nnet_7.3-12                   lazyeval_0.2.1                mime_0.5                      survival_2.41-3               magrittr_1.5                  memoise_1.1.0               
[50] foreign_0.8-69                BiocInstaller_1.28.0          tools_3.4.2                   data.table_1.10.4-3           prettyunits_1.0.2             matrixStats_0.53.0            stringr_1.2.0               
[57] munsell_0.4.3                 cluster_2.0.6                 DelayedArray_0.4.1            ensembldb_2.2.0               AnnotationDbi_1.40.0          Biostrings_2.46.0             compiler_3.4.2              
[64] rlang_0.1.6                   RCurl_1.95-4.10               dichromat_2.0-0               rstudioapi_0.7                VariantAnnotation_1.24.5      htmlwidgets_1.0               bitops_1.0-6                
[71] base64enc_0.1-3               gtable_0.2.0                  curl_3.1                      DBI_0.7                       R6_2.2.2                      GenomicAlignments_1.14.1      gridExtra_2.3               
[78] knitr_1.19                    bit_1.1-12                    Hmisc_4.1-1                   ProtGenerics_1.10.0           stringi_1.1.6                 Rcpp_0.12.15                  rpart_4.1-11                
[85] acepack_1.4.1                
ADD COMMENTlink modified 4 months ago • written 4 months ago by enricoferrero560

This might be related to gviz ideogramTrack connection error though the error message appears to be different.

ADD REPLYlink modified 4 months ago • written 4 months ago by enricoferrero560

Hopefully just a transient issue. This is a simple download of a web page, via the XML package and its embedded nanohttp library (part of libxml2).

ADD REPLYlink written 4 months ago by Michael Lawrence10.0k
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