[FIXED] Error in Gviz (actually, rtracklayer) | IdeogramTrack
7
6
Entering edit mode
Ramiro Magno ▴ 100
@ramiro-magno-12376
Last seen 5.5 years ago
CBMR, Faro, Portugal

> library(Gviz)
Loading required package: S4Vectors
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply,
    parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from ‘package:stats’:

    IQR, mad, xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, append, as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq, Filter, Find,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, Map, mapply, match, mget, order, paste, pmax,
    pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

Attaching package: ‘S4Vectors’

The following objects are masked from ‘package:hash’:

    values, values<-

The following objects are masked from ‘package:base’:

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: grid
> itrack <- IdeogramTrack(genome = "hg38" , chromosome = "chr5")
Error in getNodeSet(doc, "//table[@class='descTbl']")[[1L]] :
  subscript out of bounds
> sessionInfo()
R version 3.3.0 (2016-05-03)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Arch Linux

locale:
[1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8   
[5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8    LC_PAPER=en_US.UTF-8       LC_NAME=C                
[9] LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
[1] Gviz_1.18.1          GenomicRanges_1.26.2 GenomeInfoDb_1.10.3  IRanges_2.8.1        S4Vectors_0.12.1   
[6] BiocGenerics_0.20.0  BiocInstaller_1.24.0 hash_2.2.6           readr_1.0.0         

loaded via a namespace (and not attached):
[1] Rcpp_0.12.9                   biovizBase_1.22.0             lattice_0.20-33             
[4] Rsamtools_1.26.1              Biostrings_2.42.1             assertthat_0.1              
[7] digest_0.6.12                 mime_0.5                      R6_2.2.0                    
[10] plyr_1.8.4                    backports_1.0.5               acepack_1.4.1               
[13] RSQLite_1.1-2                 httr_1.2.1                    ggplot2_2.2.1               
[16] zlibbioc_1.20.0               GenomicFeatures_1.26.2        lazyeval_0.2.0              
[19] data.table_1.10.4             rpart_4.1-10                  Matrix_1.2-8                
[22] checkmate_1.8.2               splines_3.3.0                 BiocParallel_1.8.1          
[25] AnnotationHub_2.6.4           stringr_1.1.0                 foreign_0.8-66              
[28] htmlwidgets_0.8               RCurl_1.95-4.8                biomaRt_2.30.0              
[31] munsell_0.4.3                 shiny_1.0.0                   httpuv_1.3.3                
[34] rtracklayer_1.34.1            base64enc_0.1-3               htmltools_0.3.5             
[37] nnet_7.3-12                   SummarizedExperiment_1.4.0    interactiveDisplayBase_1.12.0
[40] tibble_1.2                    gridExtra_2.2.1               htmlTable_1.9               
[43] Hmisc_4.0-2                   matrixStats_0.51.0            XML_3.98-1.5                
[46] GenomicAlignments_1.10.0      bitops_1.0-6                  xtable_1.8-2                
[49] gtable_0.2.0                  DBI_0.5-1                     magrittr_1.5                
[52] scales_0.4.1                  stringi_1.1.2                 XVector_0.14.0              
[55] latticeExtra_0.6-28           Formula_1.2-1                 RColorBrewer_1.1-2          
[58] ensembldb_1.6.2               tools_3.3.0                   dichromat_2.0-0             
[61] BSgenome_1.42.0               Biobase_2.34.0                yaml_2.1.14                 
[64] survival_2.40-1               AnnotationDbi_1.36.2          colorspace_1.3-2            
[67] cluster_2.0.4                 memoise_1.0.0                 VariantAnnotation_1.20.2    
[70] knitr_1.15.1                 
Gviz rtracklayer • 6.3k views
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2
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I'm experiencing the same issue right now, from a pipeline that robustly worked over the past few months.

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1
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Same here. It appears that rtracklayer was updated yesterday (Feb 16).

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0
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Why do you think that? Here's the latest from the commit log:

------------------------------------------------------------------------
r123225 | m.lawrence | 2016-11-01 10:43:43 -0700 (Tue, 01 Nov 2016) | 2 lines
Changed paths:
   M /branches/RELEASE_3_4/madman/Rpacks/rtracklayer/DESCRIPTION
   M /branches/RELEASE_3_4/madman/Rpacks/rtracklayer/src/bigWig.c

port blockSize fix to release

And that was the change that brought us to the current release version:

 svn diff -r HEAD:123224 DESCRIPTION
Index: DESCRIPTION
===================================================================
--- DESCRIPTION    (revision 126778)
+++ DESCRIPTION    (revision 123224)
@@ -1,6 +1,6 @@
 Package: rtracklayer
 Title: R interface to genome browsers and their annotation tracks
-Version: 1.34.1
+Version: 1.34.0
 Author: Michael Lawrence, Vince Carey, Robert Gentleman
 Depends: R (>= 3.3), methods, GenomicRanges (>= 1.21.20)
 Imports: XML (>= 1.98-0), BiocGenerics (>= 0.13.8),

This is way more likely to be changes on UCSC's website.

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0
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Ah, my mistake. I made the assumption because the rtracklayer documentation was updated yesterday. (Rather, it has yesterday's date on it.)

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2
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I experience the same thing. Would be good to get this fixed soon... 

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1
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Any update on a fix for this? 

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@james-w-macdonald-5106
Last seen 5 hours ago
United States

I have committed a fix for this to both the release and devel versions of rtracklayer. As usual, these will take a day or so to propagate through the build servers. Or you can hang with the cool kids by getting the updates from subversion.
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I tried the subversion and the error is still there. 

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I have no idea what you mean by 'I tried the subversion' but whatever you did, it wasn't what you should have done. The fix has propagated through the build servers and you can just to

library(BiocInstaller)

biocLite(rtracklayer)

And things will work correctly.

In addition, please don't use the 'Add your answer' box below, unless you are actually adding an answer. We now have my actual answer buried by three different people who 'added answers' that are not by any stretch of the imagination actual answers...

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@james-w-macdonald-5106
Last seen 5 hours ago
United States

This is something from rtracklayer.

> rtracklayer::ucscGenomes()
Error in getNodeSet(doc, "//table[@class='descTbl']")[[1L]] :
  subscript out of bounds

Not sure if Michael Lawrence will see this thread, so I'll ping him directly.
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I was bitten by the same - and in addition, wonder whether this (currently unresolved) issue could also be due to a correlated set of updates at the UCSC website? Gviz - UcscTrack

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Let's see what Michael finds out. There have been API changes at UCSC in the past.A bit of a nightmare to keep on top of such a moving target....

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unit tests?

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guifengwei ▴ 10
@guifengwei-12886
Last seen 5.9 years ago

Hi,

Thanks to this above information. I managed to plot the IdeogramTrack.

I downloaded the cytoband info from UCSC website. for example mm10 ( http://hgdownload.cse.ucsc.edu/goldenpath/mm10/database/cytoBandIdeo.txt.gz )

Then, read this info as data.frame,

data <- read.table("cytoBandIdeo.txt", header=F, sep="\t")
colnames(data) <-c('chrom', 'chromStart', 'chromEnd', 'name', 'gieStain')
ideoTrack <- IdeogramTrack(genome="mm10",chromosome = "chr2", bands=data)
plotTracks(ideoTrack, from=143910627, to=143938620, showBandId = TRUE, cex.bands = 0.5)

 
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aina.jene ▴ 10
@ainajene-12984
Last seen 7.3 years ago
ISGlobal - Barcelona

 

Hello everybody, I have the exact same problem:

annotation.table = getAnnotation(IlluminaHumanMethylation450kanno.ilmn12.hg19)
annotY = annotation.table[annotation.table$chr == "chrY",]
gr <- GRanges(Rle(annotY$chr),
              ranges = IRanges(start = as.numeric(annotY$pos), width = 25),
              strand = Rle(annotY$strand))
chr <- unique(annotY$chr)
gen <- "hg19"
atrack <- AnnotationTrack(gr, name = "CpG")
gtrack <- GenomeAxisTrack()
itrack <- IdeogramTrack(genome = gen, chromosome = chr, name="")
plotTracks(list(itrack, gtrack, atrack))

Error in getNodeSet(doc, "//table[@class='descTbl']")[[1L]] : 
  subscript out of bounds


This is my sessionInfo()

R version 3.3.3 (2017-03-06)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X Yosemite 10.10.5

locale:
[1] ca_ES.UTF-8/ca_ES.UTF-8/ca_ES.UTF-8/C/ca_ES.UTF-8/ca_ES.UTF-8

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

other attached packages:
 [1] IlluminaHumanMethylation450kanno.ilmn12.hg19_0.2.1 minfi_1.18.6                                      
 [3] bumphunter_1.12.0                                  locfit_1.5-9.1                                    
 [5] iterators_1.0.8                                    foreach_1.4.3                                     
 [7] Biostrings_2.40.2                                  XVector_0.12.1                                    
 [9] SummarizedExperiment_1.2.3                         lattice_0.20-34                                   
[11] Biobase_2.32.0                                     Gviz_1.16.5                                       
[13] GenomicRanges_1.24.3                               GenomeInfoDb_1.8.7                                
[15] IRanges_2.6.1                                      S4Vectors_0.10.3                                  
[17] BiocGenerics_0.18.0                                biomaRt_2.28.0                                    

loaded via a namespace (and not attached):
 [1] nlme_3.1-131                  ProtGenerics_1.4.0            bitops_1.0-6                 
 [4] matrixStats_0.51.0            RColorBrewer_1.1-2            httr_1.2.1                   
 [7] tools_3.3.3                   backports_1.0.5               doRNG_1.6                    
[10] nor1mix_1.2-2                 R6_2.2.0                      rpart_4.1-10                 
[13] Hmisc_4.0-2                   DBI_0.6                       lazyeval_0.2.0               
[16] colorspace_1.3-2              nnet_7.3-12                   gridExtra_2.2.1              
[19] base64_2.0                    preprocessCore_1.34.0         htmlTable_1.9                
[22] pkgmaker_0.22                 rtracklayer_1.32.2            scales_0.4.1.9002            
[25] checkmate_1.8.2               quadprog_1.5-5                genefilter_1.54.2            
[28] stringr_1.2.0                 digest_0.6.12                 Rsamtools_1.24.0             
[31] foreign_0.8-67                illuminaio_0.14.0             siggenes_1.46.0              
[34] GEOquery_2.38.4               base64enc_0.1-3               dichromat_2.0-0              
[37] htmltools_0.3.5               limma_3.28.21                 ensembldb_1.4.7              
[40] BSgenome_1.40.1               htmlwidgets_0.8               rlang_0.1.1                  
[43] RSQLite_1.1-2                 BiocInstaller_1.22.3          shiny_1.0.3                  
[46] mclust_5.2.3                  BiocParallel_1.6.6            acepack_1.4.1                
[49] VariantAnnotation_1.18.7      RCurl_1.95-4.8                magrittr_1.5                 
[52] Formula_1.2-1                 Matrix_1.2-8                  Rcpp_0.12.12                 
[55] munsell_0.4.3                 stringi_1.1.3                 MASS_7.3-45                  
[58] zlibbioc_1.18.0               plyr_1.8.4                    AnnotationHub_2.4.2          
[61] splines_3.3.3                 annotate_1.50.1               multtest_2.28.0              
[64] GenomicFeatures_1.24.5        mzR_2.6.3                     xcms_1.48.0                  
[67] knitr_1.15.1                  beanplot_1.2                  rngtools_1.2.4               
[70] codetools_0.2-15              XML_3.98-1.5                  biovizBase_1.20.0            
[73] latticeExtra_0.6-28           data.table_1.10.4             httpuv_1.3.5                 
[76] openssl_0.9.6                 gtable_0.2.0                  reshape_0.8.6                
[79] ggplot2_2.2.1.9000            mime_0.5                      xtable_1.8-2

Any help? 

Thank you very much!

Aina

 

 

 
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Aedin Culhane ▴ 510
@aedin-culhane-1526
Last seen 5.2 years ago
United States

All fixed

 
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> itrack <- IdeogramTrack("chr1","hg38")
> sessionInfo()
R version 3.3.1 (2016-06-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux 8 (jessie)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
 [1] Gviz_1.18.1          GenomicRanges_1.26.2 GenomeInfoDb_1.10.3
 [4] pd.hta.2.0_3.12.1    DBI_0.5-1            oligo_1.38.0        
 [7] Biobase_2.34.0       oligoClasses_1.36.0  RSQLite_1.1-2       
[10] Biostrings_2.42.1    XVector_0.14.0       IRanges_2.8.1       
[13] S4Vectors_0.12.1     BiocGenerics_0.20.0
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I got what looks like the same error today. Not sure from the thread if this has been fixed or not. Any suggestions ?

Thanks

itrack <- IdeogramTrack(genome = "hg19", chromosome = "chr1")
Error in getNodeSet(doc, "//table[@class='descTbl']")[[1L]] : 
  subscript out of bounds
> traceback()
11: ucscGenomes()
10: eval(expr, envir, enclos)
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 = "chr1")
> sessionInfo()
R version 3.2.3 (2015-12-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.2 LTS

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8    LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
[1] rtracklayer_1.30.4   Gviz_1.14.7          GenomicRanges_1.22.4 GenomeInfoDb_1.6.3   IRanges_2.4.8       
[6] S4Vectors_0.8.11     BiocGenerics_0.16.1  BiocInstaller_1.20.3

loaded via a namespace (and not attached):
 [1] SummarizedExperiment_1.0.2 VariantAnnotation_1.16.4   splines_3.2.3              lattice_0.20-34           
 [5] colorspace_1.3-2           htmltools_0.3.5            GenomicFeatures_1.22.13    base64enc_0.1-3           
 [9] XML_3.98-1.5               survival_2.40-1            foreign_0.8-67             DBI_0.5-1                 
[13] BiocParallel_1.4.3         RColorBrewer_1.1-2         lambda.r_1.1.9             matrixStats_0.51.0        
[17] plyr_1.8.4                 stringr_1.2.0              zlibbioc_1.16.0            Biostrings_2.38.4         
[21] munsell_0.4.3              gtable_0.2.0               futile.logger_1.4.3        htmlwidgets_0.8           
[25] memoise_1.0.0              latticeExtra_0.6-28        Biobase_2.30.0             knitr_1.15.1              
[29] biomaRt_2.26.1             AnnotationDbi_1.32.3       htmlTable_1.9              Rcpp_0.12.9               
[33] acepack_1.4.1              BSgenome_1.38.0            scales_0.4.1               backports_1.0.5           
[37] checkmate_1.8.2            Hmisc_4.0-2                XVector_0.10.0             ggthemr_1.0.2             
[41] Rsamtools_1.22.0           gridExtra_2.2.1            ggplot2_2.2.1              digest_0.6.12             
[45] stringi_1.1.2              biovizBase_1.18.0          tools_3.2.3                bitops_1.0-6              
[49] magrittr_1.5               lazyeval_0.2.0             RCurl_1.95-4.8             tibble_1.2                
[53] RSQLite_1.1-2              dichromat_2.0-0            Formula_1.2-1              cluster_2.0.5             
[57] futile.options_1.0.0       Matrix_1.2-8               data.table_1.10.4          assertthat_0.1            
[61] rpart_4.1-10               GenomicAlignments_1.6.3    nnet_7.3-12
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Yes, it has been fixed. In the release and devel versions, as I said above. But you are using versions of R and Bioc that are almost two years out of date, which will NEVER get fixed. We only support the release and devel versions, so if you want support and bug fixes, you have to keep current.

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I still am having this error even for 

> itrack <- IdeogramTrack("chr1","hg38")

I have the most updated version of R and I have reinstalled all my packages. Not sure what else I can do, I have grabbed it from bioconductor in the normal way, I think it is because there are different versions on mac and linux? I have also been using it with a pipeline that has been very robust for the past few months. I am thinking I will have to move all my data and code to a linux machine?

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There are not different versions for MacOS and LInux. Why do you think that? What do you mean by 'I have grabbed it from bioconductor in the normal way'? You need to post the output from sessionInfo() as well.

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Aedin Culhane ▴ 510
@aedin-culhane-1526
Last seen 5.2 years ago
United States

Hi. Can you post your updated session info. It works ok on my mac

Aedin
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@jimbou-romsen-12680
Last seen 7.7 years ago

Hi all,

I'm observing this error since this week.

UcscTrack(track="foo", genome="mm9", chromosome=3, from=1000, to=10000, trackType="AnnotationTrack", id="id", feature="type", start="from", end="to")
Error: failed to load external entity "http://genome.ucsc.edu/FAQ/FAQreleases"

or

rtracklayer::ucscGenomes()
Error: failed to load external entity "http://genome.ucsc.edu/FAQ/FAQreleases"

or

itrack <- IdeogramTrack("chr1","hg38")
Error: failed to load external entity "http://genome.ucsc.edu/FAQ/FAQreleases"

Did someone else encounter this error as well?

sessionInfo()
R version 3.3.3 (2017-03-06)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

locale:
[1] LC_COLLATE=German_Germany.1252  LC_CTYPE=German_Germany.1252    LC_MONETARY=German_Germany.1252
[4] LC_NUMERIC=C                    LC_TIME=German_Germany.1252    

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

other attached packages:
[1] Gviz_1.18.2          rtracklayer_1.34.2   GenomicRanges_1.26.4 GenomeInfoDb_1.10.3 
[5] IRanges_2.8.2        S4Vectors_0.12.2     BiocGenerics_0.20.0 
[...]
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Got the same error today.

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This post is 2.4 years old! If you are having a problem, make a new post that includes a self-contained example showing the problem, plus include the output from sessionInfo

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