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Question: [FIXED] Error in Gviz (actually, rtracklayer) | IdeogramTrack
6
gravatar for Ramiro Magno
5 months ago by
Ramiro Magno60
CBMR, Faro, Portugal
Ramiro Magno60 wrote:

> 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                 

ADD COMMENTlink modified 1 day ago by aina.jene0 • written 5 months ago by Ramiro Magno60
2

I'm experiencing the same issue right now, from a pipeline that robustly worked over the past few months.

ADD REPLYlink modified 5 months ago • written 5 months ago by federico.comoglio100
1

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

ADD REPLYlink written 5 months ago by masonmlai10

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.

ADD REPLYlink written 5 months ago by James W. MacDonald43k

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

ADD REPLYlink written 5 months ago by masonmlai10
2

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

ADD REPLYlink written 5 months ago by kristianunger20
1

Any update on a fix for this? 

ADD REPLYlink written 4 months ago by Cian Murphy40
5
gravatar for James W. MacDonald
5 months ago by
United States
James W. MacDonald43k wrote:

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.

ADD COMMENTlink written 5 months ago by James W. MacDonald43k

I tried the subversion and the error is still there. 

ADD REPLYlink written 4 months ago by Cian Murphy40

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...

ADD REPLYlink written 4 months ago by James W. MacDonald43k
5
gravatar for James W. MacDonald
5 months ago by
United States
James W. MacDonald43k wrote:

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.

ADD COMMENTlink written 5 months ago by James W. MacDonald43k
1

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

ADD REPLYlink written 5 months ago by Wolfgang Huber13k
1

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....

ADD REPLYlink written 5 months ago by florian.hahne@novartis.com1.5k
1

unit tests?

ADD REPLYlink written 5 months ago by Wolfgang Huber13k
0
gravatar for Aedin Culhane
4 months ago by
Aedin Culhane510
United States
Aedin Culhane510 wrote:

All fixed

 

ADD COMMENTlink modified 4 months ago • written 4 months ago by Aedin Culhane510
> 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
ADD REPLYlink written 4 months ago by James W. MacDonald43k
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
ADD REPLYlink written 4 months ago by kevbrick0

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.

ADD REPLYlink written 4 months ago by James W. MacDonald43k

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?

ADD REPLYlink modified 4 months ago • written 4 months ago by csugai0

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.

ADD REPLYlink written 4 months ago by James W. MacDonald43k
0
gravatar for Aedin Culhane
4 months ago by
Aedin Culhane510
United States
Aedin Culhane510 wrote:

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

Aedin

ADD COMMENTlink written 4 months ago by Aedin Culhane510
0
gravatar for jimbou-romsen
3 months ago by
jimbou-romsen0 wrote:

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 
[...]
ADD COMMENTlink written 3 months ago by jimbou-romsen0
0
gravatar for guifengwei
12 weeks ago by
guifengwei0
guifengwei0 wrote:

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)

 

ADD COMMENTlink written 12 weeks ago by guifengwei0
0
gravatar for aina.jene
1 day ago by
aina.jene0
ISGlobal - Barcelona
aina.jene0 wrote:

 

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

 

 

 

ADD COMMENTlink modified 1 day ago • written 1 day ago by aina.jene0
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