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Question: [FIXED] Error in Gviz (actually, rtracklayer) | IdeogramTrack
5
gravatar for ramiro.magno
7 days ago by
ramiro.magno50
ramiro.magno50 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 Aedin Culhane510 • written 7 days ago by ramiro.magno50
1

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

ADD REPLYlink modified 7 days ago • written 7 days ago by federico.comoglio90
1

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

ADD REPLYlink written 7 days 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 7 days ago by James W. MacDonald42k

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 7 days ago by masonmlai10
1

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

ADD REPLYlink written 7 days ago by kristianunger10

Any update on a fix for this? 

ADD REPLYlink written 2 days ago by Cian Murphy30
5
gravatar for James W. MacDonald
6 days ago by
United States
James W. MacDonald42k 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 6 days ago by James W. MacDonald42k

I tried the subversion and the error is still there. 

ADD REPLYlink written 2 days ago by Cian Murphy30

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 2 days ago by James W. MacDonald42k
4
gravatar for James W. MacDonald
7 days ago by
United States
James W. MacDonald42k 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 7 days ago by James W. MacDonald42k
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 6 days ago by Wolfgang Huber12k
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 6 days ago by florian.hahne@novartis.com1.4k
1

unit tests?

ADD REPLYlink written 6 days ago by Wolfgang Huber12k
0
gravatar for Aedin Culhane
1 day ago by
Aedin Culhane510
United States
Aedin Culhane510 wrote:

All fixed

 

ADD COMMENTlink modified 1 day ago • written 1 day 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 1 day ago by James W. MacDonald42k
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