Question

Gviz IdeogramTrack Hsapiens/Mmusculus error

1

Entering edit mode

Merienne Nicolas ▴ 120

@merienne-nicolas-6729

Last seen 7.1 years ago

Switzerland

Hello all,

I have a strange error when trying to create an ideogram with Gviz IdeogramTrack function. Here is my code:

library(Gviz)

data(cpgIslands)

chr = as.character(unique(seqnames(cpgIslands)))

id = IdeogramTrack(genome = 'hg19', chromosome = chr)

Error: too deeply nested evaluations: Infinite recursion  / options(expressions =)?

For my session, options(expressions) = 5000 by default, I tried to change to 10000 or 50000. With both, the error message was not appearing, however no ideogramtrack object was created and I can not launch the plotTracks function. I found in other discussions not related to Bioconductor that it could be a problem of memory limit and often appear in infinite loop/functions. But I am not sure that this is what is done with IdeogramTrack function... Anyone has an idea of the reason of such problem?

Here is my sessionInfo():

R version 3.2.0 Patched (2015-05-27 r68420)
Platform: x86_64-apple-darwin10.8.0 (64-bit)
Running under: OS X 10.6.8 (Snow Leopard)

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

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

other attached packages:
[1] Gviz_1.12.0          GenomicRanges_1.20.4 GenomeInfoDb_1.4.0   IRanges_2.2.2        S4Vectors_0.6.0     
[6] BiocGenerics_0.14.0

loaded via a namespace (and not attached):
 [1] Rcpp_0.11.6              RColorBrewer_1.1-2       futile.logger_1.4.1      plyr_1.8.2              
 [5] XVector_0.8.0            GenomicFeatures_1.20.1   bitops_1.0-6             futile.options_1.0.0    
 [9] tools_3.2.0              zlibbioc_1.14.0          rpart_4.1-9              biomaRt_2.24.0          
[13] digest_0.6.8             BSgenome_1.36.0          biovizBase_1.16.0        RSQLite_1.0.0           
[17] gtable_0.1.2             lattice_0.20-31          DBI_0.3.1                proto_0.3-10            
[21] gridExtra_0.9.1          cluster_2.0.1            rtracklayer_1.28.4       stringr_1.0.0           
[25] Biostrings_2.36.1        nnet_7.3-9               Biobase_2.28.0           AnnotationDbi_1.30.1    
[29] survival_2.38-1          XML_3.98-1.1             BiocParallel_1.2.2       foreign_0.8-63          
[33] Formula_1.2-1            latticeExtra_0.6-26      lambda.r_1.1.7           ggplot2_1.0.1           
[37] reshape2_1.4.1           magrittr_1.5             splines_3.2.0            Hmisc_3.16-0            
[41] scales_0.2.4             Rsamtools_1.20.4         matrixStats_0.14.0       MASS_7.3-40             
[45] GenomicAlignments_1.4.1  dichromat_2.0-0          colorspace_1.2-6         stringi_0.4-1           
[49] acepack_1.3-3.3          RCurl_1.95-4.6           munsell_0.4.2            VariantAnnotation_1.14.1

Also I precise that I am using MacOS 10.6.8 Snow Leopard (I don't know if it can explain the error...)

Thank in advance,

Nicolas

gviz • 2.5k views

ADD COMMENT • link 9.6 years ago • updated 9.5 years ago Merienne Nicolas ▴ 120

score 0 · Answer 1 · 2015-06-02

0

Entering edit mode

florian.hahne@novartis.com ★ 1.6k

@florianhahnenovartiscom-3784

Last seen 6.3 years ago

Switzerland

Hi Nicolas,

I believe this is really a problem with the rtracklayer connection to UCSC.

For me this already fails when calling browserSession() directly

library(rtracklayer)
browserSession()

Can you confirm this? I have involved Michael Lawrence in this discussion to take a look on the rtracklayer side.

Florian

ADD COMMENT • link 9.6 years ago florian.hahne@novartis.com ★ 1.6k

score 0 · Answer 2 · 2015-06-02

0

Entering edit mode

florian.hahne@novartis.com ★ 1.6k

@florianhahnenovartiscom-3784

Last seen 6.3 years ago

Switzerland

Hi Nicolas,

I believe this is really a problem with the rtracklayer connection to UCSC.

For me this already fails when calling browserSession() directly

library(rtracklayer)
browserSession()

Can you confirm this? I have involved Michael Lawrence in this discussion to take a look on the rtracklayer side.

Florian

ADD COMMENT • link 9.6 years ago florian.hahne@novartis.com ★ 1.6k

0

Entering edit mode

Hi Florian,

Indeed, this fails for me too. Here is the error message :

Error in unique(unlist(lapply(dots, methods:::.class1))) :
  erreur d'évaluation de l'argument 'x' lors de la sélection d'une méthode pour la fonction 'unique' : Error in unlist(lapply(dots, methods:::.class1)) :
  erreur d'évaluation de l'argument 'x' lors de la sélection d'une méthode pour la fonction 'unlist' : Erreur : évaluations trop profondément imbriquées : récursion infinie / options(expressions=) ?

(there are part in French, do not hesitate to tell me if you need I translate it...)

I don't know if it can help you, but the version of rtracklayer is rtraclayer_1.28.4. In parallel, one of my colleague has also tried and this has worked well for both browserSession() and IdeogramTrack() functions. The main difference with my computer is that she is using the latest version of MacOSX (Yosemite_10.10) with an older version of R (R_3.1.2, 2014-10-31) and rtracklayer_1.26.3. Could it be a problem of compatibility between rtracklayer_1.28.4 and R_3.2.0?

Thank you for your help.

Nicolas

ADD REPLY • link 9.6 years ago Merienne Nicolas ▴ 120

0

Entering edit mode

I had exactly the same issue, when I downgraded to R 3.1.3 it worked perfectly.

ADD REPLY • link 9.5 years ago Tom • 0

0

Entering edit mode

Indeed, this is working for hg19 but not for mm10 or older Mus muculus genome version...

Is there something new for R 3.2.0?

Thank you

Nico

ADD REPLY • link 9.5 years ago Merienne Nicolas ▴ 120

score 0 · Answer 3 · 2015-06-18

0

Entering edit mode

florian.hahne@novartis.com ★ 1.6k

@florianhahnenovartiscom-3784

Last seen 6.3 years ago

Switzerland

Can you make sure that your rtracklayer package is up to date? This got fixed a couple of days ago.

ADD COMMENT • link 9.5 years ago florian.hahne@novartis.com ★ 1.6k

score 0 · Answer 4 · 2015-06-18

I just used biocLite to reinstall rtracklayer and Gviz but I am still getting the same error...

sessionInfo():

R version 3.2.0 Patched (2015-05-27 r68420) Platform: x86_64-apple-darwin10.8.0 (64-bit) Running under: OS X 10.6.8 (Snow Leopard)

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

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

other attached packages: [1] Gviz_1.12.0 rtracklayer_1.28.4 GenomicRanges_1.20.5 GenomeInfoDb_1.4.0 IRanges_2.2.4 [6] S4Vectors_0.6.0 BiocGenerics_0.14.0 BiocInstaller_1.18.3

loaded via a namespace (and not attached): [1] Rcpp_0.11.6 RColorBrewer_1.1-2 futile.logger_1.4.1 plyr_1.8.2 [5] XVector_0.8.0 GenomicFeatures_1.20.1 bitops_1.0-6 futile.options_1.0.0 [9] tools_3.2.0 zlibbioc_1.14.0 rpart_4.1-9 biomaRt_2.24.0 [13] digest_0.6.8 BSgenome_1.36.0 biovizBase_1.16.0 RSQLite_1.0.0 [17] gtable_0.1.2 lattice_0.20-31 DBI_0.3.1 proto_0.3-10 [21] gridExtra_0.9.1 cluster_2.0.1 stringr_1.0.0 Biostrings_2.36.1 [25] nnet_7.3-9 Biobase_2.28.0 AnnotationDbi_1.30.1 survival_2.38-1 [29] XML_3.98-1.1 BiocParallel_1.2.3 foreign_0.8-63 Formula_1.2-1 [33] latticeExtra_0.6-26 ggplot2_1.0.1 reshape2_1.4.1 lambda.r_1.1.7 [37] magrittr_1.5 splines_3.2.0 Hmisc_3.16-0 matrixStats_0.14.0 [41] scales_0.2.4 Rsamtools_1.20.4 MASS_7.3-40 GenomicAlignments_1.4.1 [45] dichromat_2.0-0 colorspace_1.2-6 stringi_0.4-1 acepack_1.3-3.3 [49] RCurl_1.95-4.6 munsell_0.4.2 VariantAnnotation_1.14.3

Do I have to use the devel version of rtracklayer?

Thank you for your help

Nico