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
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:  fr_FR.UTF-8/fr_FR.UTF-8/fr_FR.UTF-8/C/fr_FR.UTF-8/fr_FR.UTF-8 attached base packages:  grid parallel stats4 stats graphics grDevices utils datasets methods base other attached packages:  Gviz_1.12.0 GenomicRanges_1.20.4 GenomeInfoDb_1.4.0 IRanges_2.2.2 S4Vectors_0.6.0  BiocGenerics_0.14.0 loaded via a namespace (and not attached):  Rcpp_0.11.6 RColorBrewer_1.1-2 futile.logger_1.4.1 plyr_1.8.2  XVector_0.8.0 GenomicFeatures_1.20.1 bitops_1.0-6 futile.options_1.0.0  tools_3.2.0 zlibbioc_1.14.0 rpart_4.1-9 biomaRt_2.24.0  digest_0.6.8 BSgenome_1.36.0 biovizBase_1.16.0 RSQLite_1.0.0  gtable_0.1.2 lattice_0.20-31 DBI_0.3.1 proto_0.3-10  gridExtra_0.9.1 cluster_2.0.1 rtracklayer_1.28.4 stringr_1.0.0  Biostrings_2.36.1 nnet_7.3-9 Biobase_2.28.0 AnnotationDbi_1.30.1  survival_2.38-1 XML_3.98-1.1 BiocParallel_1.2.2 foreign_0.8-63  Formula_1.2-1 latticeExtra_0.6-26 lambda.r_1.1.7 ggplot2_1.0.1  reshape2_1.4.1 magrittr_1.5 splines_3.2.0 Hmisc_3.16-0  scales_0.2.4 Rsamtools_1.20.4 matrixStats_0.14.0 MASS_7.3-40  GenomicAlignments_1.4.1 dichromat_2.0-0 colorspace_1.2-6 stringi_0.4-1  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,