Entering edit mode
Hi,
I am running some code from the rtracklayer vignette. If I start a new
R session and I load the rtracklayer only, the code works fine.
Unfortunately, I need many other packages at the same time. For some
reason when loading all the other packages I get this error:
> data(targets)
> targetRanges <- IRanges(targets$start, targets$end)
> targetTrack <- GenomicData(targetRanges, targets[,
c("strand","name", "target")], chrom = paste("chr", targets$chrom,sep
= ""), genome = "hg19")
> session <- browserSession("UCSC")
> track(session, "targets") <- targetTrack
Error: evaluation nested too deeply: infinite recursion /
options(expressions=)?
I guess there is some issue with other packages. I already had similar
problems with other function, like the complement function of
Biostrings, that was replaced by the complement function in the graph
package .. so I found that the order the packages are loaded can be
critical. Not sure it is the same issue with rtracklayer though, as I
have no clue on which package, if any, is interfering.
Any suggestion?
thanks!
mattia
> sessionInfo()
R version 2.11.0 (2010-04-22)
x86_64-unknown-linux-gnu
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=C 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 stats graphics grDevices utils datasets
methods
[8] base
other attached packages:
[1] rtracklayer_1.8.1
[2] RCurl_1.4-2
[3] RMySQL_0.7-4
[4] BSgenome.Athaliana.TAIR.04232008_1.3.16
[5] BSgenome.Mmusculus.UCSC.mm9_1.3.16
[6] BSgenome.Hsapiens.UCSC.hg18_1.3.16
[7] BSgenome_1.16.1
[8] Biostrings_2.16.0
[9] GenomicRanges_1.0.1
[10] GOstats_2.14.0
[11] graph_1.26.0
[12] Category_2.14.0
[13] org.Hs.eg.db_2.4.1
[14] RSQLite_0.9-0
[15] DBI_0.2-5
[16] AnnotationDbi_1.10.1
[17] Biobase_2.8.0
[18] marray_1.26.0
[19] limma_3.4.0
[20] gplots_2.7.4
[21] caTools_1.10
[22] bitops_1.0-4.1
[23] gdata_2.8.0
[24] gtools_2.6.2
[25] nlme_3.1-96
[26] snow_0.3-3
[27] IRanges_1.6.1
loaded via a namespace (and not attached):
[1] annotate_1.26.0 genefilter_1.30.0 GO.db_2.4.1
GSEABase_1.10.0
[5] lattice_0.18-5 RBGL_1.24.0 splines_2.11.0
survival_2.35-8
[9] tools_2.11.0 XML_3.1-0 xtable_1.5-6
