[BioC] rtracklayer issues with other packages?

[mattia pelizzola]

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