[BioC] rtracklayer issues with other packages?

[Martin Morgan]

mattia pelizzola <mattia.pelizzola at gmail.com> writes:

> 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") <- targetTracktrack(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?

Hi Mattia --

traceback() after the error should be informative. This can be fixed in
the code that causes the problem, so let us know...

Martin

> 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
>
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-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

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Phone: (206) 667-2793