Hi Martin,

I am back on this rtracklayer issue after a while. There is a bug
specifically when the package graph is loaded too (before or after
rtracklayer). The code (apart from library(graph)) is from the rtracklayer
vignette:

> library(graph)
> library(rtracklayer)
Loading required package: RCurl
Loading required package: bitops

> 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=)?
> traceback()
3313: mode(expr)
3312: match(x, table, nomatch = 0L)
3311: mode(expr) %in% c("call", "expression", "(", "function")
3310: deparse(substitute(arg))
3309: eval(formal.args[[deparse(substitute(arg))]])
3308: match.arg(subformat)
3307: export.ucsc(object, con, subformat, append, ...)
3306: export.ucsc(object, con, subformat, append, ...)
3305: export.ucsc(object, con, subformat, append, ...)
3304: export.ucsc(object, con, subformat, append, ...)
.............
26: export.ucsc(object, con, subformat, append, ...)
25: export.ucsc(object, con, subformat, append, ...)
24: export.ucsc(object, con, subformat, append, ...)
23: export.ucsc(object, con, subformat, append, ...)
22: export.ucsc(object, con, subformat, append, ...)
21: export.ucsc(object[[i]], con, subformat, name = trackNames[i],
        append = append, ...)
20: export.ucsc(object[[i]], con, subformat, name = trackNames[i],
        append = append, ...)
19: .local(object, con, subformat, append, ...)
18: fun(object, con, ...)
17: fun(object, con, ...)
16: export(object, con, format, ...)
15: export(object, con, format, ...)
14: export(object, format = "ucsc", subformat = format, ...)
13: export(object, format = "ucsc", subformat = format, ...)
12: .local(object, ...)
11: ucscForm(tracks, format, ...)
10: ucscForm(tracks, format, ...)
9: FUN(X[[1L]], ...)
8: lapply(split(X, group), FUN, ...)
7: tapply(value, unlist(genomes), function(tracks) {
       form <- ucscForm(tracks, format, ...)
       response <- ucscPost(object, "custom", form)
   })
6: .local(object, ..., value = value)
5: `track<-`(`*tmp*`, name, ..., value = <S4 object of class
"RangedDataList">)
4: `track<-`(`*tmp*`, name, ..., value = <S4 object of class
"RangedDataList">)
3: .local(object, ..., value = value)
2: `track<-`(`*tmp*`, "targets", value = <S4 object of class "RangedData">)
1: `track<-`(`*tmp*`, "targets", value = <S4 object of class "RangedData">)

> sessionInfo()
R version 2.12.0 (2010-10-15)
Platform: x86_64-unknown-linux-gnu (64-bit)

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] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] rtracklayer_1.10.5 RCurl_1.5-0        bitops_1.0-4.1
graph_1.28.0

loaded via a namespace (and not attached):
[1] Biobase_2.10.0      Biostrings_2.18.2   BSgenome_1.18.2
[4] GenomicRanges_1.2.1 IRanges_1.8.5       tools_2.12.0
[7] XML_3.2-0


I can't avoid having graph loaded since it is needed by GOstats, which I
need.
Thanks for any hint,

mattia








On Fri, Jul 23, 2010 at 8:03 PM, Martin Morgan <mtmorgan@fhcrc.org> wrote:

> mattia pelizzola <mattia.pelizzola@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
> >
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor@stat.math.ethz.ch
> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> > Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
>
> --
> Martin Morgan
> Computational Biology / Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N.
> PO Box 19024 Seattle, WA 98109
>
> Location: Arnold Building M1 B861
> Phone: (206) 667-2793
>

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