[BioC] ShortRead report function crash in x86_64-apple

[Hugo Naya]

Hi,
the issue was solved in ShortRead_1.6.2.
Thank you,

Hugo

El 28/04/2010, a las 03:38 p.m., Hugo Naya escribió:

> Hi,
> I've recently installed R2.11.0 and BioC2.6 (MacBook Pro). While in  
> the i386-apple-darwin9.8.0 the package "ShortRead" works fine, when  
> I tried the same in the x86_64-apple-darwin9.8.0 the function  
> "report" crashed with the following error:
>
> *** caught segfault ***
> address 0x110c0a110000, cause 'memory not mapped'
>
> Any clue?
> TIA,
>
> Hugo
>
>
> #####  CHUNK OF CODE ####
> library(ShortRead)
> exptPath <- system.file("extdata", package = "ShortRead")
> sp <- SolexaPath(exptPath)
> qaSummary <- qa(sp)
> report(qaSummary, dest = "/Users/kangu/tmp/qareport")
>
>
>
>
> #### MY SESSION ####
>
> [R.app GUI 1.33 (5582) x86_64-apple-darwin9.8.0]
>
> > library(ShortRead)
> Loading required package: IRanges
>
> Attaching package: 'IRanges'
>
> The following object(s) are masked from 'package:base':
>
>    cbind, Map, mapply, order, paste, pmax, pmax.int, pmin, pmin.int,  
> rbind, rep.int, table
>
> Loading required package: GenomicRanges
> Loading required package: Biostrings
> Loading required package: lattice
> Loading required package: Rsamtools
> > exptPath <- system.file("extdata", package = "ShortRead")
> > sp <- SolexaPath(exptPath)
> > qaSummary <- qa(sp)
> >
> > sessionInfo()
> R version 2.11.0 (2010-04-22)
> x86_64-apple-darwin9.8.0
>
> locale:
> [1] es_ES.UTF-8/es_ES.UTF-8/C/C/es_ES.UTF-8/es_ES.UTF-8
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] ShortRead_1.6.0     Rsamtools_1.0.0     lattice_0.18-5       
> Biostrings_2.16.0   GenomicRanges_1.0.1 IRanges_1.6.0
>
> loaded via a namespace (and not attached):
> [1] Biobase_2.8.0 grid_2.11.0   hwriter_1.2
> >
> > report(qaSummary, dest = "/Users/kangu/tmp/qareport")
>
> *** caught segfault ***
> address 0x110c0a110000, cause 'memory not mapped'
>
> Traceback:
> 1: .Call(fnname, ..., PACKAGE = "grid")
> 2: grid.Call("L_textBounds", as.graphicsAnnot(x$label), x$x, x 
> $y,     resolveHJust(x$just, x$hjust), resolveVJust(x$just, x 
> $vjust),     x$rot, 0)
> 3: widthDetails.text(x)
> 4: widthDetails(x)
> 5: function (x) {    widthDetails(x)}(list(label = "", x = 0.5, y =  
> 0.5, just = "centre", hjust = NULL,     vjust = NULL, rot = 0,  
> check.overlap = FALSE, name = "GRID.text.6",     gp = list(), vp =  
> NULL))
> 6: .Call.graphics(fnname, ..., PACKAGE = "grid")
> 7: grid.Call.graphics("L_setviewport", pvp, TRUE)
> 8: push.vp.viewport(X[[1L]], ...)
> 9: FUN(X[[1L]], ...)
> 10: lapply(vps, push.vp, recording)
> 11: pushViewport(viewport(layout = page.layout, gp =  
> global.gpar,     name = trellis.vpname("toplevel", prefix = prefix)))
> 12: printFunction(x, ...)
> 13: print.trellis(fig)
> 14: print(fig)
> 15: .html_img(dir, file, .plotReadQuality(df[df$type ==  
> type, ]),     ...)
> 16: .htmlReadQuality(dest, "readQuality", qa)
> 17: func(x, dest, type, ...)
> 18: func(x, dest, type, ...)
> 19: report(qaSummary, dest = "/Users/kangu/tmp/qareport")
> 20: report(qaSummary, dest = "/Users/kangu/tmp/qareport")
>
> Possible actions:
> 1: abort (with core dump, if enabled)
> 2: normal R exit
> 3: exit R without saving workspace
> 4: exit R saving workspace
> Selection:
>
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