[BioC] ShortRead::report() breaks in mac osx

[Vincent Carey]

i fail to reproduce on 2.13 as noted below or on 2.14 -- maybe alter
locale setting?

> q
class: FastqQA(10)
QA elements (access with qa[["elt"]]):
  readCounts: data.frame(1 3)
  baseCalls: data.frame(1 5)
  readQualityScore: data.frame(1 4)
  baseQuality: data.frame(94 3)
  alignQuality: data.frame(1 3)
  frequentSequences: data.frame(1 4)
  sequenceDistribution: data.frame(1 4)
  perCycle: list(2)
    baseCall: data.frame(47 4)
    quality: data.frame(47 5)
  perTile: list(2)
    readCounts: data.frame(0 4)
    medianReadQualityScore: data.frame(0 4)
  adapterContamination: data.frame(1 2)
> sessionInfo()
R version 2.13.0 Patched (2011-04-14 r55443)
Platform: x86_64-apple-darwin10.6.0/x86_64 (64-bit)

locale:
[1] en_US.US-ASCII/en_US.US-ASCII/C/C/en_US.US-ASCII/en_US.US-ASCII

attached base packages:
[1] stats     graphics  grDevices datasets  utils     tools     methods
[8] base

other attached packages:
[1] ShortRead_1.10.4    Rsamtools_1.5.2     lattice_0.19-33
[4] Biostrings_2.20.3   GenomicRanges_1.4.8 IRanges_1.10.6
[7] weaver_1.18.0       codetools_0.2-8     digest_0.5.0

loaded via a namespace (and not attached):
[1] Biobase_2.12.2 grid_2.13.0    hwriter_1.3


On Sat, Oct 22, 2011 at 9:28 PM, Robert Castelo <robert.castelo at upf.edu> wrote:
> hi, this is what i get, the error seems to point out to something about the
> X11 font installation in my mac but i'm pretty lost about this, so any hint
> will be highly appreciated:
>
> library(ShortRead)
> q <- qa(system.file("unitTests", "cases", package="ShortRead"),
> pattern="solexa.fastq", type="fastq")
>
> rptReads <- report(q)
> Error in grid.Call("L_textBounds", as.graphicsAnnot(x$label), x$x, x$y,  :
>  could not find any X11 fonts
> Check that the Font Path is correct.
> In addition: Warning messages:
> 1: In jpeg(file.path(imgDir, jpegFile), ...) :
>  locale not supported by Xlib: some X ops will operate in C locale
> 2: In jpeg(file.path(imgDir, jpegFile), ...) :
>  X cannot set locale modifiers
> sessionInfo()
> R version 2.13.0 (2011-04-13)
> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
>
> locale:
> [1] C/UTF-8/C/C/C/C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] ShortRead_1.10.4    Rsamtools_1.4.3     lattice_0.19-33
> [4] Biostrings_2.20.4   GenomicRanges_1.4.8 IRanges_1.10.6
>
> loaded via a namespace (and not attached):
> [1] Biobase_2.12.2 grid_2.13.0    hwriter_1.3
>
>
> thanks!!
> robert.
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
>