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

[Robert Castelo]

thanks Vincent, the verification on your side confirms this is a locale 
issue and i could sort it out thanks to the following trick kindly sent 
to me by Martin:

Sys.setlocale(locale="C")

right before the call to report().

cheers,
robert.


On 10/23/11 3:55 AM, Vincent Carey wrote:
> 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.
>>
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