[BioC] error message relating to png file when running maQualityPlots

[James W. MacDonald]

I don't remember if Macs come ready to do png graphics or not, and a 
quick google doesn't clear it up for me. So the first step I would take 
is to ensure that you have the capability to do so. Try typing

capabilities()

at an R prompt and see if there is a TRUE under png. If not, you can set 
the dev argument of maQualityPlots() to a device for which you have 
capabilities. If there is a TRUE under png, then you will need to 
furnish the actual code you are running (or better yet, a reproducible 
example, which implies that I or anybody else can try and replicate what 
you have done).

Best,

Jim

On 1/3/2013 11:15 AM, Yanqing Hu [guest] wrote:
> I'm using Rstudio on my Mac. When I ran the code maQualityPlots(beta7) in Chapter 4 of Bioinformatics and Computational Biology Solutions Using R and Bioconductor, I got the mesasge "Error in plot.new() : could not open file 'diagPlot.6Hs.195.1.png'". Does anyone know how to fix this problem? Thanks a lot!
>
>   -- output of sessionInfo():
>
> R version 2.15.1 (2012-06-22)
> Platform: x86_64-redhat-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=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
>   [7] LC_PAPER=C                 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
> [7] base
>
> other attached packages:
>   [1] vsn_3.26.0            arrayQuality_1.36.0   beta7_1.0.4
>   [4] marray_1.36.0         cluster_1.14.2        BiocInstaller_1.8.2
>   [7] affycomp_1.34.0       affyPLM_1.34.0        preprocessCore_1.20.0
> [10] gcrma_2.30.0          hgu133acdf_2.11.0     hgu95av2cdf_2.11.0
> [13] AnnotationDbi_1.20.0  affydata_1.11.17      affy_1.36.0
> [16] Biobase_2.18.0        BiocGenerics_0.4.0    class_7.3-5
> [19] limma_3.14.3
>
> loaded via a namespace (and not attached):
>   [1] affyio_1.26.0      Biostrings_2.26.1  DBI_0.2-5
>   [4] grid_2.15.1        gridBase_0.4-5     hexbin_1.26.0
>   [7] IRanges_1.16.2     lattice_0.20-10    parallel_2.15.1
> [10] RColorBrewer_1.0-5 RSQLite_0.11.2     splines_2.15.1
> [13] stats4_2.15.1      tools_2.15.1       zlibbioc_1.4.0
>
> --
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>
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-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099