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

[Dan Tenenbaum]

On Thu, Jan 3, 2013 at 11:50 AM, Yanqing Hu <Yanqing.Hu at mail.wvu.edu> wrote:
> Thanks, Jim and Dan!
>
>
> To Jim: Yes, I tried capabilities and there are TRUEs under png as well as jpeg, so changing dev to other format didn't work. I also noticed that there's a FALSE under X11. Another post
> https://stat.ethz.ch/pipermail/bioconductor/2006-August/014161.html
> mentioned that png needs X11 to be running. But seems now MAC doesn't support X11 any more.
>

X11 is supported on Mac systems. If you are running Lion or newer, you
have to install XQuartz though:

http://xquartz.macosforge.org/landing/

BTW, your sessionInfo() says you are on a Red Hat Linux machine!

>
>
>
> To Dan: Yes, I  was running  the code from the beginning of that chapter. AnnBuilder is indeed obsolete, but the book mentioned that the data set beta 7 can alternatively be loaded from the data package beta7,  which is what I did and it was successful. So I guess the problem may be related to the maQualityPlots function and the MAC system themselves.
>

There is a lot of code in that file, it might be best if you post the
exact lines of code that cause the error.

Thanks,
Dan


>
>
>
>
>
>>>> Dan Tenenbaum  01/03/13 12:50 PM >>>
> On Thu, Jan 3, 2013 at 8:37 AM, James W. MacDonald  wrote:
>> 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.
>
> In general, png is supported on the mac.
>
>> 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).
>>
>
> Yes, a reproducible example would be great. I am guessing that you are
> working your way through this code:
>
> http://www.bioconductor.org/help/publications/books/bioinformatics-and-computational-biology-solutions/chapter-code/TwoColorPre.R
>
> This uses packages which are obsolete so it's not surprising that you
> are getting errors.
>
> Dan
>
>
>> 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
>>>
>>> --
>>> Sent via the guest posting facility at bioconductor.org.
>>>
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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
>>
>>
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>
>