Please ignore this request for help. I read the release notes and installed
the png package. Sorry to raise a flag without a thorough investigation of
the obvious first.
Thanks,
Dick
On Thu, Feb 24, 2011 at 10:52 AM, Richard Beyer <rpbe...@gmail.com> wrote:
> I recently updated my system to the latest aroma, and now something that
> worked in the last version is not working now.
>
> I use a script originally from Mark Robinson called doEverything. That
> seems just fine, all my usual steps work. I can use plotRle and plotNuse
> just fine. When I get to the ArrayExplorer section in order to try to
> generate array images of the residuals I get the no png error. I also tried
> this after doing library(grDevices) to make sure png() was available.
>
>
> > library(grDevices)
> > rs <- e.AndersonRat1$res
> > ae <- ArrayExplorer(rs)
> > setColorMaps(ae, c("log2,log2pos,rainbow"))
> > process(ae, interleaved="auto")
> Interleaving image...
> z:
> num [1:1050, 1:1050] NA NA NA NA NA NA NA NA NA NA ...
> - attr(*, "...instantiationTime")= POSIXct[1:1], format: "2011-02-24
> 10:50:17"
> Infering horizontal, vertical, or no interleaving...
> hOdd=0.81
> hEven=0.81
> hRatio=0.0013
> vOdd=0.81
> vEven=0.81
> vRatio=-2.5e-05
> what: none
> Infering horizontal, vertical, or no interleaving...done
> Interleaving image...done
> Error in loadNamespace(name) : there is no package called 'png'
>
>
> > sessionInfo()
> R version 2.12.1 (2010-12-16)
> Platform: x86_64-redhat-linux-gnu (64-bit)
>
> locale:
> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
> LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=C
> [6] LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8
> LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats graphics grDevices datasets utils methods base
>
> other attached packages:
> [1] abind_1.1-0 limma_3.6.6 preprocessCore_1.12.0
> affyio_1.18.0 Biobase_2.10.0 aroma.affymetrix_2.0.0
> [7] aroma.apd_0.1.8 affxparser_1.22.0 R.huge_0.2.2
> aroma.core_2.0.0 aroma.light_1.18.3 matrixStats_0.2.2
> [13] R.rsp_0.4.2 R.cache_0.4.0 R.filesets_0.9.2
> digest_0.4.2 R.utils_1.6.2 R.oo_1.7.5
> [19] EBImage_3.6.0 affy_1.28.0 R.methodsS3_1.2.1
>
> loaded via a namespace (and not attached):
> [1] tools_2.12.1
>
>
> I would be very grateful for any suggestions or help,
>
> Thanks,
> Dick
>
> *******************************************************************************
> Richard P. Beyer, Ph.D. University of Washington
> Tel.:(206) 616 7378 Env. & Occ. Health Sci. , Box 354695
> Fax: (206) 685 4696 4225 Roosevelt Way NE, # 100
> Seattle, WA 98105-6099
> http://depts.washington.edu/ceeh/members_fc_bioinfo.html
> http://staff.washington.edu/~dbeyer
>
> *******************************************************************************
>
>
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