Error in loadNamespace(name) : there is no package called 'png'

[Richard Beyer]

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
*******************************************************************************

[Richard Beyer]

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

[Henrik Bengtsson]

Hi.

Correct, installing the 'png' *package* solves your problem.

However, you did indeed spot a bug, because the png package should not
have been needed if you already have a working EBImage installation.
I've made a patch available that fixes this. The patch will be
installed if you do:

source("http://aroma-project.org/hbLite.R");
hbInstall("aroma.affymetrix");

/Henrik

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