Hi Henrik
If I just load the Cairo library and do a PNG plot, the plot appears
in the png file alright (8 kb file). I also don't notice the message
about "libpng warning: Application built with libpng-1.2.41 but running with
1.5.7"
So there appears to be something amiss in aroma.affymetrix
in its interface to Cairo devices. Does this provide any clues?
I have not gone through the aroma source to understand
how aroma interacts with Cairo.
Steve
R version 2.14.1 (2011-12-22)
Copyright (C) 2011 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: x86_64-apple-darwin10.8.0/x86_64 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
Natural language support but running in an English locale
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> .help.ESS <- help
> options(STERM='iESS', editor='emacsclient')
> require("Cairo")
Loading required package: Cairo
> CairoPNG("foo.png", width=840, height=640); plot(1:10); dev.off();
null device
1
>
Steven McKinney
________________________________________
From: Steven McKinney
Sent: January 17, 2012 8:59 PM
To: aroma-affymetrix@googlegroups.com
Subject: RE: [aroma.affymetrix] ChromosomeExplorer producing zero byte png files
Hi Henrik,
Running the commands you provided, I get an empty foo.png.
> print(pngDev)
function (...)
pngTyped(..., type = "cairo")
<environment: 0x103f64b88>
>
Full output below.
This is looking like a Cairo problem.
R version 2.14.1 (2011-12-22)
Copyright (C) 2011 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: x86_64-apple-darwin10.8.0/x86_64 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
Natural language support but running in an English locale
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> .help.ESS <- help
> options(STERM='iESS', editor='emacsclient')
> library("aroma.core")
Loading required package: R.methodsS3
R.methodsS3 v1.2.1 (2010-09-18) successfully loaded. See ?R.methodsS3 for help.
Loading required package: R.oo
R.oo v1.8.3 (2011-11-01) successfully loaded. See ?R.oo for help.
Attaching package: ‘R.oo’
The following object(s) are masked from ‘package:R.methodsS3’:
throw.default
The following object(s) are masked from ‘package:methods’:
getClass, getClasses, getMethods
The following object(s) are masked from ‘package:base’:
attach, detach, environment, gc, load, save
Loading required package: R.utils
R.utils v1.9.9 (2012-01-11) successfully loaded. See ?R.utils for help.
Attaching package: ‘R.utils’
The following object(s) are masked from ‘package:utils’:
timestamp
The following object(s) are masked from ‘package:base’:
cat, commandArgs, getOption, inherits, isOpen, lapply, parse,
remove, warnings
Loading required package: R.cache
R.cache v0.5.2 (2011-10-05) successfully loaded. See ?R.cache for help.
Loading required package: R.filesets
Loading required package: digest
R.filesets v1.1.4 (2011-11-19) successfully loaded. See ?R.filesets for help.
Attaching package: ‘R.filesets’
The following object(s) are masked from ‘package:R.cache’:
getChecksum
The following object(s) are masked from ‘package:base’:
append, readLines, sapply
Loading required package: R.rsp
R.rsp v0.7.1 (2011-11-28) successfully loaded. See ?R.rsp for help.
Type browseRsp() to open the RSP main menu in your browser.
Attaching package: ‘R.rsp’
The following object(s) are masked from ‘package:R.filesets’:
getHeader
The following object(s) are masked from ‘package:base’:
flush, restart, stop, write
Loading required package: matrixStats
matrixStats v0.4.3 (2011-12-11) successfully loaded. See ?matrixStats for help.
Loading required package: aroma.light
aroma.light v1.22.0 (2011-10-31) successfully loaded. See ?aroma.light for help.
aroma.core v2.4.2 (2012-01-14) successfully loaded. See ?aroma.core for help.
Attaching package: ‘aroma.core’
The following object(s) are masked from ‘package:base’:
.Machine, append, apply, colMeans, colSums, library, require,
sapply
> pngDev <- findPngDevice(transparent=FALSE)
Loading required package: Cairo
libpng warning: Application built with libpng-1.2.41 but running with 1.5.7
> pngDev("foo.png", width=840, height=640); plot(1:10); dev.off();
libpng warning: Application built with libpng-1.2.41 but running with 1.5.7
null device
1
> print(pngDev)
function (...)
pngTyped(..., type = "cairo")
<environment: 0x103f64b88>
>
> sessionInfo()
R version 2.14.1 (2011-12-22)
Platform: x86_64-apple-darwin10.8.0/x86_64 (64-bit)
locale:
[1] en_CA/en_CA/en_CA/C/en_CA/en_CA
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] Cairo_1.5-1 aroma.core_2.4.2 aroma.light_1.22.0 matrixStats_0.4.3
[5] R.rsp_0.7.1 R.filesets_1.1.4 digest_0.5.1 R.cache_0.5.2
[9] R.utils_1.9.9 R.oo_1.8.3 R.methodsS3_1.2.1
>
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