[BioC] why is the CMA package not available for windows??

[Henrik Bengtsson]

Hi,

if I understand you correctly, you say there is nothing in the
code/implementation per se that prevents it from running on Windows,
but instead it is just the rule that a binary should not be built if
it does not pass R CMD pass.  Is that correct?  If it is just that one
example code that prevent from getting a Windows binary, why not put a
\dontrun{} on it as a quick fix?

The only problem I see with this fix is that you might forget about
it.  Redundancy testing you can achieve using tests/ and there you run
the test conditionally on OS (skipping Windows for now).  You can even
say "skip test on Windows and package version is older than March
2009" - that way the problem won't be forgotten about in the future.

"Forced" as-is Windows binaries for CMA release and devel (without
passing R CMD check):

source("http://www.braju.com/R/hbLite.R");
installPackages("http://www.braju.com/R/repos/CMA_1.0.0.zip"); # release
installPackages("http://www.braju.com/R/repos/CMA_1.1.1.zip"); # devel

My $.02

Henrik

On Mon, Feb 9, 2009 at 9:56 AM, Patrick Aboyoun <paboyoun at fhcrc.org> wrote:
> Maria,
> The reason is because CMA fails to pass check on Windows due to MikTex
> issues when processing the examples in the *.Rd man pages. I spent some time
> during the
>  BioC 2.3 release and realized untangling this issue would take longer than
> I had to spend. When BioC 2.4 is ready to release in a couple of months,
> I'll probably spend some time again trying to fix CMA so it builds on
> Windows. If, however, someone has a chance to work on this package before
> then, we can make this package available on Windows sooner. This package
> doesn't require 3rd party libraries or code compilation, so in that respects
> it is easy to work with.
>
>
> D:\sandbox>D:\biocbld\bbs-2.4-bioc\R\bin\R CMD check CMA_1.1.1.tar.gz
> ...
> * checking examples ... ERROR
> Running examples in 'CMA-Ex.R' failed.
> The error most likely occurred in:
>
>> ### * ElasticNetCMA
>>
>> flush(stderr()); flush(stdout())
>>
>> ### Name: ElasticNetCMA
>> ### Title: Classification and variable selection by the ElasticNet
>> ### Aliases: ElasticNetCMA
>> ### Keywords: multivariate
>>
>> ### ** Examples
>>
>> ### load Golub AML/ALL data
>> data(golub)
>> ### extract class labels
>> golubY <- golub[,1]
>> ### extract gene expression
>> golubX <- as.matrix(golub[,-1])
>> ### select learningset
>> ratio <- 2/3
>> set.seed(111)
>> learnind <- sample(length(golubY), size=floor(ratio*length(golubY)))
>> ### run ElasticNet - penalized logistic regression (no tuning)
>> result <- ElasticNetCMA(X=golubX, y=golubY, learnind=learnind,
>> norm.fraction = 0.2, lambda2=0.01)
>
> Loading required package: survival
> Loading required package: splines
>>
>> AML/ALL data
>
> Error: unexpected symbol in "AML/ALL data"
> Execution halted
>
>
>
> Quoting "Ortiz, Maria" <mortiz at ceit.es>:
>
>> Hi!
>>
>> I was wondering why CMA is not available for Windows.
>>
>> Thanks,
>>
>> Maria O.
>>
>>        [[alternative HTML version deleted]]
>>
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