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

[Patrick Aboyoun]

Henrik,
As inconvenient as it may be, having a standard set of rules for all 
packages ensures a modicum of reassurance that a typical installation of 
R will run the packages hosted at bioconductor.org. Also from an 
administrative perspective, if we make exceptions for one package, then 
we open the door for other packages to receive special management as 
well. [For the package maintainers out there, please do not use 
\dontrun{} to prevent bug surfacing during R CMD check. The whole point 
of R CMD check is to find problems in packages and we even take warnings 
seriously given that they may be indicative of more serious issues.]

Fortunately, CMA can be fixed to build on Windows through simple, yet 
time intensive, checking of each of the *.Rd files to see which ones 
have the offensive end-of-line character, markup tag, etc. that is 
causing R CMD check to fail. If someone puts in the time to fix the *.Rd 
files, I, or the package maintainer, would be happy to check them in so 
they can build on Windows.


Patrick


Henrik Bengtsson wrote:
> 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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