[BioC] GRENITS won't run with example data

[Edward Morrissey]

Hi,

The error with reshape is down to backward compatibility problems with 
ggplot2 0.9.0. (which now uses package reshape2). I've adapted the next 
version of GRENITS for the latest version of
ggplot2/reshape2.

The tilde error is from the c++ code. I assumed it would be able to 
handle that syntax. Sorry, my mistake. I'll fix that when I have a moment.

Regards,
Edward

On 27/03/12 13:25, Benilton Carvalho wrote:
> dummy reply so the maintainer can get a copy of the thread...
>
> On 26 March 2012 16:50, Vincent Carey<stvjc at channing.harvard.edu>  wrote:
>
>> This looks like a problem related to the use of tilde in the output folder
>> name.  Contact the developer if you really need
>> this functionality.  In my very brief inspection using an absolute pathname
>> led to success; using the tilde led to segfault.  Failing on a tilde is
>> indicative of failure of the package code to fully respect the relevant
>> APIs.  Good candidate for obligatory test of software adequacy.
>>
>> On Sun, Mar 25, 2012 at 10:44 PM, Tyler Funnell<tyler.funnell at gmail.com
>>> wrote:
>>> Hello,
>>>
>>> I've been having trouble getting the GRENITS package to run so I tried
>>> running just their example code on their included sample data.
>>> Here is the outputP
>>>
>>>> library(GRENITS)
>>> Loading required package: Rcpp
>>> Loading required package: RcppArmadillo
>>> Loading required package: ggplot2
>>>> data(Athaliana_ODE)
>>>> output.folder<- paste(tempdir(), "/Example_LinearNet", sep="")
>>>> LinearNet(output.folder, Athaliana_ODE)
>>> Created folder
>>>
>> /var/folders/ty/9l9tb3g54614cx23_clq3tnr0000gn/T//RtmpTPnsMW/Example_LinearNet
>>> Started MCMC chain 1  =============
>>> Estimated runtime = 0.0531906 min
>>> 25% completed
>>> 50% completed
>>> 75% completed
>>> MCMC chain 1 finished!
>>> Started MCMC chain 2  =============
>>> Estimated runtime = 0.0521771 min
>>> 25% completed
>>> 50% completed
>>> 75% completed
>>> MCMC chain 2 finished!
>>>> analyse.output(output.folder)
>>> Error in UseMethod("melt", data) :
>>>   no applicable method for 'melt' applied to an object of class
>>> "c('matrix', 'double', 'numeric')"
>>> I noticed on the project page that it says it imports the reshape
>> library.
>>> When I load the reshape library and try the example it works.
>>> However, when I set the output.folder to a directory in my desktop and
>> run
>>> the analysis I get a segfault.
>>>
>>>> output.folder<- paste("~/Desktop", "/Example_LinearNet", sep="")
>>>> LinearNet(output.folder, Athaliana_ODE)
>>> Created folder ~/Desktop/Example_LinearNet
>>> Started MCMC chain 1  =============
>>>
>>>   *** caught segfault ***
>>> address 0x10, cause 'memory not mapped'
>>>
>>> Traceback:
>>>   1: .Call("callAR1", timeSeries, resultsFolder.i, ParamVec, fixMe,
>>> PACKAGE = "GRENITS")
>>>   2: LinearNet(output.folder, Athaliana_ODE)
>>>
>>>
>>> Cheers,
>>> Tyler
>>>
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