From morkus at protonmail.com  Sat Oct 28 14:59:51 2017
From: morkus at protonmail.com (Morkus)
Date: Sat, 28 Oct 2017 08:59:51 -0400
Subject: [Rd] Cannot Compute Box's M (Three Days Trying...)
In-Reply-To: <ee03e49f-9c97-5e34-d12e-7623effcf062@gmail.com>
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Hey Duncan,

Hard to debug? That's an understatement. Eyes bleeding....

In any case, I tried all your suggestions. To get "integer" for the final column, I had to change the code to get integers instead of strings.

double[] d1 = ((REXPVector) ((RList) tableRead).get(0)).asDoubles();
double[] d2 = ((REXPVector) ((RList) tableRead).get(1)).asDoubles();
double[] d3 = ((REXPVector) ((RList) tableRead).get(2)).asDoubles();
double[] d4 = ((REXPVector) ((RList) tableRead).get(3)).asDoubles();
int[] d5 = ((REXPVector) ((RList) tableRead).get(4)).asIntegers();

// create data frame with data.REXP myDf = REXP.createDataFrame(new RList(
new REXP[]
{
new REXPDouble(d1),
new REXPDouble(d2),
new REXPDouble(d3),
new REXPDouble(d4),
new REXPInteger(d5)
}));

Here are the results from the eval debug code.

head(boxMVariable)  ? Gives the high level 5 objects.

typeof(boxMVariable): ?list?

class(boxMVariable) : ?data.frame?

names(boxMVariable)  ? String object returned (couldn't evaluate it)

ncol(boxMVariable)  - 5

nrow(boxMVariable)   - 150

typeof(boxMVariable)

for (i in 1:5) print(typeof(boxMVariable[[i]]))
I get:
1 ?> double
2 ?> double
3  ?> double
4 ?> double
5 ->  integer

Is this problem "debug-proof"?

Does anyone out there actually use Java and R?

Sigh...

Sent from [ProtonMail](https://protonmail.com), Swiss-based encrypted email.

> -------- Original Message --------
> Subject: Re: [Rd] Cannot Compute Box's M (Three Days Trying...)
> Local Time: October 28, 2017 7:31 AM
> UTC Time: October 28, 2017 11:31 AM
> From: murdoch.duncan at gmail.com
> To: Morkus <morkus at protonmail.com>
> r-devel at r-project.org <r-devel at r-project.org>
>
> On 28/10/2017 7:12 AM, Morkus wrote:
>
>> Thanks Duncan. Awesome ideas!
>> I think we're getting closer!
>> I tried what you suggested and got a possibly better error...
>> .
>> .
>> .
>> rConnection.assign("boxMVariable", myDf);
>> *String resultBV *= "str(boxMVariable)"; // your suggestion.
>> RESULTING ERROR:
>> Error in format.default(nam.ob, width = max(ncn), justify = "left") :
>> invalid 'width' argument
>> (No idea what this means).
>>
>> That looks like an error occurring in the str() function. I've never
>> seen such a think in a regular R session, so I would guess that either
>> your boxMVariable object is set up in a weird way that is confusing
>> str(), or your R session in Java is messed up.
>>
>> This is likely to be pretty hard to debug. As a general strategy, I'd
>> try to find out exactly what is in boxMVariable first. Since str()
>> doesn't work, try printing things like
>>
>> head(boxMVariable)
>> class(boxMVariable)
>> names(boxMVariable)
>> ncol(boxMVariable)
>> nrow(boxMVariable)
>> typeof(boxMVariable)
>> for (i in 1:5)
>> print(typeof(boxMVariable[[i]]))
>>
>> etc.
>>
>> Make sure the values match what you see in a regular R session:
>>
>> boxMVariable <- iris
>> head(boxMVariable)
>> Sepal.Length Sepal.Width Petal.Length Petal.Width Species
>> 1 5.1 3.5 1.4 0.2 setosa
>> 2 4.9 3.0 1.4 0.2 setosa
>> 3 4.7 3.2 1.3 0.2 setosa
>> 4 4.6 3.1 1.5 0.2 setosa
>> 5 5.0 3.6 1.4 0.2 setosa
>> 6 5.4 3.9 1.7 0.4 setosa
>> class(boxMVariable)
>> [1] "data.frame"
>> names(boxMVariable)
>> [1] "Sepal.Length" "Sepal.Width" "Petal.Length" "Petal.Width"
>> "Species"
>> ncol(boxMVariable)
>> [1] 5
>> nrow(boxMVariable)
>> [1] 150
>> typeof(boxMVariable)
>> [1] "list"
>> for (i in 1:5)
>
> - print(typeof(boxMVariable[[i]]))
> [1] "double"
> [1] "double"
> [1] "double"
> [1] "double"
> [1] "integer"
>
>> For testing, I'm using the same standard IRIS dataset as the Box's M
>> documentation shows in biotools:
>> Examples
>> data(iris)
>> boxM(iris[, -5], iris[, 5])
>> -------
>> **
>> Now, in the debugger, the built values of myDf are these:
>> myDf = {org.rosuda.REngine.REXPGenericVector at 562}
>> "org.rosuda.REngine.REXPGenericVector at 17d99928+[5]?
>
>> ? payload = {org.rosuda.REngine.RList at 566} size = 5
>> ? 0 = {org.rosuda.REngine.REXPDouble at 570}
>> "org.rosuda.REngine.REXPDouble at 6fffcba5[150]"
>> ? 1 = {org.rosuda.REngine.REXPDouble at 571}
>> "org.rosuda.REngine.REXPDouble at 34340fab[150]?
>> ? 2 = {org.rosuda.REngine.REXPDouble at 572}
>> "org.rosuda.REngine.REXPDouble at 2aafb23c[150]"
>> ? 3 = {org.rosuda.REngine.REXPDouble at 573}
>> "org.rosuda.REngine.REXPDouble at 2b80d80f[150]?
>> ? 4 = {org.rosuda.REngine.REXPString at 574}
>> "org.rosuda.REngine.REXPString at 3ab39c39[150]?
>> Does this help?
>> Please let me know what else I can try.
>> Thanks,
>> Sent from ProtonMail https://protonmail.com, Swiss-based encrypted email.
>>
>>> -------- Original Message --------
>>> Subject: Re: [Rd] Cannot Compute Box's M (Three Days Trying...)
>>> Local Time: October 28, 2017 6:48 AM
>>> UTC Time: October 28, 2017 10:48 AM
>>> From: murdoch.duncan at gmail.com
>>> To: Morkus morkus at protonmail.com
>>> r-devel at r-project.org r-devel at r-project.org
>>> On 28/10/2017 6:26 AM, Morkus wrote:
>>>
>>> I'm not sure what you mean. Could you please be more specific?
>>>
>>> You were trying to eval an expression that you constructed in Java. I
>>> was suggesting that before you eval it, you print it.
>>> If I print the string, I get: /boxM(boxMVariable[, -5],
>>> boxMVariable[, 5])/
>>>
>>> Right, that's what I was suggesting you do. Now you've fixed the
>>> syntax
>>> error, that looks okay.
>>>
>>> If I'm reading these messages in the right order, your latest error is
>>>
>>> Error in |[.data.frame|(boxMVariable, , -5) : undefined columns
>>> selected
>>>
>>> The expression there is a funny way of printing boxMVariable[,-5]. So
>>> now you need to figure out why it thinks you've selected undefined
>>> columns. This is a little perplexing, because you're asking for all
>>> columns except column 5, and that works whether or not you have a
>>> column
>>>
>>> -
>>>
>>> So I'd guess there's something weird about boxMVariable. You should ask
>>> R to print it, and to print str(boxMVariable), to make sure it's a
>>> regular dataframe containing 4 numeric columns and one factor or
>>> character column.
>>> Duncan Murdoch
>>>
>>> From this code:
>>> .
>>> .
>>> .
>>> /// assign the data to a variable.
>>> /rConnection.assign("boxMVariable", myDf);
>>> /// create a string command with that variable name.
>>> /String boxVariable = "boxM(boxMVariable[, -5], boxMVariable[, 5])";
>>> /System/./out/./println/(/boxVariable/);  // print the string? Not
>>> sure
>>> what is meant.
>>> Sorry if I didn't understand your suggestion.
>>> Look forward to hearing back from you.
>>> Thanks,
>>> Sent from ProtonMail https://protonmail.com, Swiss-based encrypted
>>> email.
>>>
>>>     -------- Original Message --------
>>>     Subject: Re: [Rd] Cannot Compute Box's M (Three Days Trying...)
>>>     Local Time: October 27, 2017 6:09 PM
>>>     UTC Time: October 27, 2017 10:09 PM
>>>     From: murdoch.duncan at gmail.com <mailto:murdoch.duncan at gmail.com>
>>>     To: Morkus morkus at protonmail.com
>>>     <mailto:morkus at protonmail.com>, r-devel at r-project.org
>>>     <mailto:r-devel at r-project.org>
>>>     r-devel at r-project.org <mailto:r-devel at r-project.org>
>>>     Just print the string you are asking to R to evaluate. It
>>>     doesn't make
>>>     any sense as an R expression. Fix that, and things will work.
>>>     Duncan Murdoch
>>>     On 27/10/2017 3:41 PM, Morkus via R-devel wrote:
>>>
>>>     |It can't be this hard, right? I really need a shove in the
>>>     right direction here. Been spinning wheels for three days.
>>>     Cannot get past the errors. I'm doing something wrong,
>>>     obviously, since I can easily compute the Box's M right there
>>>     in RStudio But I don't see what is wrong below with the coding
>>>     equivalent. The entire code snippet is below. The code fails
>>>     below on the call to the boxM statistic call. PLEASE HELP!!!
>>>     Thanks in advance,
>>>     ------------------------------------------------------------------------
>>>     rConnection.eval("library('biotools')"); String inputIris =
>>>     "5.1,3.5,1.4,0.2,setosa\n" + "4.9,3,1.4,0.2,setosa\n" +
>>>     "4.7,3.2,1.3,0.2,setosa\n" + "4.6,3.1,1.5,0.2,setosa\n" +
>>>     "5,3.6,1.4,0.2,setosa\n" + "5.4,3.9,1.7,0.4,setosa\n" +
>>>     "4.6,3.4,1.4,0.3,setosa\n" + "5,3.4,1.5,0.2,setosa\n" +
>>>     "4.4,2.9,1.4,0.2,setosa\n" + "4.9,3.1,1.5,0.1,setosa\n" +
>>>     "5.4,3.7,1.5,0.2,setosa\n" + "4.8,3.4,1.6,0.2,setosa\n" +
>>>     "4.8,3,1.4,0.1,setosa\n" + "4.3,3,1.1,0.1,setosa\n" +
>>>     "5.8,4,1.2,0.2,setosa\n" + "5.7,4.4,1.5,0.4,setosa\n" +
>>>     "5.4,3.9,1.3,0.4,setosa\n" + "5.1,3.5,1.4,0.3,setosa\n" +
>>>     "5.7,3.8,1.7,0.3,setosa\n" + "5.1,3.8,1.5,0.3,setosa\n" +
>>>     "5.4,3.4,1.7,0.2,setosa\n" + "5.1,3.7,1.5,0.4,setosa\n" +
>>>     "4.6,3.6,1,0.2,setosa\n" + "5.1,3.3,1.7,0.5,setosa\n" +
>>>     "4.8,3.4,1.9,0.2,setosa\n" + "5,3,1.6,0.2,setosa\n" +
>>>     "5,3.4,1.6,0.4,setosa\n" + "5.2,3.5,1.5,0.2,setosa\n" +
>>>     "5.2,3.4,1.4,0.2,setosa\n" + "4.7,3.2,1.6,0.2,setosa\n" +
>>>     "4.8,3.1,1.6,0.2,setosa\n" + "5.4,3.4,1.5,0.4,setosa\n" +
>>>     "5.2,4.1,1.5,0.1,setosa\n" + "5.5,4.2,1.4,0.2,setosa\n" +
>>>     "4.9,3.1,1.5,0.2,setosa\n" + "5,3.2,1.2,0.2,setosa\n" +
>>>     "5.5,3.5,1.3,0.2,setosa\n" + "4.9,3.6,1.4,0.1,setosa\n" +
>>>     "4.4,3,1.3,0.2,setosa\n" + "5.1,3.4,1.5,0.2,setosa\n" +
>>>     "5,3.5,1.3,0.3,setosa\n" + "4.5,2.3,1.3,0.3,setosa\n" +
>>>     "4.4,3.2,1.3,0.2,setosa\n" + "5,3.5,1.6,0.6,setosa\n" +
>>>     "5.1,3.8,1.9,0.4,setosa\n" + "4.8,3,1.4,0.3,setosa\n" +
>>>     "5.1,3.8,1.6,0.2,setosa\n" + "4.6,3.2,1.4,0.2,setosa\n" +
>>>     "5.3,3.7,1.5,0.2,setosa\n" + "5,3.3,1.4,0.2,setosa\n" +
>>>     "7,3.2,4.7,1.4,versicolor\n" + "6.4,3.2,4.5,1.5,versicolor\n"
>>>     + "6.9,3.1,4.9,1.5,versicolor\n" +
>>>     "5.5,2.3,4,1.3,versicolor\n" + "6.5,2.8,4.6,1.5,versicolor\n"
>>>     + "5.7,2.8,4.5,1.3,versicolor\n" +
>>>     "6.3,3.3,4.7,1.6,versicolor\n" + "4.9,2.4,3.3,1,versicolor\n"
>>>     + "6.6,2.9,4.6,1.3,versicolor\n" +
>>>     "5.2,2.7,3.9,1.4,versicolor\n" + "5,2,3.5,1,versicolor\n" +
>>>     "5.9,3,4.2,1.5,versicolor\n" + "6,2.2,4,1,versicolor\n" +
>>>     "6.1,2.9,4.7,1.4,versicolor\n" +
>>>     "5.6,2.9,3.6,1.3,versicolor\n" +
>>>     "6.7,3.1,4.4,1.4,versicolor\n" + "5.6,3,4.5,1.5,versicolor\n"
>>>     + "5.8,2.7,4.1,1,versicolor\n" +
>>>     "6.2,2.2,4.5,1.5,versicolor\n" +
>>>     "5.6,2.5,3.9,1.1,versicolor\n" +
>>>     "5.9,3.2,4.8,1.8,versicolor\n" + "6.1,2.8,4,1.3,versicolor\n"
>>>     + "6.3,2.5,4.9,1.5,versicolor\n" +
>>>     "6.1,2.8,4.7,1.2,versicolor\n" +
>>>     "6.4,2.9,4.3,1.3,versicolor\n" + "6.6,3,4.4,1.4,versicolor\n"
>>>     + "6.8,2.8,4.8,1.4,versicolor\n" + "6.7,3,5,1.7,versicolor\n"
>>>     + "6,2.9,4.5,1.5,versicolor\n" + "5.7,2.6,3.5,1,versicolor\n"
>>>     + "5.5,2.4,3.8,1.1,versicolor\n" +
>>>     "5.5,2.4,3.7,1,versicolor\n" + "5.8,2.7,3.9,1.2,versicolor\n"
>>>     + "6,2.7,5.1,1.6,versicolor\n" + "5.4,3,4.5,1.5,versicolor\n"
>>>     + "6,3.4,4.5,1.6,versicolor\n" +
>>>     "6.7,3.1,4.7,1.5,versicolor\n" +
>>>     "6.3,2.3,4.4,1.3,versicolor\n" + "5.6,3,4.1,1.3,versicolor\n"
>>>     + "5.5,2.5,4,1.3,versicolor\n" +
>>>     "5.5,2.6,4.4,1.2,versicolor\n" + "6.1,3,4.6,1.4,versicolor\n"
>>>     + "5.8,2.6,4,1.2,versicolor\n" + "5,2.3,3.3,1,versicolor\n" +
>>>     "5.6,2.7,4.2,1.3,versicolor\n" + "5.7,3,4.2,1.2,versicolor\n"
>>>     + "5.7,2.9,4.2,1.3,versicolor\n" +
>>>     "6.2,2.9,4.3,1.3,versicolor\n" + "5.1,2.5,3,1.1,versicolor\n"
>>>     + "5.7,2.8,4.1,1.3,versicolor\n" + "6.3,3.3,6,2.5,virginica\n"
>>>     + "5.8,2.7,5.1,1.9,virginica\n" + "7.1,3,5.9,2.1,virginica\n"
>>>     + "6.3,2.9,5.6,1.8,virginica\n" + "6.5,3,5.8,2.2,virginica\n"
>>>     + "7.6,3,6.6,2.1,virginica\n" + "4.9,2.5,4.5,1.7,virginica\n"
>>>     + "7.3,2.9,6.3,1.8,virginica\n" +
>>>     "6.7,2.5,5.8,1.8,virginica\n" + "7.2,3.6,6.1,2.5,virginica\n"
>>>     + "6.5,3.2,5.1,2,virginica\n" + "6.4,2.7,5.3,1.9,virginica\n"
>>>     + "6.8,3,5.5,2.1,virginica\n" + "5.7,2.5,5,2,virginica\n" +
>>>     "5.8,2.8,5.1,2.4,virginica\n" + "6.4,3.2,5.3,2.3,virginica\n"
>>>     + "6.5,3,5.5,1.8,virginica\n" + "7.7,3.8,6.7,2.2,virginica\n"
>>>     + "7.7,2.6,6.9,2.3,virginica\n" + "6,2.2,5,1.5,virginica\n" +
>>>     "6.9,3.2,5.7,2.3,virginica\n" + "5.6,2.8,4.9,2,virginica\n" +
>>>     "7.7,2.8,6.7,2,virginica\n" + "6.3,2.7,4.9,1.8,virginica\n" +
>>>     "6.7,3.3,5.7,2.1,virginica\n" + "7.2,3.2,6,1.8,virginica\n" +
>>>     "6.2,2.8,4.8,1.8,virginica\n" + "6.1,3,4.9,1.8,virginica\n" +
>>>     "6.4,2.8,5.6,2.1,virginica\n" + "7.2,3,5.8,1.6,virginica\n" +
>>>     "7.4,2.8,6.1,1.9,virginica\n" + "7.9,3.8,6.4,2,virginica\n" +
>>>     "6.4,2.8,5.6,2.2,virginica\n" + "6.3,2.8,5.1,1.5,virginica\n"
>>>     + "6.1,2.6,5.6,1.4,virginica\n" + "7.7,3,6.1,2.3,virginica\n"
>>>     + "6.3,3.4,5.6,2.4,virginica\n" +
>>>     "6.4,3.1,5.5,1.8,virginica\n" + "6,3,4.8,1.8,virginica\n" +
>>>     "6.9,3.1,5.4,2.1,virginica\n" + "6.7,3.1,5.6,2.4,virginica\n"
>>>     + "6.9,3.1,5.1,2.3,virginica\n" +
>>>     "5.8,2.7,5.1,1.9,virginica\n" + "6.8,3.2,5.9,2.3,virginica\n"
>>>     + "6.7,3.3,5.7,2.5,virginica\n" + "6.7,3,5.2,2.3,virginica\n"
>>>     + "6.3,2.5,5,1.9,virginica\n" + "6.5,3,5.2,2,virginica\n" +
>>>     "6.2,3.4,5.4,2.3,virginica\n" + "5.9,3,5.1,1.8,virginica\n";
>>>     List tableRead = rConnection.eval( "read.csv(textConnection(""
>>>     + inputIris + ""), header = FALSE)").asList(); // works!
>>>     double[] d1 = ((REXPVector) ((RList)
>>>     tableRead).get(0)).asDoubles(); double[] d2 = ((REXPVector)
>>>     ((RList) tableRead).get(1)).asDoubles(); double[] d3 =
>>>     ((REXPVector) ((RList) tableRead).get(2)).asDoubles();
>>>     double[] d4 = ((REXPVector) ((RList)
>>>     tableRead).get(3)).asDoubles(); String[] d5 = ((REXPVector)
>>>     ((RList) tableRead).get(4)).asStrings(); // create data frame
>>>     with data.REXP myDf = REXP.createDataFrame(new RList( new
>>>     REXP[] { new REXPDouble(d1), new REXPDouble(d2), new
>>>     REXPDouble(d3), new REXPDouble(d4), new REXPString(d5) })); //
>>>     assign the data to a variable as was
>>>     suggested.rConnection.assign("boxMVariable", myDf); // create
>>>     a string command with that variable name.String boxVariable =
>>>     "boxM(boxMVariable [,-5], boxMVariable[,5]"; // try to execute
>>>     the command... // FAILS with
>>>     org.rosuda.REngine.Rserve.RserveException: eval failed,
>>>     request status: R parser: input incomplete>>>> FAILS ! >>>>
>>>     REXP theBoxMResult = rConnection.eval(boxVariable); <<<< FAILS
>>>     <<<<< sent from ProtonMail <https://protonmail.com>,
>>>     Swiss-based encrypted email. [[alternative HTML version
>>>     deleted]]
>>>     ------------------------------------------------------------------------
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>>>     list https://stat.ethz.ch/mailman/listinfo/r-devel |
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[Rd] Cannot Compute Box's M (Three Days Trying...)
Morkus