Cannot Compute Box's M (Three Days Trying...)

-------- 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
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