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Morkus

2017-Oct-28 12:59 UTC

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

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]]
>>>    
------------------------------------------------------------------------
>>>     R-devel at r-project.org <mailto:R-devel at
r-project.org> mailing
>>>     list https://stat.ethz.ch/mailman/listinfo/r-devel |	[[alternative HTML version deleted]]

Duncan Murdoch

2017-Oct-28 20:51 UTC

head link

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

On 28/10/2017 8:59 AM, Morkus wrote:> 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.
The last column in iris is actually a factor.  That's stored as an 
S3-classed integer vector with an attribute listing the levels.  Using 
strings instead can cause problems in a few R functions (they want 
factors, and don't do automatic conversions), but the errors you're 
seeing seem more fundamental.
> 
> 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)
That sounds like it could be serious.  Dataframe names shouldn't be 
particularly complicated, so there shouldn't be a problem evaluating 
them.  (But maybe this is just hard in Java for some reason.  As I've 
mentioned, I'm not familiar with the R Java interface.)  If there really 
is a problem with the way the names have been constructed, that would 
explain the error in str(), and would lead to lots of other weird problems.

Another way to look at R objects from within R is to use 
.Internal(inspect( x )).  For example,

 > .Internal(inspect(names(iris)))
@7f898ff9e2e8 16 STRSXP g0c4 [NAM(2)] (len=5, tl=0)
   @7f8992c41878 09 CHARSXP g0c2 [gp=0x61,ATT] [ASCII] [cached] 
"Sepal.Length"
   @7f8992c41840 09 CHARSXP g0c2 [gp=0x61] [ASCII] [cached]
"Sepal.Width"
   @7f8992c41808 09 CHARSXP g0c2 [gp=0x61,ATT] [ASCII] [cached] 
"Petal.Length"
   @7f898ba99f78 09 CHARSXP g0c2 [gp=0x61,ATT] [ASCII] [cached] 
"Petal.Width"
   @7f898b9a3468 09 CHARSXP g0c1 [gp=0x61,ATT] [ASCII] [cached]
"Species"

You can also look at R objects while in a debugger like gdb using the 
R_PV() function; see Writing R Extensions for details if this is 
something available to you.
> 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?
I don't know anyone who does that.  It seems like a bad idea just 
because it's always easiest to do what everyone else does.

I think it's more common to call Java from R than the reverse.

Duncan Murdoch
> 
> 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/@17d99928+[5]?
>>
>>     ? payload = {org.rosuda.REngine./RList/@566} size = 5
>>     ? 0 = {org.rosuda.REngine.REXPDouble at 570}
>>     "org.rosuda.REngine./REXPDouble/@6fffcba5[150]"
>>     ? 1 = {org.rosuda.REngine.REXPDouble at 571}
>>     "org.rosuda.REngine./REXPDouble/@34340fab[150]?
>>     ? 2 = {org.rosuda.REngine.REXPDouble at 572}
>>     "org.rosuda.REngine./REXPDouble/@2aafb23c[150]"
>>     ? 3 = {org.rosuda.REngine.REXPDouble at 573}
>>     "org.rosuda.REngine./REXPDouble/@2b80d80f[150]?
>>     ? 4 = {org.rosuda.REngine.REXPString at 574}
>>     "org.rosuda.REngine./REXPString/@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 <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>
>>         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 |
>>
>>         5.
>>
>>
>>         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]]
>>        
------------------------------------------------------------------------
>>         R-devel at r-project.org <mailto:R-devel at
r-project.org> mailing
>>         list https://stat.ethz.ch/mailman/listinfo/r-devel | |
>>
>>
>

Morkus

2017-Oct-29 11:26 UTC

head link

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

Thanks Duncan. I can't tell you how helpful all your terrific replies have
been.

I think the biggest surprise is that nobody appears to be using Java and R
together like I"m trying to do. I suppose it should be a surprise since
there are no books on the subject and almost no technical documentation other
than a few sites here and there.

-----

I originally had the "int" as the return type for the factors, but
that didn't make any difference.

So, let me ask you. What I can get working is calling an R Script from Java.
Literally opening the ".R" file and reading it line by line and
evaluating it. That works. Is there any reason why that's not a viable way
to go?

The one thing I don't know how to do is pass a parameter to an RScript from
Java. Is it possible to pass a parameter to an RScript from Java? If I can pass
a parameter to an RScript, then it's not static and I could use it as a
"function" to call for different values.

Look forward to your reply.

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 4:51 PM
> UTC Time: October 28, 2017 8:51 PM
> 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 8:59 AM, Morkus wrote:
>
>> 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.
>>
>> The last column in iris is actually a factor. That's stored as an
>> S3-classed integer vector with an attribute listing the levels. Using
>> strings instead can cause problems in a few R functions (they want
>> factors, and don't do automatic conversions), but the errors
you're
>> seeing seem more fundamental.
>> 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)
>>
>> That sounds like it could be serious. Dataframe names shouldn't be
>> particularly complicated, so there shouldn't be a problem
evaluating
>> them. (But maybe this is just hard in Java for some reason. As I've
>> mentioned, I'm not familiar with the R Java interface.) If there
really
>> is a problem with the way the names have been constructed, that would
>> explain the error in str(), and would lead to lots of other weird
problems.
>>
>> Another way to look at R objects from within R is to use
>> .Internal(inspect( x )). For example,
>>
>> .Internal(inspect(names(iris)))
>> @7f898ff9e2e8 16 STRSXP g0c4 [NAM(2)] (len=5, tl=0)
>> @7f8992c41878 09 CHARSXP g0c2 [gp=0x61,ATT] [ASCII] [cached]
>> "Sepal.Length"
>> @7f8992c41840 09 CHARSXP g0c2 [gp=0x61] [ASCII] [cached]
"Sepal.Width"
>> @7f8992c41808 09 CHARSXP g0c2 [gp=0x61,ATT] [ASCII] [cached]
>> "Petal.Length"
>> @7f898ba99f78 09 CHARSXP g0c2 [gp=0x61,ATT] [ASCII] [cached]
>> "Petal.Width"
>> @7f898b9a3468 09 CHARSXP g0c1 [gp=0x61,ATT] [ASCII] [cached]
"Species"
>>
>> You can also look at R objects while in a debugger like gdb using the
>> R_PV() function; see Writing R Extensions for details if this is
>> something available to you.
>>
>> 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?
>>
>> I don't know anyone who does that. It seems like a bad idea just
>> because it's always easiest to do what everyone else does.
>>
>> I think it's more common to call Java from R than the reverse.
>>
>> Duncan Murdoch
>> 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/@17d99928+[5]?
>>> ? payload = {org.rosuda.REngine./RList/@566} size = 5
>>> ? 0 = {org.rosuda.REngine.REXPDouble at 570}
>>> "org.rosuda.REngine./REXPDouble/@6fffcba5[150]"
>>> ? 1 = {org.rosuda.REngine.REXPDouble at 571}
>>> "org.rosuda.REngine./REXPDouble/@34340fab[150]?
>>> ? 2 = {org.rosuda.REngine.REXPDouble at 572}
>>> "org.rosuda.REngine./REXPDouble/@2aafb23c[150]"
>>> ? 3 = {org.rosuda.REngine.REXPDouble at 573}
>>> "org.rosuda.REngine./REXPDouble/@2b80d80f[150]?
>>> ? 4 = {org.rosuda.REngine.REXPString at 574}
>>> "org.rosuda.REngine./REXPString/@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 <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>
>>>  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 |
>>>
>>>  5.
>>>
>>>  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]]
>>> 
------------------------------------------------------------------------
>>>  R-devel at r-project.org <mailto:R-devel at r-project.org>
mailing
>>>  list https://stat.ethz.ch/mailman/listinfo/r-devel | |	[[alternative HTML version deleted]]

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