-------- 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.dun...@gmail.com
To: Morkus <mor...@protonmail.com>
r-devel@r-project.org <r-devel@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@562}
"org.rosuda.REngine./REXPGenericVector/@17d99928+[5]”
▼ payload = {org.rosuda.REngine./RList/@566} size = 5
► 0 = {org.rosuda.REngine.REXPDouble@570}
"org.rosuda.REngine./REXPDouble/@6fffcba5[150]"
► 1 = {org.rosuda.REngine.REXPDouble@571}
"org.rosuda.REngine./REXPDouble/@34340fab[150]”
► 2 = {org.rosuda.REngine.REXPDouble@572}
"org.rosuda.REngine./REXPDouble/@2aafb23c[150]"
► 3 = {org.rosuda.REngine.REXPDouble@573}
"org.rosuda.REngine./REXPDouble/@2b80d80f[150]”
► 4 = {org.rosuda.REngine.REXPString@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.dun...@gmail.com <mailto:murdoch.dun...@gmail.com>
To: Morkus mor...@protonmail.com <mailto:mor...@protonmail.com>
r-devel@r-project.org <mailto:r-devel@r-project.org>
r-devel@r-project.org <mailto:r-devel@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.dun...@gmail.com
<mailto:murdoch.dun...@gmail.com> To: Morkus
mor...@protonmail.com <mailto:mor...@protonmail.com>,
r-devel@r-project.org <mailto:r-devel@r-project.org>
r-devel@r-project.org <mailto:r-devel@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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