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

Sat, Oct 28, 2017 1:51 PM

On 28/10/2017 8:59 AM, Morkus wrote:

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.

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.

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
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Thread (14 messages)

Morkus Cannot Compute Box's M (Three Days Trying...) Oct 27 William Dunlap Cannot Compute Box's M (Three Days Trying...) Oct 27 Duncan Murdoch Cannot Compute Box's M (Three Days Trying...) Oct 27 Morkus Cannot Compute Box's M (Three Days Trying...) Oct 28 Morkus Cannot Compute Box's M (Three Days Trying...) Oct 28 Duncan Murdoch Cannot Compute Box's M (Three Days Trying...) Oct 28 Morkus Cannot Compute Box's M (Three Days Trying...) Oct 28 Duncan Murdoch Cannot Compute Box's M (Three Days Trying...) Oct 28 Morkus Cannot Compute Box's M (Three Days Trying...) Oct 28 Duncan Murdoch Cannot Compute Box's M (Three Days Trying...) Oct 28 Morkus Cannot Compute Box's M (Three Days Trying...) Oct 29 Duncan Murdoch Cannot Compute Box's M (Three Days Trying...) Oct 29 Morkus Cannot Compute Box's M (Three Days Trying...) Oct 29 Duncan Temple Lang Cannot Compute Box's M (Three Days Trying...) Oct 29