From murdoch.duncan at gmail.com  Sat Oct 28 22:51:04 2017
From: murdoch.duncan at gmail.com (Duncan Murdoch)
Date: Sat, 28 Oct 2017 16:51:04 -0400
Subject: [Rd] Cannot Compute Box's M (Three Days Trying...)
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Message-ID: <abe44eb4-e08a-087a-1870-dc73d1e59da4@gmail.com>

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 | |
>>
>>
>



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