[R] debugging R code and dealing with dependencies

[David Winsemius]

> On Dec 25, 2014, at 1:04 AM, Mike Miller <mbmiller+l at gmail.com> wrote:
> 
> I just wanted to put this out there.  It's just some of my observations about things that happen with R, or happened in this particular investigation.  There were definitely some lessons for me in this, and maybe that will be true of someone else.  The main thing I picked up is that it is good to put plenty of checks into our code -- if we expect input of a certain type or class, then I should either coerce input into that structure or test the input and throw an error.  If the function works very differently for different kinds of input, this should be documented.  The more people are doing this, the better things will go for everyone.
> 
> 
> I was working with a CRAN package called RFGLS...
> 
> http://cran.r-project.org/web/packages/RFGLS/index.html
> 
> ...and I was getting an error.  After a few rounds of testing I realized that the error was caused by a FAMID variable that was of character type.

But The Details section of the help page does say that the accepted FTYPES are all integers between 1 and 6 and the INDIV variables are integers in range 1:4.

> The problem seemed to be that gls.batch() expected FAMID to be integers, but the default ought to be character type because family and individual IDs in nearly all genetic-analysis software are character strings (they might even be people's names).

You are making up rules that were not in accord with the documentation.

> This was the error:
> 
> Error in sum(blocksize) : invalid 'type' (character) of argument
> Calls: gls.batch -> bdsmatrix
> 
> To figure out more about it, I spent a bunch of time to go from CMD BATCH mode to an interactive session so that I could look at traceback().  

Generally the first thing to check is the help page. And if there is a worked example to look at its data:

> data(pedigree, package="RFGLS")
> str(pedigree)
'data.frame':	4050 obs. of  5 variables:
 $ FAMID: int  10 10 10 10 20 20 20 20 30 30 ...
 $ ID   : int  11 12 13 14 21 22 23 24 31 32 ...
 $ PID  : int  14 14 0 0 24 24 0 0 34 34 ...
 $ MID  : int  13 13 0 0 23 23 0 0 33 33 ...
 $ SEX  : num  1 1 2 1 2 2 2 1 2 2 …

— 
David.

> That got me this additional info:
> 
>> traceback()
> 2: bdsmatrix(sizelist, lme.out$sigma at blocks, dimnames = list(id, id))
> 
> bdsmatrix() is from a package on which RFGLS depends:
> 
> http://cran.r-project.org/web/packages/bdsmatrix/index.html
> 
> The problem is that RFGLS's gls.batch() function is sending something to bdsmatrix's bdsmatrix() that it can't handle.  So I look at the code for bdsmatrix() and I see this:
> 
>     if (any(blocksize <= 0))
>         stop("Block sizes must be >0")
>     if (any(as.integer(blocksize) != blocksize))
>         stop("Block sizes must be integers")
>     n1 <- as.integer(sum(blocksize))
> 
> The condition any(as.integer(blocksize) != blocksize)) fails (is TRUE) only if blocksize contains one or more noninteger numeric values.  It doesn't fail if blocksize is character or logical if the character strings are integers.  Example:
> 
>> 4=="4"
> [1] TRUE
> 
> That's an interesting feature of R, but I guess that's how it works. Also this:
> 
>> 1=="1"
> [1] TRUE
>> 1==TRUE
> [1] TRUE
>> "1"==TRUE
> [1] FALSE
> 
> bdsmatrix() has no test that blocksize is numeric, so it fails when sum(blocksize) cannot sum character strings.
> 
> Next I had to figure out where RFGLS's gls.batch() is going wrong in producing sizelist.  It is created in a number of steps, but I identified this line as especially suspicious:
> 
> test.dat$famsize[test.dat$FTYPE!=6]=ave(test.dat$FAMID[test.dat$FTYPE!=6],test.dat$FAMID[test.dat$FTYPE!=6],FUN=length)
> 
> famsize was later converted to sizelist, and this line also includes FAMID, so this is likely where the problem originates.  Of course this is the big problem with debugging -- it's hard to find the source of an error that occurs far downstream in another function from a different package. I see that ave() is used, so I have to understand ave().
> 
> William Dunlap provided some guidance:
> 
> "ave() uses its first argument, 'x', to set the length of its output and to make an initial guess at the type of its output.  The return value of FUN can alter the type, but only in an 'upward' direction where logical<integer<numeric<complex<character<list.  (This is the same rule that x[i]<-newvalue uses.)"
> 
> In other words, if x is of character type, the output cannot be of integer or numeric type even if the output of FUN is always of integer or numeric type.  Looking at the ave() code, I can understand that choice:
> 
> function (x, ..., FUN = mean)
> {
>    if (missing(...))
>        x[] <- FUN(x)
>    else {
>        g <- interaction(...)
>        split(x, g) <- lapply(split(x, g), FUN)
>    }
>    x
> }
> 
> If the factor is missing an element, then the corresponding element of X is not changed in the output:
> 
>> fact <- gl(2,2)
>> fact[3] <- NA
>> fact
> [1] 1    1    <NA> 2
> Levels: 1 2
>> ave(1:4, fact)
> [1] 1.5 1.5 3.0 4.0
> 
> That's a reasonable plan, but it isn't the documented functioning of ave().  From the document...
> 
> https://stat.ethz.ch/R-manual/R-devel/library/stats/html/ave.html
> 
> ...you get next to nothing about what the function actually does.  It does say that x is "a numeric," but the function does not throw an error when x is not numeric.  So if someone writes code expecting numeric x, but a user provides a non-numeric x, there may be trouble.
> 
> I suspect that the programmer saw that the code worked in her examples and she went on to other things.  I can't blame the documentation for that, but it is possible that if it said something about the relation between the type of the input and the type of the output she might have written it differently.  In addition, I probably would have caught it sooner and I would have understood the problem.
> 
> This is how I'll recommend they fix the bug in the code (thanks to those of you who helped with this):
> 
> temp.vec <- as.character( test.dat$FAMID[ test.dat$FTYPE != 6 ] )
> test.dat$famsize[ test.dat$FTYPE != 6 ] <- as.vector( table( temp.vec )[ temp.vec ] )
> rm(temp.vec)
> 
> I think we should force FAMID to be character from the beginning, though.
> 
> Best,
> Mike
> 
> FYI -- RFGLS code that fails in RFGLS version 1.1:
> 
> library(RFGLS)
> 
> data(pheno)
> data(geno)
> data(map)
> data(pedigree)
> data(rescovmtx)
> #comment out the following two lines and it will run correctly
> pedigree$FAMID <- as.character(pedigree$FAMID)
> pheno$FAMID <- as.character(pheno$FAMID)
> minigwas <- gls.batch(phenfile=pheno,genfile=data.frame(t(geno)),
>  pedifile=pedigree,
>  snp.names=map[,2],input.mode=c(1,2,3),pediheader=FALSE,
>  pedicolname=c("FAMID","ID","PID","MID","SEX"),
>  phen="Zscore",covars="IsFemale",
>  outfile=NULL,col.names=TRUE,return.value=TRUE)
> str(minigwas)
> 
> Mike
> 
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