[R-sig-Debian] make check reg-tests-1b.R fails with Ubuntu R

[Michael Rutter]

On 09/14/2011 10:18 AM, Andrew Piskorski wrote:
> Today I built R from source on a 32-bit Ubuntu 10.04.3 LTS box, and
> saw that the "make check" tests/reg-tests-1b.R failed.  From the
> output at the end of my "tests/reg-tests-1b.Rout.fail" file, the
> problem is appearing in the "identical(z, x %*% t(y))" test code
> below.
>
> I then tried the stock R provided by the Ubuntu r-base-core binary
> package, and to my surprise, it failed the test in exactly the same
> way!
>
> So this is NOT solely a problem with my from-source build (I merely
> happened to notice it first that way).  It probably indicates some
> sort of system-wide bug or misconfiguration, at least on my machine,
> perhaps on others' too.
>
> Could someone please advise me:  What is the significance of this test
> from reg-tests-1b.R failing, and what should I do to further track it
> down and fix it?
>
> Thanks!  Much more detail is below.
>
> ------------------------------------------------------------
>
> # Here's the excerpt from the "make check" output where I first
> # noticed the problem:
>
> running regression tests ...
> make[3]: Entering directory `/net/brain/home/local-x86_32-ubuntu/nobackup/co-R/R-2-12-branch/Build-x86_32/tests'
> running code in '../../tests/reg-tests-1.R' ... OK
> running code in '../../tests/reg-tests-1b.R' ...make[3]: *** [reg-tests-1b.Rout] Error 1
> make[3]: Leaving directory `/net/brain/home/local-x86_32-ubuntu/nobackup/co-R/R-2-12-branch/Build-x86_32/tests'
> make[2]: *** [test-Reg] Error 2
> make[2]: Leaving directory `/net/brain/home/local-x86_32-ubuntu/nobackup/co-R/R-2-12-branch/Build-x86_32/tests'
> make[1]: *** [test-all-basics] Error 1
> make[1]: Leaving directory `/net/brain/home/local-x86_32-ubuntu/nobackup/co-R/R-2-12-branch/Build-x86_32/tests'
> make: *** [check] Error 2
>
>
> # This is the Ubuntu machine where I found the error:
>
> andy at n88:~$ lsb_release -d
> Description:	Ubuntu 10.04.3 LTS
> andy at n88:~$ uname -a
> Linux n88 2.6.32-33-generic #72-Ubuntu SMP Fri Jul 29 21:08:37 UTC 2011 i686 GNU/Linux
> andy at n88:~$ dpkg -l r-base-core | grep r-base
> ii  r-base-core   2.10.1-2   GNU R core of statistical computation and graphics system
>
>
> # Stock Ubuntu-provided R has the same failure:
>
> andy at n88:~$ /usr/bin/R -q --vanilla
>> dtk.R.version()
> [1] "R 2.10.1, 2009-12-14, svn.rev 50720, i486-pc-linux-gnu"
>> x<- matrix(c(1, 0, NA, 1), 2, 2) ; y<- matrix(c(1, 0, 0, 2, 1, 0), 3, 2)
>> (z<- tcrossprod(x, y))
>       [,1] [,2] [,3]
> [1,]   NA   NA    0
> [2,]    2    1    0
>> identical(z, x %*% t(y))
> [1] FALSE
>
>
> # R I just built from scratch, same failure as stock R:
>
> andy at n88:~$ /usr/local/pkg/R-2.12-branch-20110914/bin/R -q --vanilla
>> dtk.R.version()
> [1] "R 2.12.2 (Patched), 2011-03-18, svn.rev 57004, i686-pc-linux-gnu"
>> x<- matrix(c(1, 0, NA, 1), 2, 2) ; y<- matrix(c(1, 0, 0, 2, 1, 0), 3, 2)
>> (z<- tcrossprod(x, y))
>       [,1] [,2] [,3]
> [1,]   NA   NA    0
> [2,]    2    1    0
>> identical(z, x %*% t(y))
> [1] FALSE
>
>
> # Apparently the correct output is supposed to look like this:
>
> andy at dax:~$ /usr/bin/R -q --vanilla
>> x<- matrix(c(1, 0, NA, 1), 2, 2) ; y<- matrix(c(1, 0, 0, 2, 1, 0), 3, 2)
>> (z<- tcrossprod(x, y))
>       [,1] [,2] [,3]
> [1,]   NA   NA   NA
> [2,]    2    1    0
>> identical(z, x %*% t(y))
> [1] TRUE
>
> # Note that the correct output above was run on a different machine,
> # which happens to be x86-64:
>
> andy at dax:~$ lsb_release -d
> Description:	Ubuntu 10.04.3 LTS
> andy at dax:~$ uname -a
> Linux dax 2.6.32.29+drm33.13-custom #1 SMP Fri Apr 8 13:42:18 EDT 2011 x86_64 GNU/Linux
>
>
> # Function I used to print out the version number info above:
> dtk.R.version<- function() {
>     patched.str<- version$status
>     if (patched.str != "")
>        patched.str<- paste(" (" ,patched.str ,")" ,sep="")
>     paste(paste(version$language  ," "
>                 ,paste(version[c("major","minor")] ,collapse=".")
>                 ,patched.str  ,sep="")
>           ,paste(version[c("year","month","day")] ,collapse="-")
>           ,paste("svn.rev" ,version$"svn rev")
>           ,version$platform
>           ,sep=", " ,collapse=" ")
> }

On my i386 machine:

~/D/R> lsb_release -d
Description:	Ubuntu 10.04.3 LTS

I get the following:

 > dtk.R.version()
[1] "R 2.13.1, 2011-07-08, svn.rev 56322, i486-pc-linux-gnu"
 > x <- matrix(c(1, 0, NA, 1), 2, 2)
 > y <- matrix(c(1, 0, 0, 2, 1, 0), 3, 2)
 > (z <- tcrossprod(x, y))
 > identical(z, x %*% t(y))
      [,1] [,2] [,3]
[1,]   NA   NA   NA
[2,]    2    1    0
[1] TRUE

This is using the R available on CRAN.  I can think of two possible causes:

1.  It is an error that was found prior to 2.13.1 and has been fixed.
2.  You have installed a non-standard, math-related library on your 
machine that is causing the error. A LAPACK library or the Revolution 
computing libraries available in Ubuntu are examples.

To test, I downgraded my R back to 2.10.1-2, the version from Ubuntu, 
not from CRAN.  Here are my results:

 > x <- matrix(c(1, 0, NA, 1), 2, 2)
 > y <- matrix(c(1, 0, 0, 2, 1, 0), 3, 2)
 > (z <- tcrossprod(x, y))
      [,1] [,2] [,3]
[1,]   NA   NA   NA
[2,]    2    1    0
 > identical(z, x %*% t(y))
[1] TRUE
 > dtk.R.version()
[1] "R 2.10.1, 2009-12-14, svn.rev 50720, i486-pc-linux-gnu"

This leads me to believe cause number 2 is the likely culprit.

Michael

-- 
Dr. Michael A. Rutter
School of Science
Penn State Erie, The Behrend College
Station Road
Erie, PA 16563
http://math.bd.psu.edu/faculty/rutter