From radford at cs.toronto.edu  Tue Jun 24 13:40:05 2014
From: radford at cs.toronto.edu (Radford Neal)
Date: Tue, 24 Jun 2014 07:40:05 -0400
Subject: [Rd] Unfixed bugs in latest R-patched
In-Reply-To: <53A926BE.4030205@gmail.com>
References: <20140623152435.GA22211@cs.toronto.edu>
	<53A926BE.4030205@gmail.com>
Message-ID: <20140624114005.GA10010@cs.toronto.edu>

On Tue, Jun 24, 2014 at 09:20:30AM +0200, Duncan Murdoch wrote:
> It's hardly fair to call these "unfixed bugs".  Most of them are better
> described as "unreported bugs", or, after this posting, "bugs reported
> with insufficient detail".  We can't fix them if we don't know what they
> are, and it's not easy to determine that for most of the items below.

I think most of them are pretty clear.  For the ones referring to lack
of protection or argument error checking code, I suggesting doing a
"diff" on the source files to find where I made changes.

If your complaint is that your time is more valuable than my time, so
I should be producing a nice patch for you, then I don't agree.  I went 
to the effort of verifing that the bugs are still present in r66002.  
That's as much as I'm willing to do.  It's up to you what you do.

   Radford Neal


> On 23/06/2014, 5:24 PM, Radford Neal wrote:
> > A new version of pqR is now available at pqR-project.org, which fixes
> > several bugs that are also present in the latest R Core patch release
> > (r66002).  A number of bugs found previously during pqR development
> > are also unfixed in the latest R Core release.  Here is the list of
> > these bugs that are unfixed in r66002 (including documentation
> > deficiencies), taken from the pqR bug fix and documentation update
> > sections of the pqR NEWS file (pqR-project.org/NEWS.txt):
> > 
> >     o The documentation for c now says how the names for the result are
> >       determined, including previously missing information on the
> >       use.names argument, and on the role of the names of arguments in
> >       the call of c.  This documentation is missing in R-2.15.0 and
> >       R-3.1.0.
> > 
> >     o The documentaton for diag now documents that a diagonal matrix is
> >       always created with type double or complex, and that the names of
> >       an extracted diagonal vector are taken from a names attribute (if
> >       present), if not from the row and column names.  This information
> >       is absent in the documentation in R-2.15.1 and R-3.1.0.
> > 
> >     o Incorrect information regarding the pointer protection stack was
> >       removed from help(Memory).  This incorrect information is present
> >       in R-2.15.0 and R-3.1.0 as well.
> > 
> >     o There is now information in help(Arithmetic) regarding what
> >       happens when the operands of an arithmetic operation are NA or
> >       NaN, including the arbitrary nature of the result when one
> >       operand is NA and the other is NaN.  There is no discussion of
> >       this issue in the documentation for R-2.15.0 and R-3.1.0.
> > 
> >     o Fixed lack of protection bugs in the equal and greater functions
> >       in sort.c.  These bugs are also present in R-2.15.0 and R-3.1.0.
> > 
> >     o Fixed lack of protection bugs in the D function in deriv.c.
> >       These bugs are also present in R-2.15.0 and R-3.1.0.
> > 
> >     o Fixed argument error-checking bugs in getGraphicsEventEnv and
> >       setGraphicsEventEnv (also present in R-2.15.0 and R-3.1.0).
> > 
> >     o Fixed the following bug (also present in R-2.15.0 and R-3.0.2):
> >       
> >           x <- t(5)
> >           print (x %*% c(3,4))
> >           print (crossprod(5,c(3,4)))
> > 
> >       The call of crossprod produced an error, whereas the
> >       corresponding use of %*% does not.
> > 
> >       In pqR-2013-12-29, this bug also affected the expression t(5) %*%
> >       c(3,4), since it is converted to the equivalent of
> >       crossprod(5,c(3,4)).
> > 
> >     o Fixed a problem in R_AllocStringBuffer that could result in a
> >       crash due to an invalid memory access.  (This bug is also present
> >       in R-2.15.0 and R-3.0.2.)
> > 
> >     o The documentation for aperm now says that the default method does
> >       not copy attributes (other than dimensions and dimnames).
> >       Previously, it incorrecty said it did (as is the case also in
> >       R-2.15.0 and R-3.0.2).
> > 
> >     o Fixed the following bug (also present in R-2.15.0 and R-3.0.2):
> >       
> >          v <- c(1,2)
> >          m <- matrix(c(3,4),1,2)
> >          print(t(m)%*%v)
> >          print(crossprod(m,v))
> > 
> >       in which crossprod gave an error rather than produce the answer
> >       for the corresponding use of %*%.
> > 
> >     o Raising -Inf to a large value (eg, (-Inf)^(1e16)) no longer
> >       produces an incomprehensible warning.  As before, the value
> >       returned is Inf, because (due to their limited-precision
> >       floating-point representation) all such large numbers are even
> >       integers.
> > 
> >     o Fixed a bug (also present in R-2.15.0 and R-3.0.1) illustrated by
> >       the following code:
> >       
> >          > a <- list(x=c(1,2),y=c(3,4))
> >          > b <- as.pairlist(a)
> >          > b$x[1] <- 9
> >          > print(a)
> >          $x
> >          [1] 9 2
> >          
> >          $y
> >          [1] 3 4
> > 
> >       The value printed for a has a$x[1] changed to 9, when it should
> >       still be 1. See pqR issue #14.
> > 
> >     o Fixed several bugs (also present in R-2.15.0 and R-3.0.1)
> >       illustrated by the code below (see pqR issue #16):
> >       
> >          v <- c(10,20,30)
> >          v[[2]] <- NULL        # wrong error message
> >          
> >          x <- pairlist(list(1,2))
> >          x[[c(1,2)]] <- NULL   # wrongly gives an error, referring to misuse
> >                                # of the internal SET_VECTOR_ELT procedure
> >          
> >          v<-list(1)
> >          v[[quote(abc)]] <- 2  # internal error, this time for SET_STRING_ELT
> >          
> >          a <- pairlist(10,20,30,40,50,60)
> >          dim(a) <- c(2,3)
> >          dimnames(a) <- list(c("a","b"),c("x","y","z"))
> >          print(a)              # doesn't print names
> >          
> >          a[["a","x"]] <- 0     # crashes with a segmentation fault
> > 
> >     o Fixed a bug where, for example, log(base=4) returned the natural
> >       log of 4, rather than signalling an error.
> > 
> >     o The documentation on what MARGIN arguments are allowed for apply
> >       has been clarified, and checks for validity added.  The call
> >       
> >          > apply(array(1:24,c(2,3,4)),-3,sum)
> > 
> >       now produces correct results (the same as when MARGIN is 1:2).
> > 
> >     o Fixed a bug in which Im(matrix(complex(0),3,4)) returned a matrix
> >       of zero elements rather than a matrix of NA elements.
> > 
> >     o Now check for bad arguments for .rowSums, .colSums, .rowMeans,
> >       and .rowMeans (would previously segfault if n*p too big).
> > 
> >     o Fixed a bug where excess warning messages may be produced on
> >       conversion to RAW.  For instance:
> >       
> >          > as.raw(1e40)
> >          [1] 00
> >          Warning messages:
> >          1: NAs introduced by coercion 
> >          2: out-of-range values treated as 0 in coercion to raw 
> > 
> >       Now, only the second warning message is produced.
> > 
> >     o A bug has been fixed in which rbind would not handle non-vector
> >       objects such as function closures, whereas cbind did handle them,
> >       and both were documented to do so.
> > 
> > Regards,
> > 
> >    Radford Neal
> > 
> > ______________________________________________
> > R-devel at r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-devel
> > 
>



[Rd] Unfixed bugs in latest R-patched
Radford Neal