From radford at cs.toronto.edu  Mon Jun 23 17:24:35 2014
From: radford at cs.toronto.edu (Radford Neal)
Date: Mon, 23 Jun 2014 11:24:35 -0400
Subject: [Rd] Unfixed bugs in latest R-patched
Message-ID: <20140623152435.GA22211@cs.toronto.edu>

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



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