From murdoch.duncan at gmail.com  Tue Jun 24 15:34:44 2014
From: murdoch.duncan at gmail.com (Duncan Murdoch)
Date: Tue, 24 Jun 2014 15:34:44 +0200
Subject: [Rd] Unfixed bugs in latest R-patched
In-Reply-To: <20140624114005.GA10010@cs.toronto.edu>
References: <20140623152435.GA22211@cs.toronto.edu>
	<53A926BE.4030205@gmail.com>
	<20140624114005.GA10010@cs.toronto.edu>
Message-ID: <53A97E74.1050107@gmail.com>

On 24/06/2014, 1:40 PM, Radford Neal wrote:
> 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.

No, I don't think it's reasonable to expect you to write a patch, but
reporting the bugs in the R bug reporting system isn't that hard to do,
and does lead to fixes pretty rapidly in cases where the report contains
sample code to reproduce the problem.

I don't know if pqR has a similar bug reporting system, but if it does,
a reference to a report there would also be fine.  But something like
"Fixed a problem in R_AllocStringBuffer that could result in a crash due
to an invalid memory access" sounds serious, but is just too vague to
follow up.  I would expect that doing a diff on the source files is
going to find all sorts of stuff:  pqR isn't just R with bugs fixed, it
has a lot of other changes too.

I can understand that from your point of view saying "R has bugs that
have been fixed in pqR" is a form of advertising, but it would be more
helpful to the community if the bugs actually got fixed.  I think all of
the bugs that you reported last June got fixed within a couple of weeks
(though not all of the speedups were incorporated).  Why not report them
more frequently than annually, and give the details you already have so
they are easier to fix?

Duncan Murdoch


> 
>    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
Duncan Murdoch