From ripley at stats.ox.ac.uk  Thu Jun  7 10:57:59 2012
From: ripley at stats.ox.ac.uk (Prof Brian Ripley)
Date: Thu, 7 Jun 2012 09:57:59 +0100
Subject: [Rd] 7 arguments passed to .Internal(identical) which requires 6
In-Reply-To: <87AF97BC-EF06-4017-887C-49A5EA800A81@gmail.com>
References: <CAF42j20RBW9SGRCA1t-uOTB330RoyRN43Yjv5GBR4580ugOxVw@mail.gmail.com>
	<loom.20120606T194231-377@post.gmane.org>
	<alpine.DEB.2.02.1206061329380.2432@luke-Latitude>
	<87AF97BC-EF06-4017-887C-49A5EA800A81@gmail.com>
Message-ID: <4FD06D17.8060206@stats.ox.ac.uk>

On 06/06/2012 21:04, peter dalgaard wrote:
> FYI, Brian has backed out the changes to identical() in r59533 of R-patched. Please retry your test codes with the new version. (Due to some ISP mess-up, Brian is temporarily unable to reply in detail himself.)
>
> -pd

Some comments (now my ISP has repaired its network and I can send from 
the machine on which I did this):

- AFAICS this only applies to binary distributions, not mentioned by the OP.

- There has never been any guarantee of forwards compatibility.  If you 
want a package to run under 2.x.y, install it under 2.x.y.  There is 
limited support for backwards compatibility, so packages installed under 
2.x.y will _normally_ run under 2.x.z for z > y.

So the whining appeared to be specious: if BioC want to distribute 
binary packages which run under all 2.15.x, they need to build them 
under 2.15.0, *and* check that they run under later versions.  (AFAIK 
the CRAN binary package providers expect users to be using the current 
version of R.)

R-patched should be thought of as having an intermediate version number 
for this purpose, e.g. currently > 2.15.0, < 2.15.1.

- The issue is package installations which copy code from the current 
version of R into the package. That is not a good idea, and in general 
not recommended.  We see 3 main circumstances:

+ S4 methods.  This was first reported many years ago, and bites 
frequently.  It was deemed a 'feature'.  The usual instance is that the 
default method is copied from a function in another contributed package 
which is subsequently updated, but it can also apply to the packages in 
R itself.

+ Some packages making functions into S3 default methods.  The advice 
there has changed a while ago, to write a wrapper instead of using
foo.default <- base::foo
but there are lots of packages not doing that.

+ Byte compilation, which in some cases removes the closure wrappers 
from simple .Internal calls, and so captures the .Internal call at the 
time of compilation.

- In the particular case of identical(), the C code has generally been 
written for backwards and attempted future compatibility, but that was 
not the case for the version in 2.15.0.  (It is the case for the version 
in R-devel and that now in R-patched: I didn't back out all the changes.)

But because identical() seems to be captured more than we anticipated 
and the change was not that important, I reverted it.  But if a similar 
change is needed for an important enough bug fix, it will go into 
R-patched (and there is one there now).


So the general principles are

- install a package under the current version of R, or perhaps an 
earlier patch release of the same series.  If using R-devel, be prepared 
to re-install any package you use (in practice this is rare: for example 
XML, compositions, timeDate and timeSeries needed to be re-installed 
since 2-15-branch was branched).

- if any dependency of an S4-using package changes, re-install the 
package.  And this includes the standard packages (which is why they 
should be listed in Depends:).   Uwe's CRAN Windows binary builder does 
do that, so you may need to re-install the binary package even though 
its version number has not changed.


>
> On Jun 6, 2012, at 20:29 ,<luke-tierney at uiowa.edu>  <luke-tierney at uiowa.edu>  wrote:
>
>> On Wed, 6 Jun 2012, Matthew Dowle wrote:
>>
>>> Dan Tenenbaum<dtenenba<at>  fhcrc.org>  writes:
>>>
>>>>
>>>> I know this has come up before on R-help
>>>> (http://r.789695.n4.nabble.com/7-arguments-passed-to-Internal-identical-which-
>>> requires-6-td4548460.html)
>>>> but I have a concise reproducible case that I wanted to share.
>>>>
>>>> Also, please note the Bioconductor scenario which is potentially
>>>> seriously impacted by this.
>>>> The issue arises when a binary version of a package (like my example
>>>> package below) is built under R 2.15.0 Patched but then installed
>>>> under R 2.15.0.  Our package AnnotationDbi (which hundreds of other
>>>> packages depend on) is impacted by this issue to the extent that
>>>> calling virtually any function in it will return something like this:
>>>> Error in ls(2) :
>>>>   7 arguments passed to .Internal(identical) which requires 6
>>>>
>>>> My concern is that when R 2.15.1 is released and Bioconductor starts
>>>> building all its packages under it, that R 2.15.0 users will start to
>>>> experience this problem. We can ask all users to upgrade to R 2.15.1
>>>> if we have to, but it's not usually the case that a minor point
>>>> release MUST be installed in order to run packages built under it
>>>> (please correct me if I'm wrong). We would much prefer a workaround or
>>>> fix to make an upgrade unnecessary.
>>>>
>>>
>>> I'm seeing the same issue. Installing the latest R-Forge .zip of data.table
>>> built using 2.15.0 patched, on R 2.15.0 (or 2.14.1 same issue), then running
>>> data.table(a=1:3) produces the "7 arguments passed to .Internal(identical)
>>> which requires 6" error.  traceback() and debugger() just display the top level
>>> call. debug(data.table) and stepping through reveals it is a call to identical
>>> () but just a regular one. No .Internal() call in the package, let alone
>>> passing 6 or 7 arguments to .Internal.
>>>
>>> Not sure how else to debug or trace it. R-Forge is byte compiling data.table
>>> using R 2.15.0 patched (iiuc), would that make a difference when the byte code
>>> is loaded into 2.15.0 which doesn't have the new argument in identical()?
>>
>> Yes it would.
>>
>> luke
>>
>>>
>>> Matthew


-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595



[Rd] 7 arguments passed to .Internal(identical) which requires 6
Prof Brian Ripley