From pdalgd at gmail.com  Wed Jun  6 22:04:03 2012
From: pdalgd at gmail.com (peter dalgaard)
Date: Wed, 6 Jun 2012 22:04:03 +0200
Subject: [Rd] 7 arguments passed to .Internal(identical) which requires 6
In-Reply-To: <alpine.DEB.2.02.1206061329380.2432@luke-Latitude>
References: <CAF42j20RBW9SGRCA1t-uOTB330RoyRN43Yjv5GBR4580ugOxVw@mail.gmail.com>
	<loom.20120606T194231-377@post.gmane.org>
	<alpine.DEB.2.02.1206061329380.2432@luke-Latitude>
Message-ID: <87AF97BC-EF06-4017-887C-49A5EA800A81@gmail.com>

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


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
>> 
>> ______________________________________________
>> R-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
>> 
> 
> -- 
> Luke Tierney
> Chair, Statistics and Actuarial Science
> Ralph E. Wareham Professor of Mathematical Sciences
> University of Iowa                  Phone:             319-335-3386
> Department of Statistics and        Fax:               319-335-3017
>   Actuarial Science
> 241 Schaeffer Hall                  email:   luke-tierney at uiowa.edu
> Iowa City, IA 52242                 WWW:  http://www.stat.uiowa.edu
> 
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel

-- 
Peter Dalgaard, Professor,
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Email: pd.mes at cbs.dk  Priv: PDalgd at gmail.com



[Rd] 7 arguments passed to .Internal(identical) which requires 6
peter dalgaard