From mdowle at mdowle.plus.com  Thu Jun  7 02:30:33 2012
From: mdowle at mdowle.plus.com (Matthew Dowle)
Date: Thu, 7 Jun 2012 01:30:33 +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: <1339029033.2573.27.camel@netbook>

I built R-trunk (rev 59537), ran 'Rtrunk CMD build data.table',
installed the resulting tar.gz into R release and it ran tests ok. So it
seems ok now, if that tested it right. Will check R-Forge again when it
catches up. Thanks.
Matthew

On Wed, 2012-06-06 at 22:04 +0200, 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
> 
> 
> 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
>



[Rd] 7 arguments passed to .Internal(identical) which requires 6
Matthew Dowle