Re: [Rd] Found explanation for R-2.15.2 slowdown in one case; caution for any users of La_chol

From: Paul Johnson <>
Date: Sat, 15 Dec 2012 22:29:32 -0600

On Sat, Dec 15, 2012 at 11:44 AM, Uwe Ligges <> wrote:
> On 14.12.2012 23:31, Paul Johnson wrote:
> That is the reason why R CMD check gives a WARNING in the checks of your
> package for quite some time now:

> checking foreign function calls ... WARNING
> Foreign function calls with 'PACKAGE' argument in a base package:
> .Call("La_chol", ..., PACKAGE = "base")
> .Call("La_chol2inv", ..., PACKAGE = "base")
> Packages should not make .C/.Call/.Fortran calls to base packages. They

> are not part of the API, for use only by R itself and subject to change
> without notice.

Just to be clear. Its not *my* package. It is a package we use A LOT I had to get to the bottom of the problem. I'm *very glad* to understand it.

>From a user perspective, I wonder if CRAN could warn me somehow?
Would it be a reasonable wishlist request to have the build process take a snapshot of warnings and then have the installer play them back to the user when the package is installed? That would have saved me some time this week.

Now, when I install that, I don't see a warning. (see below).

> install.packages("Amelia")

Installing package(s) into ‘/home/pauljohn/R/x86_64-pc-linux-gnu-library/2.15’ (as ‘lib’ is unspecified)
--- Please select a CRAN mirror for use in this session --- Loading Tcl/Tk interface ... done
trying URL '' Content type 'application/x-gzip' length 1060878 bytes (1.0 Mb) opened URL

downloaded 1.0 Mb

The downloaded source packages are in

> So time to fix that. See also:
> Best,
> Uwe Ligges

Paul E. Johnson
Professor, Political Science      Assoc. Director
1541 Lilac Lane, Room 504      Center for Research Methods
University of Kansas                 University of Kansas     

______________________________________________ mailing list
Received on Sun 16 Dec 2012 - 04:37:58 GMT

This quarter's messages: by month, or sorted: [ by date ] [ by thread ] [ by subject ] [ by author ]

All messages

Archive maintained by Robert King, hosted by the discipline of statistics at the University of Newcastle, Australia.
Archive generated by hypermail 2.2.0, at Sun 16 Dec 2012 - 11:12:59 GMT.

Mailing list information is available at Please read the posting guide before posting to the list.

list of date sections of archive