From pauljohn32 at gmail.com  Sun Dec 16 05:29:32 2012
From: pauljohn32 at gmail.com (Paul Johnson)
Date: Sat, 15 Dec 2012 22:29:32 -0600
Subject: [Rd] Found explanation for R-2.15.2 slowdown in one case;
 caution for any users of La_chol
In-Reply-To: <50CCB6E9.8070800@statistik.tu-dortmund.de>
References: <CAErODj_5cvD78nmC1RBAWGgjKSvPpVwpVsNZMjcQgyjqSraQ3w@mail.gmail.com>
	<50CCB6E9.8070800@statistik.tu-dortmund.de>
Message-ID: <CAErODj8vXaVc5m1XJHkN6dXHZ+C36XambdN4fy6n0um1y7EftQ@mail.gmail.com>

On Sat, Dec 15, 2012 at 11:44 AM, Uwe Ligges
<ligges at statistik.tu-dortmund.de> 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 'http://rweb.quant.ku.edu/cran/src/contrib/Amelia_1.6.3.tar.gz'
Content type 'application/x-gzip' length 1060878 bytes (1.0 Mb)
opened URL
==================================================
downloaded 1.0 Mb

* installing *source* package ?Amelia? ...
** package ?Amelia? successfully unpacked and MD5 sums checked
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   ?amelia.Rnw?
** testing if installed package can be loaded

* DONE (Amelia)

The downloaded source packages are in
        ?/tmp/Rtmpi0CLZe/downloaded_packages?
>
> So time to fix that. See also:
> http://cran.r-project.org/web/checks/check_results_Amelia.html
>
>
> 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
http://pj.freefaculty.org               http://quant.ku.edu



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