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

Paul Johnson pauljohn32 at gmail.com
Sun Dec 16 05:29:32 CET 2012

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
** testing if installed package can be loaded

* DONE (Amelia)

The downloaded source packages are in
> 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

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