On Fri, Jun 26, 2009 at 2:43 PM, Paul Johnson<pauljohn32 at gmail.com> wrote:
Hello, again.
I'm interested to learn how programmers develop & test C/C++ code with
R packages in Linux. I've been reading R source and the manual on
Writing R Extensions but there are just a couple of details I can't
understand. I wish I could watch over a developer's shoulder to see
how people actually do this.
I've tested a bit. I am able to take package.tar.gz file, open it up,
fiddle the source code, and then run
R CMD check package-dir
from the directory above "package-dir" ,
R CMD build package-dir
and
R CMD INSTALL
For your purposes it is probably better to avoid building a new tar.gz
file and combine the last two steps as
R CMD INSTALL package-dir
The install process uses the make utility which will check which of
the object files need to be recompiled. If you only modify one source
file it will be the only file recompiled.
on the tarball that is produced. Then in R, I can load the package and use it.
That part is "all good", but somewhat tedious. I don't want to
entirely recompile and reinstall the whole package just to test one
function. I notice that R CMD check creates a new directory called
"package.Rcheck" and the shared objects and example code of the
package are in there. Can I force R to use those *.so files instead
of the ones in /usr/lib/R ?
I also wonder "what is wrong with gprof? In the Writing R Extensions
manual, it describes "oprofile" and "sprof" for Linux. I will try
them, but they are unfamilar to me. I've used gprof in the past in C
projects, and it is a pretty painless thing to add a compiler flag
-pg, run the program, and then review gmon.out. The Writing R
Extensions manual does not mention gprof in its section on Linux, but
it does mention it under Solaris. There is a somewhat ambiguous
statement:
3.4.2 Solaris
On 64-bit (only) Solaris, the standard profiling tool gprof collects
information from shared libraries compiled with -pg.
Does "(only)" here mean to differentiate Solaris from other Linux/Unix
systems? Or does it differentiate 64bit Solaris from other Solaris?
But this draws me back to the basic question. I don't want to run R
CMD INSTALL 20 times per hour. How do developers "actually" test
their code?
pj
--
Paul E. Johnson
Professor, Political Science
1541 Lilac Lane, Room 504
University of Kansas