[R] Re: packaging a package addon

[Ross Boylan]

I have some mixed results to report.  I went ahead and built a package
with the dependency, my changed files, and a few headers.  I left the
headers in the same directory as the C files.

My first attempt passed R CMD check, though there were no examples to
exercise the code.  When I tried to run it, it couldn't find the C
routine.  I had neglected to provide a .First.lib for my new library.

When I corrected that, R cmd check failed with
* checking generic/method consistency ... WARNING
Error in .loadPackageQuietly(package, lib.loc) : 
	Error in library(package, lib.loc = lib.loc, character.only = TRUE,
verbose = FALSE) : 
	.First.lib failed
Execution halted
* checking for assignment functions with final arg not named 'value' ...
WARNING
Error in .loadPackageQuietly(package, lib.loc) : 
	Error in library(package, lib.loc = lib.loc, character.only = TRUE,
verbose = FALSE) : 
	.First.lib failed
Execution halted
* checking Rd files ... OK
* checking for undocumented objects ... ERROR
Error in .loadPackageQuietly(package, lib.loc) : 

Hoping this was only a problem for check because it didn't know how to
load dependencies, I tried running the resulting code in a regular R
session.  My first discovery was that dependent libraries need to be
loaded by hand.  After I did that, when I ran my code I got
> library("survival")
> library("survivalrds", lib.loc="/home/ross/src/survivalrds.Rcheck/")
Error in dyn.load(x, as.logical(local), as.logical(now)) : 
	unable to load shared library
"/home/ross/src/survivalrds.Rcheck/survivalrds/libs/survivalrds.so":
  /home/ross/src/survivalrds.Rcheck/survivalrds/libs/survivalrds.so:
undefined symbol: cholesky2
Error in library("survivalrds", lib.loc =
"/home/ross/src/survivalrds.Rcheck/") : 
	.First.lib failed

cholesky2 is one of the entry points in survival referenced by
survivalrds.  I tried adding an "external" to the declaration of
cholesky2 (I think it's redundant) and redoing everything; it didn't
help.

In short, I'm having some dynamic linkage problems.  Any suggestions? 
(I'm on a linux system with the gcc 3.3 toolchain, but obviously it
would be better to solve this portably).
-- 
Ross Boylan                                      wk:  (415) 502-4031
530 Parnassus Avenue (Library) rm 115-4          ross at biostat.ucsf.edu
Dept of Epidemiology and Biostatistics           fax: (415) 476-9856
University of California, San Francisco
San Francisco, CA 94143-0840                     hm:  (415) 550-1062