[R] Re: packaging a package addon

[A.J. Rossini]

You might need to install before checking.  Sometimes that helps.  I
still havn't figured out exactly why...

Ross Boylan <ross at biostat.ucsf.edu> writes:

> 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
>
> ______________________________________________
> R-help at stat.math.ethz.ch mailing list
> https://www.stat.math.ethz.ch/mailman/listinfo/r-help
>

-- 
rossini at u.washington.edu            http://www.analytics.washington.edu/ 
Biomedical and Health Informatics   University of Washington
Biostatistics, SCHARP/HVTN          Fred Hutchinson Cancer Research Center
UW (Tu/Th/F): 206-616-7630 FAX=206-543-3461 | Voicemail is unreliable
FHCRC  (M/W): 206-667-7025 FAX=206-667-4812 | use Email

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