From therneau at mayo.edu  Thu Jul  9 19:26:40 2015
From: therneau at mayo.edu (Therneau, Terry M., Ph.D.)
Date: Thu, 09 Jul 2015 12:26:40 -0500
Subject: [Rd] R CMD build failure
Message-ID: <2f3a88$105o53@ironport10.mayo.edu>

I have a local library 'dart' that imports "httr".  It has routines that access central 
patient data such as birth date, so it is heavily used locally but of no interest to 
anyone else.

The httr library (and 300 others) are in a shared directory, referenced by everyone in the 
biostatistics group via adding this location to the .libPaths in their default .Rprofile.  
(Actually, their .Rprofile starts by running material from a central one, the libPaths is 
there).

When I run R (3.2.0) all is fine, but R CMD build fails with  the text below

* creating vignettes ... ERROR
Error: processing vignette 'dart.Rnw' failed with diagnostics:
  chunk 2 (label = auth1)
Error : package ?httr? required by ?dart? could not be found
Execution halted


If I add the requiste directory to my R_LIBS_USER environment variable then all is fine.  
However, that's a nuisance since the location changes over time (e.g. R releases).  The 
system admins have a whole process that keeps .bashrc, .Rprofle and etc dot references up 
to date.   Plugging into this is why we use .Rprofile.  They are quite willing to make 
select changes in the central file, but with >1000 users any suggested changes in the 
overall process do not get a warm welcome.

Any ideas?  There is no mention in the Writing R Extentions manual that it ignores the 
Rprofile file.  If "suck it up and use R_LIBS_USER" is the answer, well, there are only a 
few who build packages.

PS, I can't use RHOME:/etc/Rprofile.site since the biostat group is not the only set of R 
users.  Some other groups, for instance, cannot even see our central area.

Terry T.



[Rd] R CMD build failure
Therneau, Terry M., Ph.D.