From Setzer.Woodrow at epamail.epa.gov  Mon Feb  2 22:56:57 2009
From: Setzer.Woodrow at epamail.epa.gov (Setzer.Woodrow at epamail.epa.gov)
Date: Mon, 2 Feb 2009 16:56:57 -0500
Subject: [Rd] Getting 'LinkingTo' to find the right library
In-Reply-To: <alpine.LFD.2.00.0902022117590.19068@gannet.stats.ox.ac.uk>
References: <OF513E9410.5EB7FB0A-ON85257551.006C7BAD-85257551.00717734@epamail.epa.gov>
	<alpine.LFD.2.00.0902022117590.19068@gannet.stats.ox.ac.uk>
Message-ID: <OF9980EE67.A5FB411A-ON85257551.0076417C-85257551.007891D3@epamail.epa.gov>

(I just realized that when "they" upgraded my mail program, "they" reset
my preferences to send html and text for internet mail.  I have fixed
the preferences to text only, and apologize).
Well, where would I get the idea it was NOT reading .Rprofile, since it
clearly IS reading Rprofile.site?  However, I mainly thought that the
library being installed to would be used to find the dependent package,
because of this bug fix entry for version 2.7.2:
o The use of multiple packages in 'LinkingTo' works again, and
????????????now works when the dependent packages are in the library to
be
????????????installed to (but not in the library path seen by R
--vanilla).

Also, in this paragraph from the INSTALL help item:

     To install into the library tree 'lib', use 'R CMD INSTALL -l lib
     pkgs'.  This prepends 'lib' to 'R_LIBS' for duration of the
     install, so required packages in the installation directory will
     be found (and used in preference to those in other libraries).

Setting R_LIBS works (I DID try this before, but must have fumbled
something).

R. Woodrow Setzer, Ph. D.
National Center for Computational Toxicology
http://www.epa.gov/comptox
US Environmental Protection Agency
Mail Drop B205-01/US EPA/RTP, NC 27711
Ph: (919) 541-0128    Fax: (919) 541-1194).

Prof Brian Ripley <ripley at stats.ox.ac.uk> wrote on 02/02/2009 04:22:52
PM:

> [image removed]
>
> Re: [Rd] Getting 'LinkingTo' to find the right library
>
> Prof Brian Ripley
>
> to:
>
> Woodrow Setzer
>
> 02/02/2009 04:22 PM
>
> Cc:
>
> r-devel
>
> Where did you get the idea that R CMD INSTALL is reading .Rprofile?
> (AFAIR it does so only to find the installation library, as R CMD
> INSTALL --help says it will.)
>
> You need to set R_LIBS in the environment to get the library path you
> want.  This is not specific to 'LinkingTo'.
>
> On Mon, 2 Feb 2009, Setzer.Woodrow at epamail.epa.gov wrote:
>
> >
> > I am experimenting with exporting pointers to some of the functions
in
> > deSolve so that other packages may import them, using the
> > 'R_RegisterCCallable' mechanism.  I have added a header file and
some
> > other C code in inst/include of the deSolve source package that need
to
> > be accessible to other packages.  I have a site-library set up in
> > Rprofile.site where all installed packages go, and as long as my
> > experimental version of deSolve is installed there,  I'd like to
install
> > my modified copy of deSolve in a test library.  However, when I try
to
> > install my test package (which includes both Depends: deSolve and
> > LinkingTo: deSolve, in its Description file, as described in 'R
> > Extensions'), compilation fails, because the appropriate C code
cannot
> > be found (there is also an unrelated problem in deSolve_stubs.c
> > triggering the "unexpected ')' before '*' token" error).
> >
> > [test]$ R CMD INSTALL -l C:/home/Rlib-test dma
> >
> >
> > ---------- Making package dma ------------
> >  adding build stamp to DESCRIPTION
> >  installing NAMESPACE file and metadata
> >  making DLL ...
> > gcc  -std=gnu99  -Ic:/PROGRA~1/R/R-28~1.1PA/include
> > -I"C:/PROGRA~1/R/site-librar
> > y/deSolve/include"    -O3 -Wall  -c R_init_dma.c -o R_init_dma.o
> > R_init_dma.c:1:27: error: deSolve_stubs.c: No such file or directory
> > R_init_dma.c:3: error: expected ')' before '*' token
> > make[3]: *** [R_init_dma.o] Error 1
> > make[2]: *** [srcDynlib] Error 2
> > make[1]: *** [all] Error 2
> > make: *** [pkg-dma] Error 2
> > *** Installation of dma failed ***
> >
> > Removing 'C:/home/Rlib-test/dma'
> >
> > It seems that although the 'site-library/deSolve/include' folder is
> > included in the search list for included files, the
> > 'Rlib-test/deSolve/include' folder is not.  The folder that includes
> > both the experimental version of deSolve and the test package dma
also
> > contains a .Rprofile file which places 'C:/home/Rlib-test' at the
front
> > of the library search path, and I have confirmed that this is so (in
> > fact, the above INSTALL command does not need the '-l ' argument;
the
> > default install location is Rlib-test for installs from this
folder).
> > It looks as if the code in INSTALL that sets up the -I arguments to
gcc
> > does not find the library path defined for this folder.  Can someone
> > point me to the right way to do this?
> >
> > System information:
> > Version:
> > platform = i386-pc-mingw32
> > arch = i386
> > os = mingw32
> > system = i386, mingw32
> > status = Patched
> > major = 2
> > minor = 8.1
> > year = 2009
> > month = 01
> > day = 04
> > svn rev = 47474
> > language = R
> > version.string = R version 2.8.1 Patched (2009-01-04 r47474)
> >
> > Windows XP (build 2600) Service Pack 2
> >
> > Locale:
> > LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
> > States.1252;LC_MONETARY=English_United
> > States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
> >
> > Search Path:
> > .GlobalEnv, package:stats, package:graphics, package:grDevices,
> > package:utils, package:datasets, package:methods, Autoloads,
> > package:base
> > R. Woodrow Setzer, Ph. D.
> > National Center for Computational Toxicology
> > http://www.epa.gov/comptox
> > US Environmental Protection Agency
> > Mail Drop B205-01/US EPA/RTP, NC 27711
> > Ph: (919) 541-0128    Fax: (919) 541-1194
> >
> > ______________________________________________
> > R-devel at r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-devel
> >
>
> --
> Brian D. Ripley,                  ripley at stats.ox.ac.uk
> Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
> University of Oxford,             Tel:  +44 1865 272861 (self)
> 1 South Parks Road,                     +44 1865 272866 (PA)
> Oxford OX1 3TG, UK                Fax:  +44 1865 272595


[Rd] Getting 'LinkingTo' to find the right library
Setzer.Woodrow at epamail.epa.gov