Getting 'LinkingTo' to find the right library
(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
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-- 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