Aldi Kraja
2004-Oct-10 03:07 UTC
[R] How to install a package that needs to see oher pkg dependencies:
Hi, I am trying to install the genetics package on a server with Linux, Fedora. I installed it in a PC and worked fine. In a server since I am not used with R, I am not sure what do I need to change so genetics pkg can see some package dependencies: Any suggestion is appreciated, Aldi Note: genetics expects gregmisc and mvtnorm to be installed already. gregmisc creates gdata etc dependencies. So here is what I have done: Retrieved the base R and installed and compiled it with make under : /users/genetics/aldi/r/R/R-2.0.0 Under it directories: /mvtnorm /gregmisc /genetics are created. Installed mvtnorm and gregmisc with no problem, but genetics is not recognizing the location of /gregmisc/gdata The command I am using to install genetics package is the following: ../bin/R CMD ../bin/INSTALL genetics_1.1.0.tar.gz Here is the problem: genetics at genxeon1:/users/genetics/aldi/r/R-2.0.0/genetics% ../bin/R CMD ../bin/INSTALL -l . genetics_1.1.0.tar.gz * Installing *source* package 'genetics' ... ** R ** data ** inst ** preparing package for lazy loading Error in loadNamespace(i[[1]], c(lib.loc, .libPaths()), keep.source) : There is no package called 'gdata' Execution halted ERROR: lazy loading failed for package 'genetics' genetics at genxeon1:/users/genetics/aldi/r/R-2.0.0/genetics%
Prof Brian Ripley
2004-Oct-10 06:35 UTC
[R] How to install a package that needs to see oher pkg dependencies:
On Sat, 9 Oct 2004, Aldi Kraja wrote:> Hi, > I am trying to install the genetics package on a server with Linux, > Fedora. I installed it in a PC and worked fine. > > In a server since I am not used with R, I am not sure what do I need to > change so genetics pkg can see some package dependencies: > Any suggestion is appreciated, Aldi > > Note: > genetics expects gregmisc and mvtnorm to be installed already. gregmisc > creates gdata etc dependencies. > So here is what I have done: > Retrieved the base R and installed and compiled it with make under : > /users/genetics/aldi/r/R/R-2.0.0 > > Under it directories: > /mvtnorm > /gregmisc > /genetics > are created. > Installed mvtnorm and gregmisc with no problem, but genetics is not > recognizing the location of /gregmisc/gdata > > The command I am using to install genetics package is the following: > ../bin/R CMD ../bin/INSTALL genetics_1.1.0.tar.gz > > Here is the problem: > > genetics at genxeon1:/users/genetics/aldi/r/R-2.0.0/genetics% ../bin/R CMD > ../bin/INSTALL -l . genetics_1.1.0.tar.gzThe correct commands are R CMD INSTALL gregmisc_2.0.0.tar.gz R CMD INSTALL genetics_1.1.0.tar.gz Wherever did you get `../bin/INSTALL -l .' from? You need to install into a library that is in the library path for the package to be usable, and the system library (the default) is the best choice. (This is no different from S-PLUS, on which you have been asking questions on s-news for many years.) -- 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