[BioC] Installing genefilter

[Kasper Daniel Hansen]

Well, there are a few different issues here.

First of, the first messages indicates that you do not have genefilter 
installed. This might be because the download failed (you downloaded an 
incomplete file) or because of issues explained below.

The 404 error you get is because right now there the repository is being 
moved from Boston to Seattle and everything is not working perfctly yet. 
It does not matter because it is the bioconductor mirror of CRAN it 
cannot find , and you need access to bioconductor itself.

Ok, so that was the two first issues.

When you install an R package you can either install it as a source 
package or as a binary. For most R packages there is not much 
difference, because the package itself on contains help files and R 
code. limma is on of those packages.

Some packages contain C code, and this code either has to be compiled 
(if you do a source installation) or it comes precompiled (you get a 
binary). You are doing a source installation of genefilter and it fails 
in the C compilation step. You cannot compare with limma because limma 
does not contain C code.

In order to fix this problems you have to do one of two things
1) setup your MacOS X so that it can compile C, this entails installing 
tools from the developer CD, and you may read something about it in the 
R/MacOS X FAQ in the section "Compiling R from sources".
2) download a binary version of the package (easiest).

Now, I am not a Mac user (unfortunately) and I have no idea on hów to 
get a binary version using the command line (I would love to get a hint 
though). But I know that if you use the Aqua interface, and use the 
package manager from the toolbar, you can choose where you get the 
packages from. One of the choices is called something like "Mac OSX 
binaries".

Kasper


On Thu, Feb 10, 2005 at 02:07:30PM -0600, Monnie McGee wrote:
> Dear Bioc help,
> 
> I would like to use the package genefilter  in order to do some 
> nonspecific filtering of a microarray expression set (eset).  When I 
> typed "library(genefilter)" into R, I received the following error 
> message:
> 
> Error in library.dynam(lib, package, package.lib) :
>         shared library 'genefilter' not found
> In addition: Warning message:
> Package  'genefilter' contains no R code in: loadNamespace(package, 
> c(which.lib.loc, lib.loc))
> Error in library(genefilter) : package/namespace load failed for 
> 'genefilter'
> 
> I thought that genefilter should have been downloaded by default when I 
> downloaded bioconductor with "getBioC()".  But, I tried to download it 
> using "install.packages2".  Here's what I did:
> 
> if (interactive()){
> z <- repositories
> install.packages2("genefilter",repEntry=
> z)}
> 
> I then received the message:
> 
> Warning message:
> cannot open: HTTP status was `404 Not Found'
> Note: http://www.bioconductor.org/CRANrepository does not seem to have 
> a valid repository, skipping
> Warning message:
> Failed to read replisting at http://www.bioconductor.org/CRANrepository 
> in: getReplisting(repURL, repFile, method = method)
> 
> But, a few seconds later, the list of repositories appeared.  When it 
> did, I typed 1 for "Release 1.5 source repository" and hit return.
> 
> Then, I received the following message:
> 
> [1] "Attempting to download genefilter from 
> http://www.bioconductor.org/repository/release1.5/package/Source"
> [1] "Download complete."
> [1] "Installing genefilter"
> * Installing *source* package 'genefilter' ...
> ** libs
> gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include 
>  -I/usr/local/include   -fno-common  -g -O2 -c genedist.c -o genedist.o
> gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include 
>  -I/usr/local/include   -fno-common  -g -O2 -c init.c -o init.o
> g77   -fno-common  -g -O2 -c ttest.f -o ttest.o
> gcc -bundle -flat_namespace -undefined suppress -L/usr/local/lib -o 
> genefilter.so genedist.o init.o ttest.o  -L/usr/local/lib 
> -L/usr/local/lib/gcc/powerpc-apple-darwin6.8/3.4.2 
> -L/usr/local/lib/gcc/powerpc-apple-darwin6.8/3.4.2/../../.. -lfrtbegin 
> -lg2c -lSystem -lcc_dynamic -framework R
> ld: warning -L: directory name (/usr/local/lib) does not exist
> ld: warning -L: directory name (/usr/local/lib) does not exist
> ld: warning -L: directory name 
> (/usr/local/lib/gcc/powerpc-apple-darwin6.8/3.4.2) does not exist
> ld: warning -L: directory name 
> (/usr/local/lib/gcc/powerpc-apple-darwin6.8/3.4.2/../../..) does not 
> exist
> ld: can't locate file for: -lfrtbegin
> make: *** [genefilter.so] Error 1
> ERROR: compilation failed for package 'genefilter'
> ** Removing '/private/tmp/RtmppOfGwL/file615be850/genefilter'
> ** Restoring previous '/private/tmp/RtmppOfGwL/file615be850/genefilter'
> From URL:  
> http://www.bioconductor.org/repository/release1.5/package/Source
>         genefilter version 1.5.0
> 
> Warning message:
> Installation of package genefilter had non-zero exit status in: 
> installPkg(fileName, pkg, pkgVer, type, lib, repEntry, versForce)
> >
> 
> The upshot of all of this is that I do not have genefilter installed on 
> my machine (a powerbook G4, by the way).
> 
> I tried the exact same procedure with the package "limma" and was 
> successful.  Genefilter is the only package that gives me this problem 
> - and "multtest", but that is because multtest needs genefilter to run.
> 
> Please help!
> Thank You,
> Monnie McGee
> 
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-- 
Kasper Daniel Hansen, Research Assistant
Department of Biostatistics, University of Copenhagen