[BioC] Installing genefilter

[Robert Gentleman]

On Feb 10, 2005, at 12:07 PM, 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)}
>

Why do you want to do this?
Why not simply

  library(reposTools)
install.packages2("genefilter")



> 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)
>

So, this looks like it was a few days ago, as the bug in the  
CRANrepository was fixed
a few days ago. Is this still happening for you?

> 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
>

  So it looks like you are using a binary installation of R, on OS X and  
you do not have the appropriate tools for building R packages. Here,  
you will need to go to the R FAQ for OS X
and follow the instructions there (exactly - these are very explicit  
and it will work if you do
what you are told to).

> 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.

  No, I think every package that has C code will fail for the same  
reason as genefilter did. You may just not have found it yet.

  Our next goal is to provide binary versions of all packages for OS X,  
but that will take a couple of weeks to get working properly.

  Robert


>
> Please help!
> Thank You,
> Monnie McGee
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
>
>
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| Robert Gentleman              phone: (206) 667-7700                    
          |
| Head, Program in Computational Biology   fax:  (206) 667-1319   |
| Division of Public Health Sciences       office: M2-B865               
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| Fred Hutchinson Cancer Research Center                                 
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| email: rgentlem at fhcrc.org                                              
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