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

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 h?w 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 > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor -- Kasper Daniel Hansen, Research Assistant Department of Biostatistics, University of Copenhagen

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@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > > +--------------------------------------------------------------------- -- ----------------+ | Robert Gentleman phone: (206) 667-7700 | | Head, Program in Computational Biology fax: (206) 667-1319 | | Division of Public Health Sciences office: M2-B865 | | Fred Hutchinson Cancer Research Center | | email: rgentlem@fhcrc.org | +--------------------------------------------------------------------- -- ----------------+

Thank you very much. I used the package manager in R-Aqua to install the binaries on my Mac and everything seems to be working now. Monnie McGee, Ph.D. Assistant Professor Department of Statistical Science Southern Methodist University Ph: 214-768-2462 Fax: 214-768-4035 -----Original Message----- From: Kasper Daniel Hansen [mailto:k.hansen@biostat.ku.dk] Sent: Fri 2/11/2005 10:35 AM To: McGee, Monnie Cc: bioconductor@stat.math.ethz.ch Subject: Re: [BioC] Installing genefilter 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 h?w 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 > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor -- Kasper Daniel Hansen, Research Assistant Department of Biostatistics, University of Copenhagen