Hello, I'm running BioC 1.3 and R 1.8.1. I've tried to install the EBarrays pacckage from the devel branch, but get the following error: > install.packages2('EBarrays', force=T) Note: You did not specify a download type. Using a default value of: Source This will be fine for almost all users [1] "Attempting to download EBarrays from http://www.bioconductor.org/repository/devel/package/Source" [1] "Download complete." [1] "Installing EBarrays" * Installing *source* package 'EBarrays' ... ** libs gcc -I/tgx/soft/lib/R/include -I/usr/local/include -D__NO_MATH_INLINES -mieee-fp -fPIC -g -O2 -c ebarrays.c -o ebarrays.o gcc -shared -L/usr/local/lib -o EBarrays.so ebarrays.o -L/tgx/soft/lib/R/bin -lR ** R ** data ** demo ** inst ** save image Error: Requires utils to run properly In addition: Warning message: There is no package called 'utils' in: library(package, character.only = TRUE, logical = TRUE, warn.conflicts = warn.conflicts, Execution halted /tgx/soft/lib/R/bin/INSTALL: line -116: 2881 Broken pipe cat "/tgx/soft/lib/R/library/EBarrays/R/EBarrays" ERROR: execution of package source for 'EBarrays' failed ** Removing '/tgx/soft/lib/R/library/EBarrays' Warning message: Installation of package EBarrays had non-zero exit status in: installPkg(fileName, pkg, pkgVer, type, lib, repEntry, versForce) >From URL: http://www.bioconductor.org/repository/devel/package/Source EBarrays version 1.0-17 I cannot find the utils package, where is it locatd in the BioC repositories? Can I install EBarrays without installing the complete develompent branch? kind regards + thank for your help, Arne -- Arne Muller, Ph.D. Toxicogenomics, Aventis Pharma arne dot muller domain=aventis com

you must use R 1.9.0 to work with the devel branch. > Hello, > > I'm running BioC 1.3 and R 1.8.1. I've tried to install the EBarrays > pacckage from the devel branch, but get the following error: > > > install.packages2('EBarrays', force=T) > Note: You did not specify a download type. Using a default value of: Source > This will be fine for almost all users > > [1] "Attempting to download EBarrays from > http://www.bioconductor.org/repository/devel/package/Source" > [1] "Download complete." > [1] "Installing EBarrays" > * Installing *source* package 'EBarrays' ... > ** libs > gcc -I/tgx/soft/lib/R/include -I/usr/local/include -D__NO_MATH_INLINES > -mieee-fp -fPIC -g -O2 -c ebarrays.c -o ebarrays.o > gcc -shared -L/usr/local/lib -o EBarrays.so ebarrays.o > -L/tgx/soft/lib/R/bin -lR > ** R > ** data > ** demo > ** inst > ** save image > Error: Requires utils to run properly > In addition: Warning message: > There is no package called 'utils' in: library(package, character.only = > TRUE, logical = TRUE, warn.conflicts = warn.conflicts, > Execution halted > /tgx/soft/lib/R/bin/INSTALL: line -116: 2881 Broken pipe cat > "/tgx/soft/lib/R/library/EBarrays/R/EBarrays" > ERROR: execution of package source for 'EBarrays' failed > ** Removing '/tgx/soft/lib/R/library/EBarrays' > Warning message: > Installation of package EBarrays had non-zero exit status in: > installPkg(fileName, pkg, pkgVer, type, lib, repEntry, versForce) > >From URL: http://www.bioconductor.org/repository/devel/package/Source > EBarrays version 1.0-17 > > I cannot find the utils package, where is it locatd in the BioC repositories? > Can I install EBarrays without installing the complete develompent branch? > > kind regards + thank for your help, > > Arne > > -- > Arne Muller, Ph.D. > Toxicogenomics, Aventis Pharma > arne dot muller domain=aventis com > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor >

As I tried to write clearly in my last email about the upcoming release, you MUST use the Devel branch of R with packages in the devel branch of Bioconductor. best, -tony <arne.muller@aventis.com> writes: > Hello, > > I'm running BioC 1.3 and R 1.8.1. I've tried to install the EBarrays > pacckage from the devel branch, but get the following error: > >> install.packages2('EBarrays', force=T) > Note: You did not specify a download type. Using a default value of: Source > This will be fine for almost all users > > [1] "Attempting to download EBarrays from > http://www.bioconductor.org/repository/devel/package/Source" > [1] "Download complete." > [1] "Installing EBarrays" > * Installing *source* package 'EBarrays' ... > ** libs > gcc -I/tgx/soft/lib/R/include -I/usr/local/include -D__NO_MATH_INLINES > -mieee-fp -fPIC -g -O2 -c ebarrays.c -o ebarrays.o > gcc -shared -L/usr/local/lib -o EBarrays.so ebarrays.o > -L/tgx/soft/lib/R/bin -lR > ** R > ** data > ** demo > ** inst > ** save image > Error: Requires utils to run properly > In addition: Warning message: > There is no package called 'utils' in: library(package, character.only = > TRUE, logical = TRUE, warn.conflicts = warn.conflicts, > Execution halted > /tgx/soft/lib/R/bin/INSTALL: line -116: 2881 Broken pipe cat > "/tgx/soft/lib/R/library/EBarrays/R/EBarrays" > ERROR: execution of package source for 'EBarrays' failed > ** Removing '/tgx/soft/lib/R/library/EBarrays' > Warning message: > Installation of package EBarrays had non-zero exit status in: > installPkg(fileName, pkg, pkgVer, type, lib, repEntry, versForce) >>From URL: http://www.bioconductor.org/repository/devel/package/Source > EBarrays version 1.0-17 > > I cannot find the utils package, where is it locatd in the BioC repositories? > Can I install EBarrays without installing the complete develompent branch? > > kind regards + thank for your help, > > Arne > > -- > Arne Muller, Ph.D. > Toxicogenomics, Aventis Pharma > arne dot muller domain=aventis com > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > -- rossini@u.washington.edu http://www.analytics.washington.edu/ Biomedical and Health Informatics University of Washington Biostatistics, SCHARP/HVTN Fred Hutchinson Cancer Research Center UW (Tu/Th/F): 206-616-7630 FAX=206-543-3461 | Voicemail is unreliable FHCRC (M/W): 206-667-7025 FAX=206-667-4812 | use Email CONFIDENTIALITY NOTICE: This e-mail message and any attachme...{{dropped}}

Hi, You can also try installing EBarrays version 1.0-16 which does not require the complete development branch available at Christina Kendziorski's ftp site ftp://ftp.biostat.wisc.edu/pub/kendzior/EBARRAYS/ . I have it (installed from the command line) on redhat linux, > package.description("EBarrays", fields="Version") [1] "1.0-16" > package.description("base", fields="Version") [1] "1.8.1" > no guarantees of success though, marcus >>> <arne.muller@aventis.com> 16/03/2004 12:48:53 AM >>> Hello, I'm running BioC 1.3 and R 1.8.1. I've tried to install the EBarrays pacckage from the devel branch, but get the following error: > install.packages2('EBarrays', force=T) Note: You did not specify a download type. Using a default value of: Source This will be fine for almost all users [1] "Attempting to download EBarrays from http://www.bioconductor.org/repository/devel/package/Source" [1] "Download complete." [1] "Installing EBarrays" * Installing *source* package 'EBarrays' ... ** libs gcc -I/tgx/soft/lib/R/include -I/usr/local/include -D__NO_MATH_INLINES -mieee-fp -fPIC -g -O2 -c ebarrays.c -o ebarrays.o gcc -shared -L/usr/local/lib -o EBarrays.so ebarrays.o -L/tgx/soft/lib/R/bin -lR ** R ** data ** demo ** inst ** save image Error: Requires utils to run properly In addition: Warning message: There is no package called 'utils' in: library(package, character.only = TRUE, logical = TRUE, warn.conflicts = warn.conflicts, Execution halted /tgx/soft/lib/R/bin/INSTALL: line -116: 2881 Broken pipe cat "/tgx/soft/lib/R/library/EBarrays/R/EBarrays" ERROR: execution of package source for 'EBarrays' failed ** Removing '/tgx/soft/lib/R/library/EBarrays' Warning message: Installation of package EBarrays had non-zero exit status in: installPkg(fileName, pkg, pkgVer, type, lib, repEntry, versForce) >From URL: http://www.bioconductor.org/repository/devel/package/Source EBarrays version 1.0-17 I cannot find the utils package, where is it locatd in the BioC repositories? Can I install EBarrays without installing the complete develompent branch? kind regards + thank for your help, Arne -- Arne Muller, Ph.D. Toxicogenomics, Aventis Pharma arne dot muller domain=aventis com _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor ______________________________________________________ The contents of this e-mail are privileged and/or confidenti...{{dropped}}