Hi, I've been trying to install a number of Bioconductor packages and keep getting error messages. Can someone tell me a)what I'm doing wrong, b)How to fix it. I'm using a Mac G4 and OS X 10.3, on which I have installed RAqua. As I only installed it and the base Bioconductor package yesterday I am assuming I have the latest Bioc.R thing - can't figure out how to get it if not. On base install, XML and MAGEML did not install properly. Example of me trying to install the database package : > getBioC(libName="database", relLevel="release", getAllDeps=TRUE) Running getBioC version 1.2.46.... If you encounter problems, first make sure that you are running the latest version of getBioC() which can be found at: www.bioconductor.org/getBioC.R Please direct any concerns or questions to bioconductor@stat.math.ethz.ch. Please select an installation directory: 1:~/Library/RAqua/library 2:/Applications/StartR.app/RAqua.app/Contents/library Selection: 2 Synching your local package management information ... Packages which have been removed: XML MAGEML 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 XML from http://www.bioconductor.org//CRANrepository" [1] "Download complete." [1] "Installing XML" Warning message: Installation of package XML had non-zero exit status in: installPkg(fileName, pkg, pkgVer, type, lib, repEntry, versForce) [1] "Attempting to download AnnBuilder from http://www.bioconductor.org/repository/release1.3/package/Source" [1] "Download complete." [1] "Installing AnnBuilder" Warning message: Installation of package AnnBuilder had non-zero exit status in: installPkg(fileName, pkg, pkgVer, type, lib, repEntry, versForce) [1] "Attempting to download SAGElyzer from http://www.bioconductor.org/repository/release1.3/package/Source" [1] "Download complete." [1] "Installing SAGElyzer" [1] "Installation complete" [1] "Attempting to download Rdbi from http://www.bioconductor.org//CRANrepository" [1] "Download complete." [1] "Installing Rdbi" [1] "Installation complete" [1] "Attempting to download RdbiPgSQL from http://www.bioconductor.org/repository/release1.3/package/Source" [1] "Download complete." [1] "Installing RdbiPgSQL" Warning message: Installation of package RdbiPgSQL had non-zero exit status in: installPkg(fileName, pkg, pkgVer, type, lib, repEntry, versForce) From URL: http://www.bioconductor.org//CRANrepository XML version 0.95-4 Rdbi version 0.1-2 From URL: http://www.bioconductor.org/repository/release1.3/package/Source AnnBuilder version 1.3.3 SAGElyzer version 1.3.0 RdbiPgSQL version 1.0.2 Bronwyn Carlisle Biochemistry Department University of Otago Dunedin New Zealand Tel 64 3 479 7704 -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: text/enriched Size: 2938 bytes Desc: not available Url : https://www.stat.math.ethz.ch/pipermail/bioconductor/attachments /20031210/718ef49a/attachment.bin

Thoughts: XML installation is tough. Try manually downloading the package source .gz for as many versions as you can find, then install that. Try installing the R XML package (not just the Bioconductor XML package). Only the "devel" version of AnnBuilder, I think 1.3.5, installed for me. Good luck, Michael Benjamin, MD Emory University -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces@stat.math.ethz.ch] On Behalf Of Bronwyn Carlisle Sent: Tuesday, December 09, 2003 9:54 PM To: bioconductor@stat.math.ethz.ch Subject: [BioC] (no subject) Hi, I've been trying to install a number of Bioconductor packages and keep getting error messages. Can someone tell me a)what I'm doing wrong, b)How to fix it. I'm using a Mac G4 and OS X 10.3, on which I have installed RAqua. As I only installed it and the base Bioconductor package yesterday I am assuming I have the latest Bioc.R thing - can't figure out how to get it if not. On base install, XML and MAGEML did not install properly. Example of me trying to install the database package : > getBioC(libName="database", relLevel="release", getAllDeps=TRUE) Running getBioC version 1.2.46.... If you encounter problems, first make sure that you are running the latest version of getBioC() which can be found at: www.bioconductor.org/getBioC.R Please direct any concerns or questions to bioconductor@stat.math.ethz.ch. Please select an installation directory: 1:~/Library/RAqua/library 2:/Applications/StartR.app/RAqua.app/Contents/library Selection: 2 Synching your local package management information ... Packages which have been removed: XML MAGEML 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 XML from http://www.bioconductor.org//CRANrepository" [1] "Download complete." [1] "Installing XML" Warning message: Installation of package XML had non-zero exit status in: installPkg(fileName, pkg, pkgVer, type, lib, repEntry, versForce) [1] "Attempting to download AnnBuilder from http://www.bioconductor.org/repository/release1.3/package/Source" [1] "Download complete." [1] "Installing AnnBuilder" Warning message: Installation of package AnnBuilder had non-zero exit status in: installPkg(fileName, pkg, pkgVer, type, lib, repEntry, versForce) [1] "Attempting to download SAGElyzer from http://www.bioconductor.org/repository/release1.3/package/Source" [1] "Download complete." [1] "Installing SAGElyzer" [1] "Installation complete" [1] "Attempting to download Rdbi from http://www.bioconductor.org//CRANrepository" [1] "Download complete." [1] "Installing Rdbi" [1] "Installation complete" [1] "Attempting to download RdbiPgSQL from http://www.bioconductor.org/repository/release1.3/package/Source" [1] "Download complete." [1] "Installing RdbiPgSQL" Warning message: Installation of package RdbiPgSQL had non-zero exit status in: installPkg(fileName, pkg, pkgVer, type, lib, repEntry, versForce) >From URL: http://www.bioconductor.org//CRANrepository XML version 0.95-4 Rdbi version 0.1-2 >From URL: http://www.bioconductor.org/repository/release1.3/package/Source AnnBuilder version 1.3.3 SAGElyzer version 1.3.0 RdbiPgSQL version 1.0.2 Bronwyn Carlisle Biochemistry Department University of Otago Dunedin New Zealand Tel 64 3 479 7704 [[alternative HTML version deleted]]

Dear Sir/Madam: I got the following error message when I tried to load Bioconductor into my computer. I don't know what could be the reason. Loading required package: reposTools Synching your local package management information ... Error: restore file may be empty -- no data loaded Error in getBioC(libName = "default") : Needs reposTools to continue Thank you so much, Sincerely, Joshua Joshua Yuan Microarray Core Manager Ernest Gallo Research and Clinic Center at UCSF 5858 Horton Street, Suite 200 Emeryville, CA 94608 Email: yuans@egcrc.net Phone: 510-985-3826 FAX: 510-985-3101

Hi, you need to give a complete description of what you did, (what operating system sometimes helps as well) what commands etc and what version of R you are using, thanks, Robert On Fri, Dec 19, 2003 at 03:16:36PM -0800, Joshua (Shuhua) Yuan wrote: > Dear Sir/Madam: > > I got the following error message when I tried to load Bioconductor into my > computer. I don't know what could be the reason. > > Loading required package: reposTools > > Synching your local package management information ... > Error: restore file may be empty -- no data loaded > Error in getBioC(libName = "default") : Needs reposTools to continue > > > Thank you so much, > > Sincerely, > > Joshua > > > > > Joshua Yuan > Microarray Core Manager > Ernest Gallo Research and Clinic Center at UCSF > 5858 Horton Street, Suite 200 > Emeryville, CA 94608 > > Email: yuans@egcrc.net > Phone: 510-985-3826 > FAX: 510-985-3101 > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor -- +--------------------------------------------------------------------- ------+ | Robert Gentleman phone : (617) 632-5250 | | Associate Professor fax: (617) 632-2444 | | Department of Biostatistics office: M1B20 | | Harvard School of Public Health email: rgentlem@jimmy.harvard.edu | +--------------------------------------------------------------------- ------+