Hi all! I am a new user of bioconductor and I already have some questions and problems. I was told that the new version of R 1.8 was to be released soon. I want to install Bioconductor but on the homepage it says it requires R 1.7.1 (patched) or later and can?t find either of them. I have version 1.7.0 and have tried to install packages from bioconductor such as biobase going to "Packages - install packages from Bioconductor". I get an error that says: ------- trying URL `http://www.bioconductor.org/bin/windows/contrib/1.7/Biobase_1.3.22.zi p ' Content type `application/zip' length 444064 bytes opened URL downloaded 433Kb Error in int.unzip(zipname, NULL, dest) : destination does not exist -------- What am I doing wrong? Thanks for your help, David

I suppose you make use of a MS Win OS. For patch set look at the CRAN closer to you (I think was http://cran.at.r-project.org/). You have to download the script getBioC.R from Biocunductor site, load it with 'source r code' (for UNIX-like user type source("getBioC.R") at the R-prompt) command from File menu of R-Gui at the end type getBioC() to start script. This script should be able to download and install biocunductor packages. Good job! A.S. ---------------------------- Alessandro Semeria Models and Simulations Laboratory The Environment Research Center - Montecatini (Edison Group), Via Ciro Menotti 48, 48023 Marina di Ravenna (RA), Italy Tel. +39 544 536811 Fax. +39 544 538663 E-mail: asemeria@cramont.it

I know about some bugs on the R-1.7.0 version for Win (for the moment I use R-1.6.2 on XP and 1.7.0 on Linux RH8 without problem), then you can try with devel version http://www.stats.uwo.ca/faculty/murdoch/software/r-devel/! PS: However for me is better first to download a script getBioC.R and then source("local/getBioC.R"), to avoid connections problems. For mail-list: next time put BioC address on 'cc' field of yours e-mails... may be that wath we are talking about is suitable to someone!Thanks Good luck A.S. ---------------------------- Alessandro Semeria Models and Simulations Laboratory The Environment Research Center - Montecatini (Edison Group), Via Ciro Menotti 48, 48023 Marina di Ravenna (RA), Italy Tel. +39 544 536811 Fax. +39 544 538663 E-mail: asemeria@cramont.it

Dear Jeff, I have tried again installing BioC and now there is a new error message. This is what it says: > source("http://www.bioconductor.org/getBioC.R") > getBioC() Running getBioC version 1.2.34.... 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. [1] "Installing reposTools ..." Error in download.file(sourceUrl, fileName, mode = getMode (platform), : cannot open destfile `C:/ARCHIV~1/R/RW1071~1/library/reposTools_1.1.43.zip' Is it something that I haven?t downloaded to my R folder? Regards, David > > > [1] "Installing reposTools ..." > > > Error in getPkgDisc(relLevel) : The url: > > > http://www.bioconductor.org/repository/release1.2/package/PACKAGES > > > does not seem to have a valid PACKAGES file. > > This is the same thing from a few minutes ago on the list. I had been > trying to fix something in the web generation and it managed to break > another thing and it took a bit to regenerate all the pages. This should > be fixed fory ou now. > > -J > >

Dear Jeff, yes, using the option "Install packages from CRAN", and trying to install geneSOM it doesn?t work either. This is the error I get trying URL `http://cran.r- project.org/bin/windows/contrib/1.7/GeneSOM_0.2-5.zip' Content type `application/zip' length 373697 bytes opened URL downloaded 364Kb Error in int.unzip(zipname, NULL, dest) : destination does not exist Any ideas? David > > > On Wed, 4 Jun 2003 kfbargad@lg.ehu.es wrote: > > [1] "Installing reposTools ..." > > Error in download.file(sourceUrl, fileName, mode = getMode > > (platform), : > > cannot open destfile > > `C:/ARCHIV~1/R/RW1071~1/library/reposTools_1.1.43.zip' > > Judging from this and the earlier error you reported by attempting to use > the pulldown Packages->Install Packages from Bioconductor, I suspect that > you have some sort of permission problem with the way your R is > configured. > > Have you tried what I requested you to try earlier, IE use the pulldown > Packages->Install Packages from CRAN and try to install a package from > there? Does that work? > > -J > >

Are you able to look/write inside windows/temp of your C:\? May be a permission problem ! A.S. ---------------------------- Alessandro Semeria Models and Simulations Laboratory The Environment Research Center - Montecatini (Edison Group), Via Ciro Menotti 48, 48023 Marina di Ravenna (RA), Italy Tel. +39 544 536811 Fax. +39 544 538663 E-mail: asemeria@cramont.it