Leonor, I have found the repository locations for BioC 1.5 on bioconductor.org. The main location you can use in the R install.packages function is http://www.bioconductor.org/packages/bioc/1.5 and the underlying locations for the source, Mac OS X binary, and Windows binary packages are respectively http://www.bioconductor.org/packages/bioc/1.5/src/contrib/PACKAGES http://www.bioconductor.org/packages/bioc/1.5/bin/macosx/2.0/PACKAGES http://www.bioconductor.org/packages/bioc/1.5/bin/windows/contrib/2.0/ PACKAGES http://www.bioconductor.org/packages/bioc/1.5/bin/windows/contrib/2.1/ PACKAGES It might be easier to grab the packages the directly rather than modifying the older getBioC.R script that Jim sent you. Patrick Leonor Palmeira wrote: > James W. MacDonald a ?crit : >> Hi Leonor, >> >> I just checked, and you get getBioC.R the same way you get biocLite.R >> >> source("http://www.bioconductor.org/getBioC.R") >> >> So getting previous versions is easier than I thought... >> >> Best, >> >> Jim > > Sorry, there was an error in what I wrote. I wanted to say that > source("http://bioconductor.org/biocLite.R") makes an explicit call to > source("http://www.bioconductor.org/getBioC.R") [and not to itself...] > and that the current getBioC.R script checks for the R version. This > makes it impossible to download BioC packages with R version less than > 2.1.0 using this method. > > Getting an old getBioC.R could help, but the one available at > http://www.bioconductor.org/getBioC.R is the current one. > > [Just for archiving purposes, the old "getBioC.R" script that Jim > provided me in private (along with other old scripts) makes an > explicit call for > http://www.bioconductor.org/repository/release1.3//package//PACKAGES > which is no longer available] > > I am now trying Wolfgang's solution and will let you know. > > Thank you very much everybody, > Best, > Leonor. > >> >> >> >> Leonor Palmeira wrote: >>> [back in thread] >>> >>> Leonor Palmeira a ?crit : >>> > Hi Leonor, >>> >>> [...] >>> >>> > Actually yes. Nothing ever goes away. >>> >>> I was crossing fingers for that! However, the 'readonly' user and >>> 'readonly' password don't seem to work (403 forbidden access) to >>> access the svn depository. So, I couldn't explore this possibility. >>> >>> I also tried installing R.2.0.0 and running biocLite() from within >>> this old R. But, when calling "http://bioconductor.org/biocLite.R", >>> R calls for "http://bioconductor.org/biocLite.R" which explicitely >>> checks for the R version and returns an error (R version should be >>> above R.2.1.0). >>> >>> When taking a look at the biocLite.R script, this line caught my eye: >>> >>> ## R versions less than 2.1.0 need to use the old (BioC 1.5) version >>> of getBioC.R >>> >>> but I have no idea where to get the old version of getBioC.R. >>> Does someone know how I could get help on this? >>> >>> Thank you very much, >>> Leonor. >>> >>> > And if I am not mistaken, you can >>> > get this for yourself. All you need is a subversion client, which >>> you >>> > can get here if you aren't on Linux (if you are on Linux it is >>> easier to >>> > install using whatever package manager your distro uses): >>> > >>> > http://subversion.tigris.org/ >>> > >>> > Then you can get any of the packages from release 1.5 here: >>> > >>> > >>> https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_1_5/madma n/Rpacks >>> >>> > >>> > e.g., >>> > >>> > svn co >>> > >>> https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_1_5/madma n/Rpacks/affy >>> >>> > >>> > will get you the affy sources. You want to use the username >>> readonly and >>> > password readonly, which I think should work. >>> > >>> > You will probably need to get other packages as well, depending >>> on what >>> > the dependencies were for affy at that time. In addition, you >>> will need >>> > to get R-2.0.0, as there is no guarantee that an old affy will >>> run on >>> > current R. >>> > >>> > You might also just try installing R-2.0.0 and running >>> biocLite(). It >>> > might actually work. >>> > >>> > Best, >>> > >>> > Jim >>> >> > > >