Thanks to all of you (Robert, John, Steve, Bryan, Anna) for your comments ! Best Wishes, Chintanu ________________________________________ From: rgentlem@gmail.com [rgentlem@gmail.com] on behalf of Robert Gentleman [rgentlem@fhcrc.org] Sent: 11 May 2009 17:23 To: Sarmah, Chintanu Kumar Cc: bioconductor at stat.math.ethz.ch Subject: Re: [BioC] Upgrading R Hi Chintanu, Basically no, there is no such path. You should always upgrade R and reinstall all packages. biocLite will help you to do that. best wishes Robert On Sat, May 9, 2009 at 4:33 PM, Sarmah, Chintanu Kumar <chintanu.sarmah2 at="" lincolnuni.ac.nz=""> wrote: > Hi, > Wonder if there is a way to upgrade R. > I?m currently using R 2.7.2, and wish to ?upgrade? to the latest one via some process that doesn?t make me reinstall all the packages again !! Please let me know. > Thank you ! > Chintanu > > [[alternative HTML version deleted]] > > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Robert Gentleman, PhD Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 PO Box 19024 Seattle, Washington 98109-1024 206-667-7700 rgentlem at fhcrc.org

Hi, On May 11, 2009, at 10:46 AM, Michal Blazejczyk wrote: > Hi everyone, > > I think an interesting feature in R would be "package list dump" > option. > The way I see this working is the following: the user would issue > a command on the source R installation (say, an older version), e.g. > packages.dump("~/R/packages.dump") > Then the user would run the destination installation (say, a new > version) > and recreate the environment by issuing a command like: > packages.load("~/R/packages.dump") > This last command would go and download and install all packages that > were listed in the dump. This is already possible with a little coding on your part, and is all written up in a blog post[1] that I linked to in reply to Kumar's question, which I just noticed I sent directly to Kumar w/o CC-ing the BioC list ... sorry. Anyway, I've extracted the code from the post into some functions using nomenclature similar to what you're asking for: ======================== packages.dump <- function(dump.file) { tmp <- installed.packages() installed.old <- as.vector(tmp[is.na(tmp[,"Priority"]), 1]) save(installed.old, file=dump.file) } packages.load.R <- function(dump.file) { # Attempts to install all packages that were present in old install # into the new install. All non-cran package will return a warning # that they are not available, but will allow for the remainder # of packages to be installed load(dump.file) tmp <- installed.packages() installed.current <- as.vector(tmp[is.na(tmp[,"Priority"]), 1]) missing.packages <- setdiff(installed.old, installed.current) install.packages(missing.packages) } packages.load.bioc <- function(dump.file) { # assumes that whatever packages are missing from old install and # current install are BioC packages load(dump.file) tmp <- installed.packages() installed.current <- as.vector(tmp[is.na(tmp[,"Priority"]), 1]) missing.packages <- setdiff(installed.old, installed.current) source("http://bioconductor.org/biocLite.R") biocLite(missing.packages) } =========================== Now, when upgrading R, all you have to do is: 1. Before upgrading, run `packages.dump('/path/to/dumpfile.rda') 2. Install new R 3. Start new R and run `packages.load.R('/path/to/dumpfile.rda') 4. Run `packages.load.bioc('/path/to/dumpfile.rda')` This assumes that all of the packages in your current installation can be downloaded from CRAN, or are otherwise bioconductor packages. If this isn't true, it's rather simple to add a function to install whatever else you need to (or make one clever `packages.load` function that tries to install packages from several different repos and merge steps 3 and 4 into one func call). Anyway, hope that helps. -steve [1] Original blog post: http://onertipaday.blogspot.com/2008/10/r -upgrade-on-mac-os-x-1055-leopard.html -- Steve Lianoglou Graduate Student: Physiology, Biophysics and Systems Biology Weill Medical College of Cornell University http://cbio.mskcc.org/~lianos

It sure is: writeLines(installed.packages()[,1], con="packages.dump") recompile R packs <- readLines("packages.dump") biocLite(packs) Florian On 11.05.2009, at 07:46, Michal Blazejczyk wrote: > Hi everyone, > > I think an interesting feature in R would be "package list dump" > option. > The way I see this working is the following: the user would issue > a command on the source R installation (say, an older version), e.g. > packages.dump("~/R/packages.dump") > Then the user would run the destination installation (say, a new > version) > and recreate the environment by issuing a command like: > packages.load("~/R/packages.dump") > This last command would go and download and install all packages that > were listed in the dump. > > Or maybe this is already possible? > > Best, > Michal > > >> Hi Chintanu, >> Basically no, there is no such path. You should always upgrade R and >> reinstall all packages. biocLite will help you to do that. >> >> best wishes >> Robert >> >> >> On Sat, May 9, 2009 at 4:33 PM, Sarmah, Chintanu Kumar >> <chintanu.sarmah2 at="" lincolnuni.ac.nz=""> wrote: >>> Hi, >>> Wonder if there is a way to upgrade R. >>> I?m currently using R 2.7.2, and wish to ?upgrade? to the latest >>> one via some process that doesn?t make me reinstall all the >>> packages again !! Please let me know. >>> Thank you ! >>> Chintanu >>> >>> ? ? ? ?[[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

It's very simple to maintain a small .R script file which runs a combination of biocLite and install.packages(). You can have all the new packages installed in about 30-60 mins on a typical connection. I've done this for a number of installs and it is very efficient. Fraser -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of john seers (IFR) Sent: Monday, May 11, 2009 7:39 AM To: Sarmah, Chintanu Kumar; bioconductor at stat.math.ethz.ch Subject: Re: [BioC] Upgrading R Hi Chintanu I have struggled with this problem through several upgrades and I have not found a consensus of the best way to do it. There are quite a lot of suggestions and advice if you search around using RSiteSearch(). I think the most straightforward answer I have found is described here: http://batchfiles.googlecode.com/svn/trunk/README I have not investigated fully - perhaps copydir is the way to go? But my last upgrade I used this: Look for the README and the part that describes the alternative to copydir: "An alternative to copydir is to reinstall all packages # Alternative to copydir.bat #1 # this example is for moving from 2.4.1 to 2.5.0 # run this in R 2.5.0 setwd(R.home()) ip <- installed.packages(lib.loc = "../R-2.4.1/library") ip <- ip[ip[,1]!="base" ,1] install.packages(ip) " I hope this helps. Regards John Seers -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Sarmah, Chintanu Kumar Sent: 10 May 2009 00:33 To: bioconductor at stat.math.ethz.ch Subject: [BioC] Upgrading R Hi, Wonder if there is a way to upgrade R. I'm currently using R 2.7.2, and wish to 'upgrade' to the latest one via some process that doesn't make me reinstall all the packages again !! Please let me know. Thank you ! Chintanu [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

Hi, On Mon, May 11, 2009 at 3:47 AM, arnaud Le Cavorzin <arnaudlc at="" msn.com=""> wrote: > > Hi, > > Yes you can do it, read the R FAQ on the cran website. > > I quote it : > > > "That's a matter of taste. ?For most people the best thing to do is to > uninstall R (see the previous Q), install the new version, copy any > installed packages to the library folder in the new installation, run > update.packages(checkBuilt=TRUE, ask=FALSE) in the new R and then > delete anything left of the old installation. ?Different versions of R > are quite deliberately installed in parallel folders so you can keep old > versions around if you wish. well, for Bioconductor, since we bump all version numbers at each release, the net effect is that all Bioconductor packages will be reinstalled. Users may save a little bit of downloading doing this. Also, for Bioconductor you need to be careful to ensure that your repositories are set correctly so that update.packages finds the Bioconductor one - which is why we prefer that users simply use the directions posted on the Bioconductor site and reinstall at each upgrade of R. best wishes Robert > > > For those with a personal library (folder R\win-library\x.y > of your home directory), you will need to update that too when the minor > version of R changes (e.g. from 2.6.2 to 2.7.0). ?A simple way > to do so is to copy (say) R\win-library\2.6 to > R\win-library\2.7 before running > update.packages(checkBuilt=TRUE, ask=FALSE)." > You can install the new version, copy your package from the old R version library to the new, and after uninstall the old version. > I hope it will help you, > > Best regards > > Arnaud > > > On Sat, May 9, 2009 at 4:33 PM, Sarmah, Chintanu Kumar > <chintanu.sarmah2 at="" lincolnuni.ac.nz=""> wrote: >> Hi, >> Wonder if there is a way to upgrade R. >> I?m currently using R 2.7.2, and wish to ?upgrade? to the latest one via some process that doesn?t make me reinstall all the packages again !! Please let me know. >> Thank you ! >> Chintanu >> >> ? ? ? ?[[alternative HTML version deleted]] >> >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > > > -- > Robert Gentleman, PhD > Program in Computational Biology > Division of Public Health Sciences > Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N, M2-B876 > PO Box 19024 > Seattle, Washington 98109-1024 > 206-667-7700 > rgentlem at fhcrc.org > > > > > > > _________________________________________________________________ > > n ligne... si nouveaux qu'ils ne sont pas encore sortis officiellement sur le march? ! > > ? ? ? ?[[alternative HTML version deleted]] > > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Robert Gentleman, PhD Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 PO Box 19024 Seattle, Washington 98109-1024 206-667-7700 rgentlem at fhcrc.org