Hi all, confirming that this did the trick. Cheers, Firas. On Wed, Nov 30, 2011 at 10:26 AM, Firas Swidan <firas@biomatters.com> wrote: > Thanks. I will give that a try and let you know how it goes. > > On Wed, Nov 30, 2011 at 10:15 AM, Dan Tenenbaum <dtenenba@fhcrc.org>wrote: > >> Hi Firas, >> >> On Tue, Nov 29, 2011 at 1:06 PM, Firas Swidan <firas@biomatters.com> >> wrote: >> > I see there is a misunderstanding regarding the nature of the problem I >> am >> > trying to describe. To try and eliminate any confusing, the problem >> that I >> > am describing happens when running this command: >> > >> > 'source("http://bioconductor.org/biocLite.R")' >> > >> > not when trying later on to use the >> > >> > 'biocLite' >> > >> > command. I have been using the lib.loc argument with the biocLite >> command, >> > and that works great. >> > >> > >> > The problem is that the recent modifications to >> > the "http://bioconductor.org/biocLite.R" script make it install >> packages >> > without the user having the ability to specify the lib.loc location. >> > >> > >> > Does that help clarifying the problem? >> >> >> I understand. >> >> Have a look at the documentation for >> ?install.packages >> >> Notice that lib defaults to the first element of .libPaths(). >> If you look at ?.libPaths, you can see how to change that first >> element, namely something like this: >> >> .libPaths(c("c:/a/writeable/directory", .libPaths())) >> >> Try doing that prior to your source() line. >> >> Thanks >> Dan >> >> >> > >> > >> > On Wed, Nov 30, 2011 at 9:56 AM, Dan Tenenbaum <dtenenba@fhcrc.org> >> wrote: >> >> >> >> Hi Firas, >> >> >> >> On Tue, Nov 29, 2011 at 12:49 PM, Firas Swidan <firas@biomatters.com> >> >> wrote: >> >> > Hi all, >> >> > >> >> > thanks for the suggestions - I just got to read them after recovering >> >> > from a >> >> > bad flu. >> >> > >> >> > I think Dan's experience probably resembles most the one that I had. >> The >> >> > problem though gets more troublesome when one tries to automate the >> >> > process >> >> > through a script installation. More specifically, imagine that a >> script >> >> > needs to install a bioconduct package on different machines (running >> >> > Windows, and maybe also other OSs) on a fresh R install. Then the >> >> > 'source' >> >> > command needs to be run from inside the R script that is executed >> >> > through 'R >> >> > CMD BATCH'. In this case there is no pop-up dialog asking to create >> >> > another >> >> > user-writable directory, and the command >> >> > 'install.packages("BiocInstaller", >> >> > repos=a["BioCsoft", >> >> >> "URL"])' fails. It would be great in case one could pass an argument >> >> >> specifying the lib.loc to the 'install.packages' command above, but >> I >> >> >> understand this is not possible through 'sourcing'. The old way of >> just >> >> >> defining a 'biocLite' function in the biocLite.R script, and then >> being >> >> >> able >> >> >> to pass the lib.loc argument to it seems to fair better in this >> >> >> use-case >> >> >> model. >> >> >> >> Thanks for posting the detailed use case so we can understand the issue >> >> better. >> >> >> >> Please have a look at >> >> ?biocLite >> >> >> >> You'll see that it takes a '...' argument which is passed to >> >> install.packages, so you can pass lib (not lib.loc) to >> >> install.packages and specify where packages are to be installed. Be >> >> sure that any directory you pass here also ends up in .libPaths() so >> >> that R will look in it for packages. >> >> >> >> I don't see a need to use install.packages() directly in the situation >> >> you describe. biocLite() should do it, and you won't need to specify >> >> the repos argument. >> >> >> >> > >> >> > I do not really have access to the machines where the installation is >> >> > going >> >> > to be done, so I cannot change permissions and the like. Also, the >> >> > installed >> >> > bioconduct packages need later on to be loaded and used, so I need to >> >> > specify a specific location for their installation. The saga goes >> on, as >> >> > I >> >> > cannot use the 'R_LIBS_USER' directory because of complications on >> >> > Windows >> >> > that diving in would just clutter this post. >> >> > >> >> > I am still puzzled why the biocLite.R script had to undergo such a >> huge >> >> > change following the new R 2.14 release. Is it safe to fall back to >> the >> >> > old >> >> > behavior under this version, i.e., use the 'else' part in the script: >> >> > >> >> > source("http://bioconductor.org/getBioC.R") >> >> > biocLite <<- >> >> > function(pkgs, groupName="lite", ...) >> >> > { >> >> > if (missing(pkgs)) >> >> > biocinstall(groupName=groupName, ...) >> >> > else >> >> > biocinstall(pkgs=pkgs, groupName=groupName, ...) >> >> > } >> >> >> >> >> >> >> >> No, it's not safe, but more importantly, it won't work on R >= 2.14. >> >> >> >> Please let us know if you still are having problems. >> >> >> >> Thanks >> >> Dan >> >> >> >> >> >> >> >> >> >> > >> >> > >> >> > Thanks, >> >> > >> >> > Firas. >> >> > >> >> > >> >> > On Sun, Nov 27, 2011 at 9:57 AM, Dan Tenenbaum <dtenenba@fhcrc.org> >> >> > wrote: >> >> >> >> >> >> Hello, >> >> >> >> >> >> On Thu, Nov 24, 2011 at 6:32 PM, Firas Swidan <firas@biomatters.com>> > >> >> >> wrote: >> >> >> > Hi, >> >> >> > >> >> >> > I used to be able to install Bioconductor packages from a script >> >> >> > *without* >> >> >> > having administrator rights (e.g., on Windows) by specifying the >> >> >> > library >> >> >> > location to where the packages are to be installed. >> >> >> > >> >> >> > However, with the new R (2.14.0) and Bioconductor releases, the >> >> >> > command >> >> >> > >> >> >> > >> >> >> > >> >> >> > source("http://bioconductor.org/biocLite.R") >> >> >> > >> >> >> > >> >> >> > >> >> >> > would fail without administrator rights, because it tries to >> install >> >> >> > packages to directories that require administrator rights. >> >> >> > >> >> >> > I checked the file biocLite.R and located the line where this >> >> >> > problematic >> >> >> > install happens (install.packages("BiocInstaller", >> >> >> > repos=a["BioCsoft", >> >> >> > "URL"])) >> >> >> > >> >> >> > >> >> >> > Is there a safe way to avoid the requirement for administrator >> >> >> > rights? I >> >> >> > know that I could modify the above command and add a library >> location >> >> >> > argument, but is that safe? >> >> >> > >> >> >> > In particular I am wondering why the r-script was modified to >> require >> >> >> > the >> >> >> > administrator right? >> >> >> > >> >> >> >> >> >> The script was not modified specifically to require administrator >> >> >> rights. >> >> >> >> >> >> I tried to reproduce your situation, as I understand it, but >> perhaps I >> >> >> don't have enough information. When I (as a Windows user without >> >> >> administrative rights) ran the source() command above, I got a popup >> >> >> asking me if I wanted to create a personal library directory. If I >> >> >> said Yes, BiocInstaller installed itself just fine, and I was then >> >> >> able to install packages with biocLite(). I did get some warnings >> >> >> about packages that cannot be updated because they are installed in >> >> >> directories that are not writeable. However, those are just >> warnings; >> >> >> if you need to update any of those packages, you can install them >> >> >> yourself with biocLite(). >> >> >> >> >> >> It would be helpful if you could send the complete output of your >> >> >> session, including sessionInfo() and all the commands you tried, >> plus >> >> >> any errors/warnings. >> >> >> >> >> >> Thanks >> >> >> Dan >> >> >> >> >> >> >> >> >> >> >> >> > Thanks, >> >> >> > Firas. >> >> >> > >> >> >> > [[alternative HTML version deleted]] >> >> >> > >> >> >> > _______________________________________________ >> >> >> > Bioconductor mailing list >> >> >> > Bioconductor@r-project.org >> >> >> > https://stat.ethz.ch/mailman/listinfo/bioconductor >> >> >> > Search the archives: >> >> >> > http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> >> > >> >> > >> >> > >> >> > >> >> > >> >> > -- >> >> > Dr Firas Swidan, PhD Computer Science / Computational Biology >> >> > Bioinformatics Software Engineer >> >> > Biomatters Ltd >> >> > firas@biomatters.com >> > >> > >> > >> > >> > -- >> > Dr Firas Swidan, PhD Computer Science / Computational Biology >> > Bioinformatics Software Engineer >> > Biomatters Ltd >> > firas@biomatters.com >> > > > > -- > Dr Firas Swidan, PhD Computer Science / Computational Biology > Bioinformatics Software Engineer > Biomatters Ltd > firas@biomatters.com > -- Dr Firas Swidan, PhD Computer Science / Computational Biology Bioinformatics Software Engineer Biomatters Ltd firas@biomatters.com [[alternative HTML version deleted]]