Hi, I am running R under X11 (MacOsx) and when I try to install bioconductor (Unix/Linux procedure), I get the following message: > getBioC(libName="all") Running getBioC version 1.2.28.... 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. Error in getBioC(libName = "all") : You do not have write access to /sw/lib/R/library Please check your permissions or provide a different 'destdir' parameter Then, trying the "destdir" option, I get: > getBioC(libName="all",destdir="/Users/martinobarenco/Desktop/biocond") Running getBioC version 1.2.28.... 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: cannot write to or create directory '/sw/lib/R/library' Error in upDatePkgs(relLevel, PLATFORM, destdir, method = method) : Failed to install package Biobase What should I do? Other Information: -The version of R I use is 1.7.0 and was installed via fink: > R.version _ platform powerpc-apple-darwin6.5 arch powerpc os darwin6.5 system powerpc, darwin6.5 status major 1 minor 7.0 year 2003 month 04 day 16 language R I also tried the whole thing via the carbon version of R (1.6.2), which works fine, except that it has no widgets and the functionalities I am interested in (normalisation/summary procedures in the "affy" package) crash because of some Fortran/C thing missing. Thanks a lot Best regards Martino --------------------------------------- Martino Barenco CoMPLEX 4, Stephenson Way London NW1 2HE Tel.: +44 20 7679 5088 Fax.: +44 20 7383 5519 Email: m.barenco@ucl.ac.uk -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: text/enriched Size: 2378 bytes Desc: not available Url : https://www.stat.math.ethz.ch/pipermail/bioconductor/attachments /20030501/3410a271/attachment.bin

Martino Barenco <sejjmba@ucl.ac.uk> writes: > Hi, > > I am running R under X11 (MacOsx) and when I try to install > bioconductor (Unix/Linux procedure), I get the following message: > >> getBioC(libName="all") > Running getBioC version 1.2.28.... > 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. > > Error in getBioC(libName = "all") : You do not have write access to > /sw/lib/R/library > Please check your permissions or provide a different 'destdir' > parameter Sounds like you need to install as root, in this case, i.e. sudo R and then go on. BUT, you probably REALLY do not want to do this. I mean, REALLY do not want to do this (should I say it a 3rd time?). > Then, trying the "destdir" option, I get: > >> > getBioC(libName="all",destdir="/Users/martinobarenco/Desktop/biocond") > Running getBioC version 1.2.28.... > 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: cannot write to or create directory '/sw/lib/R/library' > Error in upDatePkgs(relLevel, PLATFORM, destdir, method = method) : > Failed to install package Biobase > > What should I do? Looks like a bug in the installer function. Jeff? best, -tony -- A.J. Rossini rossini@u.washington.edu http://software.biostat.washington.edu/ Biostatistics, U Washington and Fred Hutchinson Cancer Research Center FHCRC:Tu: 206-667-7025 (fax=4812)|Voicemail is pretty sketchy/use Email UW : Th: 206-543-1044 (fax=3286)|Change last 4 digits of phone to FAX CONFIDENTIALITY NOTICE: This e-mail message and any attachments ... {{dropped}}

It is probably a better idea to change the ownership of the library directory, so that you need not be root in order to install. Something like sudo chown username /sw/lib/R/library then do the install. -Greg > -----Original Message----- > From: rossini@blindglobe.net [mailto:rossini@blindglobe.net] > Sent: Thursday, May 01, 2003 12:28 PM > To: Martino Barenco > Cc: bioconductor@stat.math.ethz.ch > Subject: Re: [BioC] Installing bioconductor under MacOsx > > > Martino Barenco <sejjmba@ucl.ac.uk> writes: > > > > Hi, > > > > I am running R under X11 (MacOsx) and when I try to install > > bioconductor (Unix/Linux procedure), I get the following message: > > > >> getBioC(libName="all") > > Running getBioC version 1.2.28.... > > 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. > > > > Error in getBioC(libName = "all") : You do not have write access to > > /sw/lib/R/library > > Please check your permissions or provide a different 'destdir' > > parameter > > Sounds like you need to install as root, in this case, i.e. sudo R and > then go on. BUT, you probably REALLY do not want to do this. I > mean, REALLY do not want to do this (should I say it a 3rd time?). > > > > Then, trying the "destdir" option, I get: > > > >> > > > getBioC(libName="all",destdir="/Users/martinobarenco/Desktop/biocond") > > Running getBioC version 1.2.28.... > > 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: cannot write to or create directory '/sw/lib/R/library' > > Error in upDatePkgs(relLevel, PLATFORM, destdir, method = method) : > > Failed to install package Biobase > > > > What should I do? > > Looks like a bug in the installer function. Jeff? > > best, > -tony > > -- > A.J. Rossini rossini@u.washington.edu > http://software.biostat.washington.edu/ > Biostatistics, U Washington and Fred Hutchinson Cancer Research Center > > FHCRC:Tu: 206-667-7025 (fax=4812)|Voicemail is pretty > sketchy/use Email > UW : Th: 206-543-1044 (fax=3286)|Change last 4 digits of > phone to FAX > > CONFIDENTIALITY NOTICE: This e-mail message and any > attachments ... {{dropped}} > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > LEGAL NOTICE\ Unless expressly stated otherwise, this message is... {{dropped}}

> > > getBioC(libName="all",destdir="/Users/martinobarenco/Desktop/biocond") > [1] "Installing reposTools ..." > ERROR: cannot write to or create directory '/sw/lib/R/library' > Error in upDatePkgs(relLevel, PLATFORM, destdir, method = method) : > Failed to install package Biobase > What should I do? Yeap, up until a couple of days ago reposTool was not very cooperative when dealing with library directories that one didn't have write permission to. This has been fixed, but the Release 1.1 patch isn't up on the site yet. The devel version however does work, so you could install the devel reposTools and then run getBioC() (or just getBioC(relLevel="devel")). The fix to reposTools will be on the site at the very latest Sunday morning (I'll try to get a new build of our release packages before that). -J

Well, not wanting to be too contradictory, it would be better if we didn't presume that we could write all over the users machine...that will get fixed. The package managment tools need to function in environments where not all R libraries are writable by the user; an oversight on our part which we will rectify. Thanks for the bug report. Robert On Thu, May 01, 2003 at 12:35:14PM -0400, Warnes, Gregory R wrote: > > It is probably a better idea to change the ownership of the library > directory, so that you need not be root in order to install. > > Something like > > sudo chown username /sw/lib/R/library > > then do the install. > > -Greg > > > > -----Original Message----- > > From: rossini@blindglobe.net [mailto:rossini@blindglobe.net] > > Sent: Thursday, May 01, 2003 12:28 PM > > To: Martino Barenco > > Cc: bioconductor@stat.math.ethz.ch > > Subject: Re: [BioC] Installing bioconductor under MacOsx > > > > > > Martino Barenco <sejjmba@ucl.ac.uk> writes: > > > > > > > Hi, > > > > > > I am running R under X11 (MacOsx) and when I try to install > > > bioconductor (Unix/Linux procedure), I get the following message: > > > > > >> getBioC(libName="all") > > > Running getBioC version 1.2.28.... > > > 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. > > > > > > Error in getBioC(libName = "all") : You do not have write access to > > > /sw/lib/R/library > > > Please check your permissions or provide a different 'destdir' > > > parameter > > > > Sounds like you need to install as root, in this case, i.e. sudo R and > > then go on. BUT, you probably REALLY do not want to do this. I > > mean, REALLY do not want to do this (should I say it a 3rd time?). > > > > > > > Then, trying the "destdir" option, I get: > > > > > >> > > > > > getBioC(libName="all",destdir="/Users/martinobarenco/Desktop/biocond") > > > Running getBioC version 1.2.28.... > > > 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: cannot write to or create directory '/sw/lib/R/library' > > > Error in upDatePkgs(relLevel, PLATFORM, destdir, method = method) : > > > Failed to install package Biobase > > > > > > What should I do? > > > > Looks like a bug in the installer function. Jeff? > > > > best, > > -tony > > > > -- > > A.J. Rossini rossini@u.washington.edu > > http://software.biostat.washington.edu/ > > Biostatistics, U Washington and Fred Hutchinson Cancer Research Center > > > > FHCRC:Tu: 206-667-7025 (fax=4812)|Voicemail is pretty > > sketchy/use Email > > UW : Th: 206-543-1044 (fax=3286)|Change last 4 digits of > > phone to FAX > > > > CONFIDENTIALITY NOTICE: This e-mail message and any > > attachments ... {{dropped}} > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@stat.math.ethz.ch > > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > > > > > LEGAL NOTICE\ Unless expressly stated otherwise, this message is... {{dropped}} > > _______________________________________________ > 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 | +--------------------------------------------------------------------- ------+

Hi Jeff, How are read-only directories handled. For end-users, it would be ideal if they were prompted select which library directory (from the current list) should be the installation target. -Greg > -----Original Message----- > From: Jeff Gentry [mailto:jgentry@jimmy.harvard.edu] > Sent: Thursday, May 01, 2003 12:38 PM > To: Martino Barenco > Cc: bioconductor@stat.math.ethz.ch > Subject: Re: [BioC] Installing bioconductor under MacOsx > > > > > > > > getBioC(libName="all",destdir="/Users/martinobarenco/Desktop/biocond") > > [1] "Installing reposTools ..." > > ERROR: cannot write to or create directory '/sw/lib/R/library' > > Error in upDatePkgs(relLevel, PLATFORM, destdir, method = method) : > > Failed to install package Biobase > > What should I do? > > Yeap, up until a couple of days ago reposTool was not very > cooperative > when dealing with library directories that one didn't have write > permission to. > > This has been fixed, but the Release 1.1 patch isn't up on the site > yet. The devel version however does work, so you could > install the devel > reposTools and then run getBioC() (or just > getBioC(relLevel="devel")). The fix to reposTools will be on > the site at > the very latest Sunday morning (I'll try to get a new build of our > release packages before that). > > -J > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > LEGAL NOTICE\ Unless expressly stated otherwise, this message is... {{dropped}}

As others have said, you don't have write access.... Set your R_LIBS in your .tcshrc (or .bash_profile if you're a bash user). I like setenv R_LIBS /Users/<username>/Library/R using bash: export R_LIBS=/Users/<username>/Library/R This puts user installed packages (including Bioconductor---it works fine on my iBook) in ~/Library/R rather than trying to use the system repository. If you want to make the packages available to all users you might want to consider using /Users/Shared/R or something like that instead. You should make sure to mkdir ~/Library/R before you try it though :-) You can also create a file ~/.MacOSX/environment.plist which is a standard plist (search macosxhints.com for the format if you like... or use the PList editor that comes with the Developer Tools) that makes the environment variables available to _ALL_ OS X applications (after logging in and out of course). This is useful if, say, you were going to use StatPaper and wanted to have a custom R package location. Hope that Helps, B On Thursday, May 1, 2003, at 11:33 AM, Martino Barenco wrote: > Hi, > > I am running R under X11 (MacOsx) and when I try to install > bioconductor (Unix/Linux procedure), I get the following message: > > > getBioC(libName="all") > Running getBioC version 1.2.28.... > 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. > > Error in getBioC(libName = "all") : You do not have write access to > /sw/lib/R/library > Please check your permissions or provide a different 'destdir' > parameter > > Then, trying the "destdir" option, I get: > > > > getBioC(libName="all",destdir="/Users/martinobarenco/Desktop/biocond") > Running getBioC version 1.2.28.... > 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: cannot write to or create directory '/sw/lib/R/library' > Error in upDatePkgs(relLevel, PLATFORM, destdir, method = method) : > Failed to install package Biobase > > What should I do? > > Other Information: > > -The version of R I use is 1.7.0 and was installed via fink: > > > R.version > _ > platform powerpc-apple-darwin6.5 > arch powerpc > os darwin6.5 > system powerpc, darwin6.5 > status > major 1 > minor 7.0 > year 2003 > month 04 > day 16 > language R > > I also tried the whole thing via the carbon version of R (1.6.2), > which works fine, except that it has no widgets and the > functionalities I am interested in (normalisation/summary procedures > in the "affy" package) crash because of some Fortran/C thing missing. > > Thanks a lot > > Best regards > > Martino > > --------------------------------------- > Martino Barenco > CoMPLEX > 4, Stephenson Way > London NW1 2HE > Tel.: +44 20 7679 5088 > Fax.: +44 20 7383 5519 > Email: > m.barenco@ucl.ac.uk_______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > Byron Ellis (bellis@hsph.harvard.edu) "Oook" - The Librarian -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: text/enriched Size: 3795 bytes Desc: not available Url : https://www.stat.math.ethz.ch/pipermail/bioconductor/attachments /20030503/41d3ab59/attachment.bin