Dear all, I have just upgraded to R1.7.0/Bioconductor, with a little help from our local sys ad people. However, when I start R I always get the following error: >Creating a new generic function for "summary" in package >reposTools > >Synching your local package management information ... > > Note: reposTools can not access/usr/lbiosoft/lib/R/library. > This will not affect your R session unless you wish > to install/update/remove packages from this directory I presume this is a permissions problem to do with accessing the directory, however the permissions are exactly the same as they are in R1.6.2/Bioconductor 1.1 and this runs fine Furthermore, I have a .Rprofile file that runs the following commands library(affy) library(Biobase) library(ctest) library(annotate) library(genefilter) library(MASS) library(tkWidgets) library(mva) Now in the latest version of R/Bioconductor, I get the following errors when I use my .Rprofile >Welcome to Bioconductor > Vignettes contain introductory material. To view, > simply type: openVignette() > For details on reading vignettes, see > the openVignette help page. >Creating a new generic function for "summary" in package >reposTools > >Synching your local package management information ... > > Note: reposTools can not access/usr/lbiosoft/lib/R/library. > This will not affect your R session unless you wish > to install/update/remove packages from this directory > >Error in get(x, envir, mode, inherits) : variable "biplot" was not found >Error in library(MASS) : package/namespace load failed Yet when I remove my .Rprofile and load the libraries separately, I get no errors. Any hints? Thanks in advance Claire -------------------------------------------------------- This email is confidential and intended solely for the use of th... {{dropped}}

Hi Claire, You really need R 1.7.0 (patched), available at: http://www.stats.uwo.ca/faculty/murdoch/software/r-devel/ there are some bugs in R 1.7.0 that make it incompatible with much of the bioconductor software. Robert On Tue, Jun 03, 2003 at 05:50:56PM +0100, Claire Wilson wrote: > Dear all, > > I have just upgraded to R1.7.0/Bioconductor, with a little help from our local sys ad people. However, when I start R I always get the following error: > >Creating a new generic function for "summary" in package > >reposTools > > > >Synching your local package management information ... > > > > Note: reposTools can not access/usr/lbiosoft/lib/R/library. > > This will not affect your R session unless you wish > > to install/update/remove packages from this directory > > I presume this is a permissions problem to do with accessing the directory, however the permissions are exactly the same as they are in R1.6.2/Bioconductor 1.1 and this runs fine > > Furthermore, I have a .Rprofile file that runs the following commands > library(affy) > library(Biobase) > library(ctest) > library(annotate) > library(genefilter) > library(MASS) > library(tkWidgets) > library(mva) > > Now in the latest version of R/Bioconductor, I get the following errors when I use my .Rprofile > > >Welcome to Bioconductor > > Vignettes contain introductory material. To view, > > simply type: openVignette() > > For details on reading vignettes, see > > the openVignette help page. > >Creating a new generic function for "summary" in package > >reposTools > > > >Synching your local package management information ... > > > > Note: reposTools can not access/usr/lbiosoft/lib/R/library. > > This will not affect your R session unless you wish > > to install/update/remove packages from this directory > > > >Error in get(x, envir, mode, inherits) : variable "biplot" was not found > >Error in library(MASS) : package/namespace load failed > > Yet when I remove my .Rprofile and load the libraries separately, I get no errors. > > Any hints? > > Thanks in advance > > Claire > > -------------------------------------------------------- > > > This email is confidential and intended solely for the use of th... {{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 | +--------------------------------------------------------------------- ------+

As of 1.7.0, direct calls to library() should not be placed in .Rprofile. Rather, you should use options("defaultPackages"). Try putting the following in your .Rprofile: local({ orig <- getOption("defaultPackages") options(defaultPackages = c(orig, "affy","Biobase","ctest","annotate","genefilter","MASS","tkWidgets","m va")) }) -roger Claire Wilson wrote: >Dear all, > >I have just upgraded to R1.7.0/Bioconductor, with a little help from our local sys ad people. However, when I start R I always get the following error: > > >>Creating a new generic function for "summary" in package >>reposTools >> >>Synching your local package management information ... >> >> Note: reposTools can not access/usr/lbiosoft/lib/R/library. >> This will not affect your R session unless you wish >> to install/update/remove packages from this directory >> >> > >I presume this is a permissions problem to do with accessing the directory, however the permissions are exactly the same as they are in R1.6.2/Bioconductor 1.1 and this runs fine > >Furthermore, I have a .Rprofile file that runs the following commands >library(affy) >library(Biobase) >library(ctest) >library(annotate) >library(genefilter) >library(MASS) >library(tkWidgets) >library(mva) > >Now in the latest version of R/Bioconductor, I get the following errors when I use my .Rprofile > > > >>Welcome to Bioconductor >> Vignettes contain introductory material. To view, >> simply type: openVignette() >> For details on reading vignettes, see >> the openVignette help page. >>Creating a new generic function for "summary" in package >>reposTools >> >>Synching your local package management information ... >> >> Note: reposTools can not access/usr/lbiosoft/lib/R/library. >> This will not affect your R session unless you wish >> to install/update/remove packages from this directory >> >>Error in get(x, envir, mode, inherits) : variable "biplot" was not found >>Error in library(MASS) : package/namespace load failed >> >> > >Yet when I remove my .Rprofile and load the libraries separately, I get no errors. > >Any hints? > >Thanks in advance > >Claire > >-------------------------------------------------------- > > >This email is confidential and intended solely for the use of th... {{dropped}} > >_______________________________________________ >Bioconductor mailing list >Bioconductor@stat.math.ethz.ch >https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > > > >