search for: biocinstallrepo

Hello, All: Jonathan Baron is "giving up" maintaining the RSiteSearch database. This breaks three things: (1) The R Site Search web service that Baron has maintained. (2) The RSiteSearch function in the utils package. (3) The sos package, for which I'm the maintainer and lead author. Might someone else be willing to take these over? For me,

...some help from R developers and Fedora >maintainers. Here is the trick, for someone who wants to do it: > >m0 <- rownames(installed.packages()) >m1 <- m0[which(m0 %in% needed.packages)] >source("http://bioconductor.org/biocLite.R") >update.packages(oldPkgs=m1,repos=biocinstallRepos()) >update.packages(dependencies=FALSE,INSTALL_opts=c("--no-configure","--no-test-load"," >--no-R","--no-clean-on-error","--no-libs","--no-data","--no-demo","--no-exec","--html >"),repos=biocinstallR...

...ALSE needed > source("http://bioconductor.org/biocLite.R") BioC_mirror = http://www.bioconductor.org Change using chooseBioCmirror(). Warning messages: 1: In safeSource() : Redefining ?biocinstall? 2: In safeSource() : Redefining ?biocinstallPkgGroups? 3: In safeSource() : Redefining ?biocinstallRepos? > biocLite() Using R version 2.11.1, biocinstall version 2.6.7. Installing Bioconductor version 2.6 packages: [1] "affy" "affydata" "affyPLM" "affyQCReport" [5] "annaffy" "annotate" "Biobase" "biomaRt" [9] "B...

...nd vignettes only, with some help from R developers and Fedora maintainers. Here is the trick, for someone who wants to do it: m0 <- rownames(installed.packages()) m1 <- m0[which(m0 %in% needed.packages)] source("http://bioconductor.org/biocLite.R") update.packages(oldPkgs=m1,repos=biocinstallRepos()) update.packages(dependencies=FALSE,INSTALL_opts=c("--no-configure","--no-test-load","--no-R","--no-clean-on-error","--no-libs","--no-data","--no-demo","--no-exec","--html"),repos=biocinstallRepos(),ask=F)...

...aintainers. Here is the trick, for someone who wants to do it: >>> >>> m0 <- rownames(installed.packages()) >>> m1 <- m0[which(m0 %in% needed.packages)] >>> source("http://bioconductor.org/biocLite.R") >>> update.packages(oldPkgs=m1,repos=biocinstallRepos()) >>> update.packages(dependencies=FALSE,INSTALL_opts=c("--no-configure","--no-test-load", >>> >> " >>> --no-R","--no-clean-on-error","--no-libs","--no-data","--no-demo","--no-exec",&...

...ers and Fedora >>maintainers. Here is the trick, for someone who wants to do it: >> >>m0 <- rownames(installed.packages()) >>m1 <- m0[which(m0 %in% needed.packages)] >>source("http://bioconductor.org/biocLite.R") >>update.packages(oldPkgs=m1,repos=biocinstallRepos()) >>update.packages(dependencies=FALSE,INSTALL_opts=c("--no-configure","--no-test-load", >" >>--no-R","--no-clean-on-error","--no-libs","--no-data","--no-demo","--no-exec","--htm >l >>&quo...

...ants to do it: > > m0 <- rownames(installed.packages()) > m1 <- m0[which(m0 %in% needed.packages)] > source("http://bioconductor.org/biocLite.R > <http://bioconductor.org/biocLite.R>") > update.packages(oldPkgs=m1,repos=biocinstallRepos()) > update.packages(dependencies=FALSE,INSTALL_opts=c("--no-configure","--no-test-load"," > --no-R","--no-clean-on-error","--no-libs","--no-data","--no-demo","--no-exec","--html >...

...8.0.libs to the new one. 3) Update the two environment variables %R_HOME% and %R_LIBS% to point to the new R-2.8.1 and library 4) Execute R 5) Update CRAN packages via update.packages() 6) Update Bioconductor packages via source("http://bioconductor.org/biocLite.R") update.packages(repos=biocinstallRepos(), ask=FALSE) 7) Update local zip packages via Go to menu -> Packages -> Install packages from local zip -> select the zip file. 8) Done!!! > sessionInfo() R version 2.8.0 (2008-10-20) i386-pc-mingw32 locale: LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;L...

...somewhere else. The trick is: update.packages(dependencies=FALSE,INSTALL_opts=c("--no-configure","--no-test-load","--no-R","--no-clean-on-error","--no-libs","--no-data","--no-demo","--no-exec","--html"),repos=biocinstallRepos(),ask=F) and install.packages(m3,dependencies=FALSE,INSTALL_opts=c("--no-configure","--no-test-load","--no-R","--no-clean-on-error","--no-libs","--no-data","--no-demo","--no-exec","--html"),repos=biocinstal...

...t installed correctly. Please see the following sequence. Thank you in advance. Maura > source("http://bioconductor.org/biocLite.R") Warning messages: 1: In safeSource() : Redefining ‘biocinstall’ 2: In safeSource() : Redefining ‘biocinstallPkgGroups’ 3: In safeSource() : Redefining ‘biocinstallRepos’ > > biocLite("biomaRt") Running biocinstall version 2.4.11 with R version 2.9.0 Your version of R requires version 2.4 of Bioconductor. Warning in install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, : argument 'lib' is missing: using '/home/ma...

...t attached): [1] tools_2.10.1 > source("http://bioconductor.org/biocLite.R") biocLite("GenomeGraphs")Warning messages: 1: In safeSource() : Redefining 'biocinstall' 2: In safeSource() : Redefining 'biocinstallPkgGroups' 3: In safeSource() : Redefining 'biocinstallRepos' > biocLite("GenomeGraphs") Using R version 2.10.1, biocinstall version 2.5.11. Installing Bioconductor version 2.5 packages: [1] "GenomeGraphs" Please wait... Warning in install.packages(pkgs = pkgs, repos = repos, ...) : argument 'lib' is missing: using...

I currently set the Bioconductor repository in my .Rprofile using this code (which needs editing for every version number change of Bioconductor): # Choose repositories repos <- structure(c(CRAN="http://streaming.stat.iastate.edu/CRAN", CRANextra="http://www.stats.ox.ac.uk/pub/RWin",