I am having some trouble installing the bioconductor package in R, it is hanging at the "testing if installed packages can be loaded" part source("http://bioconductor.org/biocLite.R") #Installing package into ‘/homexxx/lib/R’ #(as ‘lib’ is unspecified) #trying URL 'http://www.bioconductor.org/packages/2.12/bioc/src/contrib/BiocInstal ler_1.10.2.tar.gz' #Content type 'application/x-gzip' length 13424 bytes (13 Kb) #opened URL #================================================== #downloaded 13 Kb # #* installing *source* package ‘BiocInstaller’ ... #** R #** inst #** preparing package for lazy loading #** help #*** installing help indices #** building package indices #** testing if installed package can be loaded #^C #No traceback available #* removing ‘/home/xxx/lib/R/BiocInstaller’ # #The downloaded source packages are in # ‘/tmp/Rtmpb2nVhP/downloaded_packages’ #'biocLite.R' failed to install 'BiocInstaller', use # 'install.packages("BiocInstaller", # repos="http://www.bioconductor.org/packages/2.12/bioc")' Here is R version: R --version R version 3.0.1 (2013-05-16) -- "Good Sport"Copyright (C) 2013 The R Foundation for Statistical ComputingPlatform: x86_64-pc-linux-gnu (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY.You are welcome to redistribute it under the terms of the GNU General Public License versions 2 or 3.For more information about these matters see http://www.gnu.org/licenses/. I also tried install.packages("BiocInstaller", repos=" http://www.bioconductor.org/packages/2.12/bioc") as indicated in the error message, but no luck there either. Best regards, Kaiyin ZHONG ------------------------------ Forensic Molecular Biology, Erasmus MC k.zhong@erasmusmc.nl kindlychung@gmail.com [[alternative HTML version deleted]]

On Tue, Jun 25, 2013 at 8:27 AM, Kaiyin Zhong (Victor Chung) <k.zhong at="" erasmusmc.nl=""> wrote: > I am having some trouble installing the bioconductor package in R, it is > hanging at the "testing if installed packages can be loaded" part > > source("http://bioconductor.org/biocLite.R") > #Installing package into ?/homexxx/lib/R? > #(as ?lib? is unspecified) > #trying URL > 'http://www.bioconductor.org/packages/2.12/bioc/src/contrib/BiocInst aller_1.10.2.tar.gz' > #Content type 'application/x-gzip' length 13424 bytes (13 Kb) > #opened URL > #================================================== > #downloaded 13 Kb > # > #* installing *source* package ?BiocInstaller? ... > #** R > #** inst > #** preparing package for lazy loading > #** help > #*** installing help indices > #** building package indices > #** testing if installed package can be loaded > #^C > #No traceback available > #* removing ?/home/xxx/lib/R/BiocInstaller? > # > #The downloaded source packages are in > # ?/tmp/Rtmpb2nVhP/downloaded_packages? > #'biocLite.R' failed to install 'BiocInstaller', use > # 'install.packages("BiocInstaller", > # repos="http://www.bioconductor.org/packages/2.12/bioc")' > > Here is R version: > > R --version > R version 3.0.1 (2013-05-16) -- "Good Sport"Copyright (C) 2013 The R > Foundation for Statistical ComputingPlatform: x86_64-pc-linux-gnu > (64-bit) > > R is free software and comes with ABSOLUTELY NO WARRANTY.You are > welcome to redistribute it under the terms of the > GNU General Public License versions 2 or 3.For more information about > these matters see > http://www.gnu.org/licenses/. > > > I also tried install.packages("BiocInstaller", repos=" > http://www.bioconductor.org/packages/2.12/bioc") as indicated in the error > message, but no luck there either. > The BiocInstaller package installs itself automatically; what happens if you try and install a different package; for example: source("http://bioconductor.org/biocLite.R") biocLite("Biobase") ? Dan > Best regards, > > Kaiyin ZHONG > ------------------------------ > Forensic Molecular Biology, Erasmus MC > k.zhong at erasmusmc.nl > kindlychung at gmail.com > > [[alternative HTML version deleted]] > > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

On Tue, Jun 25, 2013 at 10:04 AM, Kaiyin Zhong (Victor Chung) <k.zhong at="" erasmusmc.nl=""> wrote: > Oh, sorry, my mistake, it's still hanging with "testing if packages can be > loaded". > However, after starting R with R --vanilla, I can install Biobase without > problems. I guess there is something wrong with my .Rprofile, let me post > it here for your examination: > Without needing to look at your .Rprofile I can tell you there is something wrong with it, since installing packages works with --vanilla. I'm not sure what the problem is; maybe the CRAN mirror you've chosen is down? You can try with a fresh (empty) .Rprofile and add one line/function at a time and see where it breaks. Dan > history = function(max.show = 25, reverse = FALSE, filter = TRUE, pattern, > ...) > { > file1 <- tempfile("Rrawhist") > savehistory(file1) > rawhist <- readLines(file1) > unlink(file1) > > # the modification to stock > if (filter) > rawhist <- rawhist[cumsum(rle(rawhist)$lengths)] > # end of modification > > if (!missing(pattern)) > rawhist <- unique(grep(pattern, rawhist, value = TRUE, > ...)) > nlines <- length(rawhist) > if (nlines) { > inds <- max(1, nlines - max.show):nlines > if (reverse) > inds <- rev(inds) > } > else inds <- integer() > file2 <- tempfile("hist") > writeLines(rawhist[inds], file2) > file.show(file2, title = "R History", delete.file = TRUE) > } > > > options(papersize="a4") > options(editor="vim") > # options(pager="internal") > # R interactive prompt > options(prompt="R>") > options(continue=" ") > # to prefer Compiled HTML > # help options(chmhelp=TRUE) > # to prefer HTML help > # options(htmlhelp=TRUE) > options(tab.width = 4) > options(width = 80) > options(graphics.record=TRUE) > # If you would like to forbid conversion of strings into factors, > # uncomment the following line > options(stringsAsFactors=FALSE) > options(max.print=1000) > # number of digits to display > options(digits=5) > # traceback when error occurs > options(error=traceback) > > # set default CRAN repo > r = getOption('repos') > r["CRAN"] = "http://cran-mirror.cs.uu.nl" > options(repos=r) > rm(r) > > if(interactive()){ > } > > .First <- function(){ > } > > .Last <- function(){ > savehistory() > } > > > > > Best regards, > > Kaiyin ZHONG > ------------------------------ > Forensic Molecular Biology, Erasmus MC > k.zhong at erasmusmc.nl > kindlychung at gmail.com > > > On Tue, Jun 25, 2013 at 6:55 PM, Kaiyin Zhong (Victor Chung) < > k.zhong at erasmusmc.nl> wrote: > >> >> On Tue, Jun 25, 2013 at 6:46 PM, Dan Tenenbaum <dtenenba at="" fhcrc.org=""> wrote: >> >>> source("http://bioconductor.org/biocLite.R") >>> >> >> Problem solved after applying update to some packages, having not idea >> why it worked. My system is Ubuntu 12.04. >> >> >> >> Best regards, >> >> Kaiyin ZHONG >> ------------------------------ >> Forensic Molecular Biology, Erasmus MC >> k.zhong at erasmusmc.nl >> kindlychung at gmail.com >> > > [[alternative HTML version deleted]] > > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor