I like Florian's solution (sometime earlier this year, which I post here a somewhat differently): - before installing the new R: writeLines(installed.packages()[,1], con="~/packages.dump") - install R packs <- readLines("~/packages.dump") biocLite(packs) b On Sep 30, 2009, at 3:15 PM, Weiwei Shi wrote: > Thanks for all advice! > > Last time, I upgrade from 2.5 to 2.6, I remember it works in that > way; maybe > this time, there is some change. > > I want to make sure of my understanding, so if I follow Martin's > suggestion, > each time I upgrade my R, those 3 lines of codes can help me re- > install all > of my previous packages? > > I checked some previous posts and it seems that there is some other > way > since I have too many packages installed and re-installation might > take > really long time... > > Any suggestion about a quick re-installation? > > On Thu, Oct 1, 2009 at 2:10 AM, Sean Davis <seandavi at="" gmail.com=""> wrote: > >> On Wed, Sep 30, 2009 at 2:07 PM, Weiwei Shi <helprhelp at="" gmail.com=""> >> wrote: >>> Actually both 3 and 5 method work. >>> >>> I found that issue too. It could be because the upgrade since to >>> save my >>> previous packages, I just copy my previous packages from >>> Library/Framework/R.framework/.../2.6/resources/library to 2.9's >>> library. >> Do >>> you think that cause the problem? >> >> You shouldn't do that, and that is likely the cause of at least parts >> of the problem. >> >>> I did not reinstall base bioconductor base packages, let me try >>> that too. >> >> Each time you re-install a new version of R, it is best to reinstall >> all packages, in general, preferably using biocLite(). >> >>> The machine I am using is Macbook Pro, 2.2 GHz 4GB..., and OSX >>> 10.5.5 >>> >>> thanks, >>> >>> Weiwei >>> >>> On Thu, Oct 1, 2009 at 1:59 AM, Steve Lianoglou < >>> mailinglist.honeypot at gmail.com> wrote: >>> >>>> Hi, >>>> >>>> On Sep 30, 2009, at 1:53 PM, Weiwei Shi wrote: >>>> >>>> The installation seems to work now but the loading got some >>>> error... >>>>> >>>> >>>> 1. What did you do to get the install to work? >>>> >>>> 2. It actually seems like your problems aren't really with the lumi >> package >>>> since it looks like you're having problems with some compiled code, >> given >>>> the bus error. As far as I can see lumi has no compiled code, >>>> which just >>>> means to say I think we should be trying to debug "greater" issues. >>>> >>>> After you installed your new R (2.9.2), you reinstalled your base >>>> bioconductor base packages, right? >>>> >>>> 3. Out of curiosity, what kind of machine are you running on? >>>> >>>> -steve >>>> >>>> >>>> >>>>> >>>>>> library(lumi) >>>>> Loading required package: annotate >>>>> Loading required package: Biobase >>>>> Loading required package: tools >>>>> >>>>> Welcome to Bioconductor >>>>> >>>>> Vignettes contain introductory material. To view, type >>>>> 'openVignette()'. To cite Bioconductor, see >>>>> 'citation("Biobase")' and for packages 'citation(pkgname)'. >>>>> >>>>> Loading required package: AnnotationDbi >>>>> Loading required package: DBI >>>>> Loading required package: RSQLite >>>>> Loading required package: xtable >>>>> Loading required package: affy >>>>> Loading required package: affyio >>>>> Loading required package: preprocessCore >>>>> >>>>> *** caught bus error *** >>>>> address 0xc, cause 'non-existent physical address' >>>>> >>>>> Traceback: >>>>> 1: dyn.load(file, DLLpath = DLLpath, ...) >>>>> 2: library.dynam("preprocessCore", pkgname, libname, now = FALSE) >>>>> 3: f(libname, pkgname) >>>>> 4: firstlib(which.lib.loc, package) >>>>> 5: doTryCatch(return(expr), name, parentenv, handler) >>>>> 6: tryCatchOne(expr, names, parentenv, handlers[[1L]]) >>>>> 7: tryCatchList(expr, classes, parentenv, handlers) >>>>> 8: tryCatch(expr, error = function(e) { call <- >>>>> conditionCall(e) >> if >>>>> (!is.null(call)) { if (identical(call[[1L]], >>>>> quote(doTryCatch))) >>>>> call <- sys.call(-4L) dcall <- deparse(call)[1L] >>>>> prefix <- paste("Error in", dcall, ": ") LONG <- >>>>> 75L msg >> <- >>>>> conditionMessage(e) sm <- strsplit(msg, "\n") >>>>> [[1L]] if >> (14L + >>>>> nchar(dcall, type = "w") + nchar(sm[1L], type = "w") > >> LONG) >>>>> prefix <- paste(prefix, "\n ", sep = "") } else >>>>> prefix >> <- >>>>> "Error : " msg <- paste(prefix, conditionMessage(e), "\n", >>>>> sep = "") >>>>> .Internal(seterrmessage(msg[1L])) if (!silent && >>>>> identical(getOption("show.error.messages"), TRUE)) { >> cat(msg, >>>>> file = stderr()) .Internal(printDeferredWarnings()) } >>>>> invisible(structure(msg, class = "try-error"))}) >>>>> 9: try(firstlib(which.lib.loc, package)) >>>>> 10: library(pkg, character.only = TRUE, logical.return = TRUE, >>>>> lib.loc >> = >>>>> lib.loc) >>>>> 11: .getRequiredPackages2(pkgInfo) >>>>> 12: library(pkg, character.only = TRUE, logical.return = TRUE, >>>>> lib.loc >> = >>>>> lib.loc) >>>>> 13: .getRequiredPackages2(pkgInfo) >>>>> 14: library(lumi) >>>>> >>>>> Possible actions: >>>>> 1: abort (with core dump, if enabled) >>>>> 2: normal R exit >>>>> 3: exit R without saving workspace >>>>> 4: exit R saving workspace >>>>> Selection: >>>>> >>>>> >>>>> >>>>> On Thu, Oct 1, 2009 at 1:37 AM, Steve Lianoglou < >>>>> mailinglist.honeypot at gmail.com> wrote: >>>>> Hi, >>>>> >>>>> Wow ... weird: >>>>> >>>>> >>>>> On Sep 30, 2009, at 1:25 PM, Weiwei Shi wrote: >>>>> >>>>> still not works. >>>>> >>>>>> source("http://www.bioconductor.org/biocLite.R") >>>>>> biocLite("lumi") >>>>> Using R version 2.9.2, biocinstall version 2.4.12. >>>>> Installing Bioconductor version 2.4 packages: >>>>> [1] "lumi" >>>>> Please wait... >>>>> >>>>> Warning: unable to access index for repository >>>>> >> http://brainarray.mbni.med.umich.edu/bioc/bin/macosx/universal/cont rib/2.9 >>>>> trying URL 'http://bioconductor.org/packages/2.4/bioc/bin/macosx/ >>>>> universal/contrib/2.9/lumi_1.10.2.tgz' >>>>> Content type 'application/x-gzip' length 7082922 bytes (6.8 Mb) >>>>> opened URL >>>>> ================================================== >>>>> downloaded 6.8 Mb >>>>> >>>>> tar: Skipping to next header >>>>> tar: Archive contains obsolescent base-64 headers >>>>> >>>>> gzip: stdin: invalid compressed data--crc error >>>>> >>>>> I'm not sure why this is happening, but it looks like it can't >> uncompress >>>>> the downloaded tar correctly ... installing from both within R >>>>> (via >>>>> biocLite) and from the command line is working for me. >>>>> >>>>> Someone will likely have a better idea, but in the meantime, can >>>>> you >> try >>>>> to install the package from the command line? Like so: >>>>> >>>>> 1. Open Terminal.app >>>>> >>>>> 2. Download the package: >>>>> $ curl -O >>>>> >> http://bioconductor.org/packages/2.4/bioc/bin/macosx/universal/cont rib/2.9/lumi_1.10.2.tgz >>>>> >>>>> 3. Install into R >>>>> $ R CMD INSTALL lumi_1.10.2.tgz >>>>> >>>>> Is it still breaking? If so, continue to 4, otherwise celebrate. >>>>> >>>>> 4. Can you you simply uncompress that file? eg. does this >>>>> uncompress >>>>> successfully? (From within Terminal, we're not in R) >>>>> $ tar xvfz lumi_1.10.2.tgz >>>>> >>>>> 5. If that works, try to install the uncompressed file (it >>>>> expanded to >> a >>>>> "lumi" directory), but first remove the lumi*.tgz >>>>> >>>>> $ rm lumi_1.10.2.tgz >>>>> $ R CMD INSTALL lumi >>>>> >>>>> Anything? >>>>> >>>>> >>>>> -steve >>>>> >>>>> -- >>>>> Steve Lianoglou >>>>> Graduate Student: Computational Systems Biology >>>>> | Memorial Sloan-Kettering Cancer Center >>>>> | Weill Medical College of Cornell University >>>>> Contact Info: http://cbio.mskcc.org/~lianos/contact<http: cbio.="" mskcc.org="" %7elianos="" contact="">>>>> > >> <http: cbio.mskcc.org="" %7elianos="" contact=""> >>>>> >>>>> >>>>> >>>>> >>>>> -- >>>>> Weiwei Shi, Ph.D >>>>> Research Scientist >>>>> GeneGO, Inc. >>>>> >>>>> "Did you always know?" >>>>> "No, I did not. But I believed..." >>>>> ---Matrix III >>>>> >>>> >>>> -- >>>> Steve Lianoglou >>>> Graduate Student: Computational Systems Biology >>>> | Memorial Sloan-Kettering Cancer Center >>>> | Weill Medical College of Cornell University >>>> Contact Info: http://cbio.mskcc.org/~lianos/contact<http: cbio.m="" skcc.org="" %7elianos="" contact="">>>> > >> <http: cbio.mskcc.org="" %7elianos="" contact=""> >>>> >>>> >>> >>> >>> -- >>> Weiwei Shi, Ph.D >>> Research Scientist >>> GeneGO, Inc. >>> >>> "Did you always know?" >>> "No, I did not. But I believed..." >>> ---Matrix III >>> >>> [[alternative HTML version deleted]] >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at stat.math.ethz.ch >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >> > > > > -- > Weiwei Shi, Ph.D > Research Scientist > GeneGO, Inc. > > "Did you always know?" > "No, I did not. But I believed..." > ---Matrix III > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor