Finally it works. I think the problem I posted before are caused by: 1. the tgz file could be corrupted at the first time; 2. my way of upgrade from 2.6 to 2.9 was not right I followed Marin's method, and it works. Thanks for all the helps. Weiwei On Thu, Oct 1, 2009 at 2:25 AM, Benilton Carvalho <bcarvalh@jhsph.edu>wrote: > 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@gmail.com> wrote: >> >> On Wed, Sep 30, 2009 at 2:07 PM, Weiwei Shi <helprhelp@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@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@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/con trib/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/con trib/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=""> >>>>>> >>>>> <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.="" mskcc.org="" %7elianos="" 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 >>>> >>>> [[alternative HTML version deleted]] >>>> >>>> _______________________________________________ >>>> Bioconductor mailing list >>>> Bioconductor@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@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]]