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 wrote: > On Wed, Sep 30, 2009 at 2:07 PM, Weiwei Shi 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/contrib/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/contrib/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 > > >>> > >>> > >>> > >>> > >>> -- > >>> 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 > > >> > >> > > > > > > -- > > 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]]