[BioC] lumi package
Steve Lianoglou
mailinglist.honeypot at gmail.com
Wed Sep 30 20:09:38 CEST 2009
Hi,
On 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?
>
> I did not reinstall base bioconductor base packages, let me try that
> too.
Right, as Martin just pointed out, this is it. Once you reinstall (you
can follow his instructions), everything should be back to normal.
-steve
>
> 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/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
--
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
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