The installation seems to work now but the loading got some error...


> 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<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

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