[BioC] lumi package

[Martin Morgan]

Weiwei Shi wrote:
> The installation seems to work now but the loading got some error...

try

  source('http://bioconductor.org/biocLite.R')
  old.packages(repos=biocinstallRepos())
  update.packages(repos=biocinstallRepos(), ask=FALSE)

Martin

> 
> 
>> 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<http://cbio.mskcc.org/%7Elianos/contact>
>>
>>
> 
> 


-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
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PO Box 19024 Seattle, WA 98109

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