[BioC] lumi package

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