[BioC] lumi package

[Steve Lianoglou]

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