[BioC] lumi package

Wed Sep 30 20:10:22 CEST 2009

On Wed, Sep 30, 2009 at 2:07 PM, Weiwei Shi <helprhelp at gmail.com> 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?

You shouldn't do that, and that is likely the cause of at least parts
of the problem.

> I did not reinstall base bioconductor base packages, let me try that too.

Each time you re-install a new version of R, it is best to reinstall
all packages, in general, preferably using biocLite().

> 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<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
>>>
>>
>> --
>> 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
>
>        [[alternative HTML version deleted]]
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
>