[BioC] lumi package

Benilton Carvalho bcarvalh at jhsph.edu
Wed Sep 30 20:25:03 CEST 2009 

I like Florian's solution (sometime earlier this year, which I post  
here a somewhat differently):

- before installing the new R:

writeLines(installed.packages()[,1], con="~/packages.dump")

- install R

packs <- readLines("~/packages.dump")
biocLite(packs)


b

On Sep 30, 2009, at 3:15 PM, Weiwei Shi wrote:

> Thanks for all advice!
>
> Last time, I upgrade from 2.5 to 2.6, I remember it works in that  
> way; maybe
> this time, there is some change.
>
> I want to make sure of my understanding, so if I follow Martin's  
> suggestion,
> each time I upgrade my R, those 3 lines of codes can help me re- 
> install all
> of my previous packages?
>
> I checked some previous posts and it seems that there is some other  
> way
> since I have too many packages installed and re-installation might  
> take
> really long time...
>
> Any suggestion about a quick re-installation?
>
> On Thu, Oct 1, 2009 at 2:10 AM, Sean Davis <seandavi at gmail.com> wrote:
>
>> 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 
>>>>> >
>> <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 
>>>> >
>> <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]]
>>>
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>>>
>>
>
>
>
> --
> 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]]
>
> _______________________________________________
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