[BioC] Wow, what have I done

Tue Dec 11 05:31:26 CET 2007

Ignore question 3, sorry
Is it > load(".RData") in the directory wherein you quit


> From: Loren Engrav <engrav at u.washington.edu>
> Date: Mon, 10 Dec 2007 19:00:56 -0800
> To: "bioconductor at stat.math.ethz.ch" <bioconductor at stat.math.ethz.ch>
> Conversation: [BioC] Wow, what have I done
> Subject: Re: [BioC] Wow, what have I done
> 
> Ok
> I have a 500 or 750gig drive somewhere round here so will get it out and
> install Leopard, and then do as you say
> 
> Then three questions in the meantime
> 1) if this 2.3.1 monster G5 ppc package is serious deficient, why is it
> still up? And called experimental implying "new"?
> 2) is it possible to get affyQCReport and simpleaffy into this old 64 bit R?
> 3) when you quit R from Terminal, and save the image, where is it and what
> is it called? (.Rdata)
> 
> Thanks again
> 
> -- 
> Loren Engrav
> Univ Washington
> Seattle
> 
>> From: Kasper Daniel Hansen <khansen at stat.Berkeley.EDU>
>> Date: Mon, 10 Dec 2007 18:45:21 -0800
>> To: Loren Engrav <engrav at u.washington.edu>
>> Cc: "bioconductor at stat.math.ethz.ch" <bioconductor at stat.math.ethz.ch>
>> Subject: Re: [BioC] Wow, what have I done
>> 
>> 
>> On Dec 10, 2007, at 6:26 PM, Loren Engrav wrote:
>> 
>>> Thank you
>>> 
>>> Am using G5
>>> And I have Leopard but have not installed as "too little hard drive
>>> space"
>>> And have 32bit R version 2.6.1 (2007-11-26) which I run with R.app
>>> and is
>>> fine but fails to ReadAffy() 81 .cel files (cannot make vector...)
>>> 
>>> So am now trying for G5 ppc 64bit R to read 83 .cel files
>>> 
>>> I went to page that says...
>>> 
>>> 64-bit R for Mac OS X
>>> All binaries on this page are strictly experimental. For licenses see
>>> individual projects (basically covered by GPL). All downloads are
>>> subject to
>>> acceptance of the disclaimer below. Feedback is welcome, but please
>>> don't
>>> use R-bugs as this is not an official release!
>>> R for PowerPC 64-bit (G5) on Mac OS X 10.4 (Tiger)
>>> 
>>> And obtained the
>>> 
>>> Monster package of 64-bit R
>>> The following tar-ball includes R 2.3.1 + X11 client + binaries of
>>> all CRAN
>>> packages that build cleanly + binaries of default Bioconducductor
>>> packages
>>> that build cleanly. Packages that require external libraries that
>>> are not
>>> part of Tiger are not included.
>>> Download R-2.3.1-ppc64-monster.tar.gz (ca. 530MB!!)
>>> 
>>> And installed same and it ReadAffy() 81 cel files very nicely but
>>> BiocLite fails for some packages and affyQCReport and simpleaffy
>>> are not
>>> included
>> 
>> Yes, all of this was reasonably clear from your earlier description.
>> 
>>> So
>>> If this monster package of 2.3.1 is bad out of date, is there a
>>> monster
>>> package of 2.6.1 64bit for G5 ppc?
>> 
>> No. And this monster package you are using is more than 1.5 years out
>> of date.
>> 
>> The only way to get something current which everyone will recommend
>> (essentially if you have any problems using such an old version of R
>> people will tell you to upgrade before they help), is to do what I said:
>> 1) Install Leopard
>> 2) Install R-2.6.1 from the package on this page
>> http://r.research.att.com/
>> You probably want 2.6.1 (instead of the development version 2.7.0)
>> and you most certainly want one which under "status" says "ppc64". As
>> you see on the package, Leopard is required.
>> 3) You then need to be able to install packages "from source". This
>> includes getting Xcode-3, and tools from
>> http://r.research.att.com/tools/
>> and possibly other stuff.
>> 4) Then set
>> option(pkgtype = "source")
>> and do the usual
>> biocLite()
>> 
>> Kasper
>> 
>> 
>> 
>> 
>> 
>>>> From: Kasper Daniel Hansen <khansen at stat.Berkeley.EDU>
>>>> Date: Mon, 10 Dec 2007 17:57:55 -0800
>>>> To: Loren Engrav <engrav at u.washington.edu>
>>>> Cc: "bioconductor at stat.math.ethz.ch" <bioconductor at stat.math.ethz.ch>
>>>> Subject: Re: [BioC] Wow, what have I done
>>>> 
>>>> On Dec 10, 2007, at 5:29 PM, Loren Engrav wrote:
>>>> 
>>>>> So I did and this is half Mac list half Bio list
>>>>> 
>>>>> curl -O http://r.research.att.com/exp/R-2.3.1-ppc64.tar.gz
>>>>> sudo tar fvxz R-2.3.1-ppc64.tar.gz -C /
>>>>> sudo ln -sf /usr/local/lib64/R/bin/R /usr/local/bin/R64
>>>>> 
>>>>> As per <http://cran.fhcrc.org/>
>>>>> 
>>>>> And cool, I have 64 bit R which launches
>>>> 
>>>> But your R version is 2.3.1 - seriously outdated.
>>>> 
>>>> You should be using the build of R-2.6.1 that says "leopard only,
>>>> pp64" on
>>>> http://r.research.att.com/
>>>> You need to be using leopard
>>>> 
>>>> (I hope you are using a G5 cpu, otherwise it will not work, I can see
>>>> from earlier posts that you are using a PowerPC cpu).
>>>> 
>>>> Then you need to do
>>>>   options(pkgType = "source")
>>>> and set up your mac to install bioconductor from source (otherwise
>>>> you will not get 64bit versions of the packages, which is what you
>>>> want). This may be painful if you have not done so before. Them you
>>>> can do
>>>>   biocLite()
>>>> 
>>>> It is possible as far as I know to get 64bit R to run under Tiger,
>>>> but it is supposedly very painful. The stuff above requires you to
>>>> upgrade to Leopard however.
>>>> 
>>>> Kasper
>>>> 
>>>> 
>>>>> But the
>>>>> 
>>>>> source("http://bioconductor.org/biocLite.R")
>>>>> biocLite()
>>>>> 
>>>>>  method of installing packages failed with complicated error
>>>>> messages
>>>>> 
>>>>> So I obtained the monster 64bit package from <http://
>>>>> cran.fhcrc.org/>
>>>>>  and dragged it all into the various /usr folders
>>>>> 
>>>>> And super,
>>>>> ReadAffy now reads 81 .cel files no problem with 2.5 gig
>>>>> So the 64bit is far more efficient than the 32bit
>>>>> 
>>>>> But now 3 new questions
>>>>> 1) does the biocLite method of packages work with R64bit
>>>>> 2) affyQCReport is not in the monster, how do I get affyQCReport
>>>>> into 64 bit
>>>>> 3) when quitting R in the Terminal (Mac) I save the image but do
>>>>> not know
>>>>> where it went nor what it is named, where is it, what is it called
>>>>> 
>>>>> Thank you
>>>>> 
>>>>> -- 
>>>>> Loren Engrav
>>>>> Univ Washington
>>>>> Seattle
>>>>> 
>>>>>> From: "Marcus G. Daniels" <mdaniels at lanl.gov>
>>>>>> Date: Mon, 10 Dec 2007 12:15:53 -0700
>>>>>> To: "bioconductor at stat.math.ethz.ch"
>>>>>> <bioconductor at stat.math.ethz.ch>
>>>>>> Subject: Re: [BioC] Wow, what have I done
>>>>>> 
>>>>>> Loren Engrav wrote:
>>>>>>> 3) try 64bit R
>>>>>>> 
>>>>>> Also if you are a Linux user, you can try VMware Fusion together
>>>>>> with
>>>>>> some x86_64 distribution of Linux (e.g. Fedora 8 x86_64 has a 64
>>>>>> build
>>>>>> of R). This will get you up past the 4GB software limit (up to 8GB
>>>>>> virtual memory).
>>>>>> 
>>>>>> _______________________________________________
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>>>>> 
>>>>> _______________________________________________
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>>>>> gmane.science.biology.informatics.conductor
>>>> 
>>> 
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>> 
> 
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