Thank you so much Tomorrow when the martini's have worn off will try it But there is the one more question
I have installed from page <http://r.research.att.com/> R-2.6-branch R 2.6.1 Patched (2007-12-12) Must I install R-devel R 2.7.0 Under development (unstable) (2007-12-12) Who knows, I may one day ReadAffy on 81 .cel files Which was the original goal of all of this My wife say doing this by hand would have been quicker Thank you -- Loren Engrav Univ Washington Seattle > From: Benilton Carvalho <[EMAIL PROTECTED]> > Date: Thu, 13 Dec 2007 23:38:24 -0500 > To: Loren Engrav <[EMAIL PROTECTED]> > Cc: "[email protected]" <[email protected]> > Subject: Re: [R-SIG-Mac] Does preprocessCore do ppc64? > > Hi Loren, > > it seems you have all the tools to build the packages. > > So, this is what you need: > > 1) load R from the command line using the 64 bits mode > 2) type: source("http://www.bioconductor.org/biocLite.R";) > 3) type, note the "type" argument: > > biocLite(c("Biobase", "affy", "preprocessCore"), type="source") > > this will download the *source*, compile and install (64 bits).... > > because R is under /Library (I assume), you want to load R using "sudo" > > sudo R --arch=ppc64 > > btw, you want to repeat the same procedure for other packages you > might need > > b > > On Dec 13, 2007, at 11:29 PM, Loren Engrav wrote: > >> Thank you, maybe is coming into focus >> >>>> Then I run R.app with options(arch="ppc64") in .Rprofile >>>> That is a really bad idea (see the response you got previously). >> >> Would appear that I have proven what you say is true >> >>>> I bet you didn't install the package from sources. CRAN/BioC offer >>>> 32- >>>> bit package binaries only, so you have to install all packages from >>>> sources (i.e. you must use type='source' in install.packages). Also >>>> you need all the necessary tools for this (please read the page you >>>> got the binaries from). >> >> Couple lines up I included >> >>>>> source("http://bioconductor.org/biocLite.R";) >>>>> biocLite("preprocessCore") >> >> Again proving you correct >> >> And I see the directions on <http://r.research.att.com/> are >> changing which >> is good for R/Bio R1's >> >> So now what I wish to do is 64bit Readaffy >> And can use 64bit command line which is painful but would work >> But have no 64bit Bio packages >> >> As I understand now >> To get 64bit R.app I must get the tools and build it >> To get 64bit Bio packages I must get the tools and build them >> >> I might try this being this deep into this and finding it rather fun >> >> One question before I start >> You say >>> note that R 2.6.1 doesn't have Quartz support in 64-bit, so the GUI >>> won't be of much use. You have to use R-devel for Quartz in 64-bit. >> >> This means that from <http://r.research.att.com/> >>> R-2.6-branch >>> R 2.6.1 Patched (2007-12-12) >> Will not work, I MUST use >>> R-devel >>> R 2.7.0 Under development >>> (unstable) (2007-12-12) >> True? Even tho neither include R.app? >> >> In preparation for this I have installed >> Xcode 3 from the Leopard DVD >> And >> GNU Fortan 4.2.1 >> And >> Will install LaTeX after massive download done >> >> And did in Terminal... >> export PATH=$PATH:/usr/local/bin >> and >> curl -s -S http://r.research.att.com/readline-5.2-1-quad.tar.gz|sudo >> tar fxz >> - -C / >> and >> curl -s -S http://r.research.att.com/jpegpng-quad.tar.gz|sudo tar >> fxz - -C / >> >> >> And of course, maybe I should bag it, admit I am over my head, and >> let some >> "expert" with dChip do it >> >> But then what the hell? Why not try it, if you can tolerate my >> questions >> that is, and I am closer to ReadAffy 64bit 81 cell as I now have >> command >> line 64bit R >> >> -- >> Loren Engrav >> Univ Washington >> Seattle >> >>> From: Simon Urbanek <[EMAIL PROTECTED]> >>> Date: Thu, 13 Dec 2007 19:39:52 -0500 >>> To: Loren Engrav <[EMAIL PROTECTED]> >>> Cc: "[email protected]" <[email protected]> >>> Subject: Re: [R-SIG-Mac] Does preprocessCore do ppc64? >>> >>> >>> On Dec 13, 2007, at 5:58 PM, Loren Engrav wrote: >>> >>>> Thank you, was helpful, is complicated for this geezer, but >>>> interesting >>>> >>>> The whole goal is to ReadAffy() on 81 chips which seems to need 64 >>>> bit to >>>> avoid "cannot allocate vector...." error (or reduce chips or analyze >>>> in >>>> pieces but not yet ready to give up on this) >>>> >>>> Other advisors advised >>>> >>>> "Install Leopard 10.5.1 >>>> >>>> Now install either >>>> R-2.6-branch-leopard-universal.tar.gz >>>> or >>>> R-devel-leopard-universal.tar.gz >>>> depending on which version of BioC you want to use: the former is >>>> for BioC >>>> 2.1 (the current release) and the latter for BioC 2.2 (the current >>>> devel). >>>> >>>> Then start R with --arch=ppc64 and you will be running in 64-bit >>>> mode." >>>> >>>> So I installed Leopard and R-2.6-branch and start with R -- >>>> arch=ppc64 >>>> >>>> ========= >>>> and as you suggested while running Command Line >>>> >>>>> version >>>> _ >>>> platform powerpc-apple-darwin9.0.0 >>>> arch powerpc >>>> os darwin9.0.0 >>>> system powerpc, darwin9.0.0 >>>> status Patched >>>> major 2 >>>> minor 6.1 >>>> year 2007 >>>> month 12 >>>> day 12 >>>> svn rev 43661 >>>> language R >>>> version.string R version 2.6.1 Patched (2007-12-12 r43661) >>>> >>>>> .Machine$sizeof.pointer == 8 >>>> [1] TRUE >>>> >>>>> R.version$arch >>>> [1] "powerpc" >>>> >>>>> .Platform$r_arch >>>> [1] "ppc64" >>>> >>>> ============ >>>> Then I run R.app with options(arch="ppc64") in .Rprofile >>>> >>> >>> That is a really bad idea (see the response you got previously). You >>> cannot change the architecture in a running R and you also cannot use >>> 32-bit R.app with 64-bit R. If you want 64-bit R and the GUI, you >>> have >>> to use 64-bit R.app (which you have to build from the sources). Also >>> note that R 2.6.1 doesn't have Quartz support in 64-bit, so the GUI >>> won't be of much use. You have to use R-devel for Quartz in 64-bit. >>> >>> >>>> And get >>>> >>>>> version >>>> _ >>>> platform powerpc-apple-darwin9.1.0 >>>> arch powerpc >>>> os darwin9.1.0 >>>> system powerpc, darwin9.1.0 >>>> status Patched >>>> major 2 >>>> minor 6.1 >>>> year 2007 >>>> month 12 >>>> day 12 >>>> svn rev 43661 >>>> language R >>>> version.string R version 2.6.1 Patched (2007-12-12 r43661) >>>> >>>>> .Machine$sizeof.pointer == 8 >>>> [1] FALSE >>>> >>>>> R.version$arch >>>> [1] "powerpc" >>>> >>>>> .Platform$r_arch >>>> [1] "ppc" >>>>> >>>> >>>> So would then seem at Command Line I have 64 but in R.app I do not >>>> >>>> ============ >>>> Then I try biocLite("preprocessCore") at Command Line and returns >>>> >>>>> .Platform$r_arch >>>> [1] "ppc64" >>>>> sessionInfo() >>>> R version 2.6.1 Patched (2007-12-12 r43661) >>>> powerpc-apple-darwin9.0.0 >>>> >>>> locale: >>>> en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 >>>> >>>> attached base packages: >>>> [1] stats graphics grDevices utils datasets methods base >>>> >>>> loaded via a namespace (and not attached): >>>> [1] rcompgen_0.1-17 >>>>> source("http://bioconductor.org/biocLite.R";) >>>>> biocLite("preprocessCore") >>>> >>>> Running biocinstall version 2.1.8 with R version 2.6.1 >>>> Your version of R requires version 2.1 of Bioconductor. >>>> trying URL >>>> 'http://bioconductor.org/packages/2.1/bioc/bin/macosx/universal/contrib/2.6>>>> / >>>> preprocessCore_1.0.0.tgz' >>>> Content type 'application/x-gzip' length 157468 bytes (153 Kb) >>>> opened URL >>>> ================================================== >>>> downloaded 153 Kb >>>> >>>> >>>> The downloaded packages are in >>>> >>>> /var/folders/-O/-O2rx2VN2RWJgU+8ZMxMx++++TI/-Tmp-//RtmpHcRo5R/ >>>> downloaded_pac >>>> kages >>>>> library(preprocessCore) >>>> Error: package 'preprocessCore' is not installed for 'arch=ppc64' >>>>> >>>> >>> >>> I bet you didn't install the package from sources. CRAN/BioC offer >>> 32- >>> bit package binaries only, so you have to install all packages from >>> sources (i.e. you must use type='source' in install.packages). Also >>> you need all the necessary tools for this (please read the page you >>> got the binaries from). >>> >>> Cheers, >>> Simon >>> >>> >>>> =============== >>>> Then I try same with R.app and returns >>>> >>>>> .Platform$r_arch >>>> [1] "ppc" >>>>> sessionInfo() >>>> R version 2.6.1 Patched (2007-12-12 r43661) >>>> powerpc-apple-darwin9.1.0 >>>> >>>> locale: >>>> en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 >>>> >>>> attached base packages: >>>> [1] stats graphics grDevices utils datasets methods base >>>>> >>>> >>>>> source("http://bioconductor.org/biocLite.R";) >>>>> biocLite("preprocessCore") >>>> Running biocinstall version 2.1.8 with R version 2.6.1 >>>> Your version of R requires version 2.1 of Bioconductor. >>>> trying URL >>>> 'http://bioconductor.org/packages/2.1/bioc/bin/macosx/universal/contrib/2.6>>>> / >>>> preprocessCore_1.0.0.tgz' >>>> Content type 'application/x-gzip' length 157468 bytes (153 Kb) >>>> opened URL >>>> ================================================== >>>> downloaded 153 Kb >>>> >>>> >>>> The downloaded packages are in >>>> >>>> /var/folders/-O/-O2rx2VN2RWJgU+8ZMxMx++++TI/-Tmp-//Rtmp3VK9Rw/ >>>> downloaded_pac >>>> kages >>>> >>>> >>>>> library(preprocessCore) >>>> Error in dyn.load(file, ...) : >>>> unable to load shared library >>>> '/Library/Frameworks/R.framework/Resources/library/preprocessCore/ >>>> libs/ppc/p >>>> reprocessCore.so': >>>> >>>> dlopen(/Library/Frameworks/R.framework/Resources/library/ >>>> preprocessCore/libs >>>> /ppc/preprocessCore.so, 5): Library not loaded: >>>> /Library/Frameworks/R.framework/Versions/2.6/Resources/lib/ >>>> libgfortran.2.dyl >>>> ib >>>> Referenced from: >>>> /Library/Frameworks/R.framework/Resources/library/preprocessCore/ >>>> libs/ppc/pr >>>> eprocessCore.so >>>> Reason: image not found >>>> Error in library(preprocessCore) : .First.lib failed for >>>> 'preprocessCore' >>>> >>>> ============= >>>> So to me seems with your investigative advice >>>> 1) I have 64bit at command line >>>> 2) I do not have 64bit in R.app >>>> 3) preprocessCore is not 64bit (and other packages) >>>> >>>> So I am closer to 64bit ReadAffy of 81 files but still not there >>>> >>>> With your serious knowledge, how should I get to 64bit ReadAffy >>>> >>>> Thank you >>>> >>>> >>>> >>>> >>>> >>>>> From: Prof Brian Ripley <[EMAIL PROTECTED]> >>>>> Date: Thu, 13 Dec 2007 17:00:36 +0000 (GMT) >>>>> To: Loren Engrav <[EMAIL PROTECTED]> >>>>> Cc: "[email protected]" <[email protected]> >>>>> Subject: Re: [R-SIG-Mac] Does preprocessCore do ppc64? >>>>> >>>>> The short answer is that the BioC binary packages are not 64-bit. >>>>> But >>>>> then neither is the CRAN build of R 2.6.1 nor the CRAN binary >>>>> packages. >>>>> >>>>> And very likely you are running a 32-bit R. >>>>> >>>>> On Thu, 13 Dec 2007, Loren Engrav wrote: >>>>> >>>>>> I tried >>>>>> options(arch="ppc64") in Rprofile >>>>>> and seems to have worked, >>>>> >>>>> I am sure it 'worked' for some value of 'worked', but what do you >>>>> think it >>>>> did? You can't change the architecture of a running R process (and >>>>> you >>>>> need a running R process to use R code ...). You find out whether >>>>> the >>>>> process is 64-bit by checking >>>>> >>>>> .Machine$sizeof.pointer == 8 >>>>> >>>>> and R.version$arch will also indicate the architecture name (x86_64 >>>>> on my >>>>> Macintel builds). >>>>> >>>>> The sub-architecture (if any) of the running process is given by >>>>> .Platform$r_arch and the user cannot change it (it was set at >>>>> configure >>>>> time). From the output below, that is 'ppc'. Not only do the >>>>> architectures need to match, but do the sub-architecture settings: >>>>> this is >>>>> easy to achieve when building everything yourself, but not when >>>>> taking >>>>> binaries built on different systems by different people at >>>>> different >>>>> times. >>>>> >>>>> So, it seems >>>>> >>>>> - you are running a 32-bit R. >>>>> - you are missing a Fortran library. >>>>> >>>>> Please do try to deduce from the output what the problem is, not >>>>> guess and >>>>> never test your guesses. >>>>> >>>>>> I think R.app is ppc64 in Leopard >>>>> >>>>> The CRAN build of 2.6.1 is not, and you haven't told us which build >>>>> you >>>>> are using. >>>>> >>>>> AFAIK if you want 64-bit, you need to build packages from sources. >>>>> >>>>> How to set all this up is AFAIK not fully documented, for the very >>>>> good >>>>> reason that it is *experimental*. My understanding is that it is >>>>> intended >>>>> to support 64-bit MacOS binary builds from R 2.7.0 only. >>>>> >>>>> >>>>> >>>>>> But affy will not load as requires preprocessCore >>>>>> >>>>>> Library(preprocessCore) returns >>>>>> >>>>>> Error in dyn.load(file, ...) : >>>>>> unable to load shared library >>>>>> '/Library/Frameworks/R.framework/Resources/library/preprocessCore/ >>>>>> libs/ppc/p >>>>>> reprocessCore.so': >>>>>> >>>>>> dlopen(/Library/Frameworks/R.framework/Resources/library/ >>>>>> preprocessCore/libs >>>>>> /ppc/preprocessCore.so, 5): Library not loaded: >>>>>> /Library/Frameworks/R.framework/Versions/2.6/Resources/lib/ >>>>>> libgfortran.2.dyl >>>>>> ib >>>>>> Referenced from: >>>>>> /Library/Frameworks/R.framework/Resources/library/preprocessCore/ >>>>>> libs/ppc/pr >>>>>> eprocessCore.so >>>>>> Reason: image not found >>>>>> Error in library(preprocessCore) : .First.lib failed for >>>>>> 'preprocessCore' >>>>>> >>>>>> I check libs in preprocessCore and find i386 and ppc, no ppc64 >>>>>> >>>>>> Does this mean preprocessCore as it stands does not do ppc64? Or I >>>>>> am >>>>>> getting the wrong one? Or I must build 64bit? Or? >>>>>> >>>>>> The original thread is in Bio but this seems like a Mac specific >>>>>> question >>>>>> >>>>>> Thank you >>>>>> >>>>>> >>>>> >>>>> -- >>>>> Brian D. Ripley, [EMAIL PROTECTED] >>>>> Professor of Applied Statistics, http://www.stats.ox.ac.uk/ >>>>> ~ripley/ >>>>> University of Oxford, Tel: +44 1865 272861 (self) >>>>> 1 South Parks Road, +44 1865 272866 (PA) >>>>> Oxford OX1 3TG, UK Fax: +44 1865 272595 >>>> >>>> _______________________________________________ >>>> R-SIG-Mac mailing list >>>> [email protected] >>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac >>>> >>>> >>> >> >> _______________________________________________ >> R-SIG-Mac mailing list >> [email protected] >> https://stat.ethz.ch/mailman/listinfo/r-sig-mac > _______________________________________________ R-SIG-Mac mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/r-sig-mac
