Wow, what have I done
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Loren Engrav ★ 1.0k
@loren-engrav-2040
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@marcus-g-daniels-1474
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Loren Engrav wrote: > R(22621,0xa000ed88) malloc: *** error: can't allocate region > R(22621,0xa000ed88) malloc: *** set a breakpoint in szone_error to debug > R(22621,0xa000ed88) malloc: *** vm_allocate(size=758743040) failed (error > code=3) > R(22621,0xa000ed88) malloc: *** error: can't allocate region > R(22621,0xa000ed88) malloc: *** set a breakpoint in szone_error to debug > > I have 2.5 gb DDR SDRAM in the dual G5 Mac > > Is the only answer, buy more RAM? > These sorts of errors tend not to occur with 64 bit software. Provided you don't need to reference all of it, the fact it exceeds your actual amount of RAM isn't a cause for a crash or even slowness. In short, a 64 bit build of R for Leopard might be a solution.
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Damn, you guys are big league Am using 10.4.11 since do not have Leopard since do not have enough hard drive space although I bought the disk and As this point have no clue what "64 bit build" means and so use the provided binaries > From: "Marcus G. Daniels" <mdaniels at="" lanl.gov=""> > Date: Fri, 07 Dec 2007 22:40:11 -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: >> R(22621,0xa000ed88) malloc: *** error: can't allocate region >> R(22621,0xa000ed88) malloc: *** set a breakpoint in szone_error to debug >> R(22621,0xa000ed88) malloc: *** vm_allocate(size=758743040) failed (error >> code=3) >> R(22621,0xa000ed88) malloc: *** error: can't allocate region >> R(22621,0xa000ed88) malloc: *** set a breakpoint in szone_error to debug >> >> I have 2.5 gb DDR SDRAM in the dual G5 Mac >> >> Is the only answer, buy more RAM? >> > These sorts of errors tend not to occur with 64 bit software. Provided > you don't need to reference all of it, the fact it exceeds your actual > amount of RAM isn't a cause for a crash or even slowness. In short, a > 64 bit build of R for Leopard might be a solution. > > _______________________________________________ > 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
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@benilton-carvalho-1375
Last seen 13 months ago
Brazil/Campinas/UNICAMP
I'd first make sure that you have the latest version (of R and the packages) installed... b On Dec 7, 2007, at 11:59 PM, Loren Engrav wrote: > So I enter > >> GibranGlue70 <- ReadAffy() # to read in 70 .cel files > > And I get this, all in bright red > > Error: cannot allocate vector of size 723.6 Mb > R(22621,0xa000ed88) malloc: *** vm_allocate(size=758743040) failed > (error > code=3) > R(22621,0xa000ed88) malloc: *** error: can't allocate region > R(22621,0xa000ed88) malloc: *** set a breakpoint in szone_error to > debug > R(22621,0xa000ed88) malloc: *** vm_allocate(size=758743040) failed > (error > code=3) > R(22621,0xa000ed88) malloc: *** error: can't allocate region > R(22621,0xa000ed88) malloc: *** set a breakpoint in szone_error to > debug > > I have 2.5 gb DDR SDRAM in the dual G5 Mac > > Is the only answer, buy more RAM? > > [[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
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Thank you so much for the prompt help Having been "scolded" for this before I now use sessionInfo which returned > sessionInfo() R version 2.6.0 Patched (2007-11-09 r43408) powerpc-apple-darwin8.10.1 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] tools stats graphics grDevices utils datasets methods base other attached packages: [1] affy_1.16.0 preprocessCore_1.0.0 affyio_1.6.1 Biobase_1.16.1 > From: Benilton Carvalho <bcarvalh at="" jhsph.edu=""> > Date: Sat, 8 Dec 2007 00:06:07 -0500 > 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 > > I'd first make sure that you have the latest version (of R and the > packages) installed... > b > > On Dec 7, 2007, at 11:59 PM, Loren Engrav wrote: > >> So I enter >> >>> GibranGlue70 <- ReadAffy() # to read in 70 .cel files >> >> And I get this, all in bright red >> >> Error: cannot allocate vector of size 723.6 Mb >> R(22621,0xa000ed88) malloc: *** vm_allocate(size=758743040) failed >> (error >> code=3) >> R(22621,0xa000ed88) malloc: *** error: can't allocate region >> R(22621,0xa000ed88) malloc: *** set a breakpoint in szone_error to >> debug >> R(22621,0xa000ed88) malloc: *** vm_allocate(size=758743040) failed >> (error >> code=3) >> R(22621,0xa000ed88) malloc: *** error: can't allocate region >> R(22621,0xa000ed88) malloc: *** set a breakpoint in szone_error to >> debug >> >> I have 2.5 gb DDR SDRAM in the dual G5 Mac >> >> Is the only answer, buy more RAM? >> >> [[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
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In that case, assuming that R-2.6.1 behaves just like R-2.6.0-patched in terms of memory management, you might want to define beforehand what you're going to be doing and, probably, use functions like justRMA(). b On Dec 8, 2007, at 12:13 AM, Loren Engrav wrote: > Thank you so much for the prompt help > > Having been "scolded" for this before I now use sessionInfo which > returned > >> sessionInfo() > R version 2.6.0 Patched (2007-11-09 r43408) > powerpc-apple-darwin8.10.1 > > 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] tools stats graphics grDevices utils datasets > methods > base > > other attached packages: > [1] affy_1.16.0 preprocessCore_1.0.0 affyio_1.6.1 > Biobase_1.16.1 > > >> From: Benilton Carvalho <bcarvalh at="" jhsph.edu=""> >> Date: Sat, 8 Dec 2007 00:06:07 -0500 >> 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 >> >> I'd first make sure that you have the latest version (of R and the >> packages) installed... >> b >> >> On Dec 7, 2007, at 11:59 PM, Loren Engrav wrote: >> >>> So I enter >>> >>>> GibranGlue70 <- ReadAffy() # to read in 70 .cel files >>> >>> And I get this, all in bright red >>> >>> Error: cannot allocate vector of size 723.6 Mb >>> R(22621,0xa000ed88) malloc: *** vm_allocate(size=758743040) failed >>> (error >>> code=3) >>> R(22621,0xa000ed88) malloc: *** error: can't allocate region >>> R(22621,0xa000ed88) malloc: *** set a breakpoint in szone_error to >>> debug >>> R(22621,0xa000ed88) malloc: *** vm_allocate(size=758743040) failed >>> (error >>> code=3) >>> R(22621,0xa000ed88) malloc: *** error: can't allocate region >>> R(22621,0xa000ed88) malloc: *** set a breakpoint in szone_error to >>> debug >>> >>> I have 2.5 gb DDR SDRAM in the dual G5 Mac >>> >>> Is the only answer, buy more RAM? >>> >>> [[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 > > _______________________________________________ > 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
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Thank you again for prompt help, I am grateful Damn, you guys are big league I thought I was current having just set this up But now I am out of date I will get and try 2.6.1 binary Engrav > From: Benilton Carvalho <bcarvalh at="" jhsph.edu=""> > Date: Sat, 8 Dec 2007 00:23:10 -0500 > 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 > > In that case, assuming that R-2.6.1 behaves just like R-2.6.0-patched > in terms of memory management, you might want to define beforehand > what you're going to be doing and, probably, use functions like > justRMA(). > > b > > On Dec 8, 2007, at 12:13 AM, Loren Engrav wrote: > >> Thank you so much for the prompt help >> >> Having been "scolded" for this before I now use sessionInfo which >> returned >> >>> sessionInfo() >> R version 2.6.0 Patched (2007-11-09 r43408) >> powerpc-apple-darwin8.10.1 >> >> 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] tools stats graphics grDevices utils datasets >> methods >> base >> >> other attached packages: >> [1] affy_1.16.0 preprocessCore_1.0.0 affyio_1.6.1 >> Biobase_1.16.1 >> >> >>> From: Benilton Carvalho <bcarvalh at="" jhsph.edu=""> >>> Date: Sat, 8 Dec 2007 00:06:07 -0500 >>> 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 >>> >>> I'd first make sure that you have the latest version (of R and the >>> packages) installed... >>> b >>> >>> On Dec 7, 2007, at 11:59 PM, Loren Engrav wrote: >>> >>>> So I enter >>>> >>>>> GibranGlue70 <- ReadAffy() # to read in 70 .cel files >>>> >>>> And I get this, all in bright red >>>> >>>> Error: cannot allocate vector of size 723.6 Mb >>>> R(22621,0xa000ed88) malloc: *** vm_allocate(size=758743040) failed >>>> (error >>>> code=3) >>>> R(22621,0xa000ed88) malloc: *** error: can't allocate region >>>> R(22621,0xa000ed88) malloc: *** set a breakpoint in szone_error to >>>> debug >>>> R(22621,0xa000ed88) malloc: *** vm_allocate(size=758743040) failed >>>> (error >>>> code=3) >>>> R(22621,0xa000ed88) malloc: *** error: can't allocate region >>>> R(22621,0xa000ed88) malloc: *** set a breakpoint in szone_error to >>>> debug >>>> >>>> I have 2.5 gb DDR SDRAM in the dual G5 Mac >>>> >>>> Is the only answer, buy more RAM? >>>> >>>> [[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 >> >> _______________________________________________ >> 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
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Ok SessionInfo now returns > sessionInfo() R version 2.6.1 (2007-11-26) powerpc-apple-darwin8.10.1 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] tools stats graphics grDevices utils datasets methods base other attached packages: [1] affy_1.16.0 preprocessCore_1.0.0 affyio_1.6.1 Biobase_1.16.1 But I still get > Gibran70 <- ReadAffy() Error: cannot allocate vector of size 723.6 Mb Although not big red messages which is not quite so hostile I guess time to go to bed and in the AM buy some RAM Thank you so much for the help Engrav > From: Benilton Carvalho <bcarvalh at="" jhsph.edu=""> > Date: Sat, 8 Dec 2007 00:23:10 -0500 > 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 > > In that case, assuming that R-2.6.1 behaves just like R-2.6.0-patched > in terms of memory management, you might want to define beforehand > what you're going to be doing and, probably, use functions like > justRMA(). > > b > > On Dec 8, 2007, at 12:13 AM, Loren Engrav wrote: > >> Thank you so much for the prompt help >> >> Having been "scolded" for this before I now use sessionInfo which >> returned >> >>> sessionInfo() >> R version 2.6.0 Patched (2007-11-09 r43408) >> powerpc-apple-darwin8.10.1 >> >> 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] tools stats graphics grDevices utils datasets >> methods >> base >> >> other attached packages: >> [1] affy_1.16.0 preprocessCore_1.0.0 affyio_1.6.1 >> Biobase_1.16.1 >> >> >>> From: Benilton Carvalho <bcarvalh at="" jhsph.edu=""> >>> Date: Sat, 8 Dec 2007 00:06:07 -0500 >>> 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 >>> >>> I'd first make sure that you have the latest version (of R and the >>> packages) installed... >>> b >>> >>> On Dec 7, 2007, at 11:59 PM, Loren Engrav wrote: >>> >>>> So I enter >>>> >>>>> GibranGlue70 <- ReadAffy() # to read in 70 .cel files >>>> >>>> And I get this, all in bright red >>>> >>>> Error: cannot allocate vector of size 723.6 Mb >>>> R(22621,0xa000ed88) malloc: *** vm_allocate(size=758743040) failed >>>> (error >>>> code=3) >>>> R(22621,0xa000ed88) malloc: *** error: can't allocate region >>>> R(22621,0xa000ed88) malloc: *** set a breakpoint in szone_error to >>>> debug >>>> R(22621,0xa000ed88) malloc: *** vm_allocate(size=758743040) failed >>>> (error >>>> code=3) >>>> R(22621,0xa000ed88) malloc: *** error: can't allocate region >>>> R(22621,0xa000ed88) malloc: *** set a breakpoint in szone_error to >>>> debug >>>> >>>> I have 2.5 gb DDR SDRAM in the dual G5 Mac >>>> >>>> Is the only answer, buy more RAM? >>>> >>>> [[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 >> >> _______________________________________________ >> 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
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Thank you all and sorry for the unclear subject I did get down to this in the documentation.......... Depending on the size of your dataset and on the memory available to your system, you might experience errors like ?Cannot allocate vector . . . ?. An obvious option is to increase the memory available to your R process (by adding memory and/or closing external applications2 . An another option is to use the function justRMA. (or explore ulimit) R> eset <- justRMA() This reads the data and performs the ?RMA? way to preprocess them at the C level. One does not need to call ReadAffy, probe level data is never stored in an AffyBatch. rma continues to be the recommended function for computing RMA. So... I tried killing other processes and it went a little further but then failed with same message I then tried > library(affy) > library(hgu133plus2cdf) > GibranGlue81 <- justRMA() #load 81 .cel files And it returned Background correcting Error in density.default(x, kernel = "epanechnikov", n = 2^14) : need at least 2 points to select a bandwidth automatically And most of our previous stuff is gcrma and not sure mixing is a good idea if this is mixing And finally as per the documentation I examined "ulimit", but that might be a little aggressive for me at this point given my knowledge of unix Again > sessionInfo() R version 2.6.1 (2007-11-26) powerpc-apple-darwin8.10.1 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] tools stats graphics grDevices utils datasets methods base other attached packages: [1] hgu133plus2cdf_2.0.0 affy_1.16.0 preprocessCore_1.0.0 affyio_1.6.1 Biobase_1.16.1 > Thank you again for the help Loren Engrav Univ Washington Seattle From: Sean Davis <sdavis2@mail.nih.gov> Date: Sat, 8 Dec 2007 07:49:36 -0500 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 8, 2007 1:00 AM, Loren Engrav <engrav at="" u.washington.edu=""> wrote: > Ok > SessionInfo now returns > >> sessionInfo() > R version 2.6.1 (2007-11-26) > powerpc-apple-darwin8.10.1 > > 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] tools stats graphics grDevices utils datasets methods > base > > other attached packages: > [1] affy_1.16.0 preprocessCore_1.0.0 affyio_1.6.1 > Biobase_1.16.1 > > But I still get >> Gibran70 <- ReadAffy() > Error: cannot allocate vector of size 723.6 Mb > Although not big red messages which is not quite so hostile > > I guess time to go to bed and in the AM buy some RAM > > Thank you so much for the help > > Engrav > > >> From: Benilton Carvalho <bcarvalh at="" jhsph.edu=""> >> Date: Sat, 8 Dec 2007 00:23:10 -0500 >> To: Loren Engrav <engrav at="" u.washington.edu=""> >> Cc: "bioconductor at stat.math.ethz.ch <mailto:bioconductor at="" stat.math.ethz.ch=""> >> " <bioconductor at="" stat.math.ethz.ch=""> >> Subject: Re: [BioC] Wow, what have I done >> >> In that case, assuming that R-2.6.1 behaves just like R-2.6.0-patched >> in terms of memory management, you might want to define beforehand >> what you're going to be doing and, probably, use functions like >> justRMA(). Hi, Loren. I would really consider following the advice that Benilton gave you and use justRMA(). The reason justRMA() was created in the first place was to solve the memory problem that you are describing. I didn't see that you had tried this yet (but I might be mistaken), so I just wanted to remind you to try it. If justRMA() will not work for your particular application for some reason, it is probably worth outlining for us what you want to do, as it may not be necessary to load all the arrays at once to accomplish the task. In the end, you may want to buy RAM for other reasons, but I think a solution might have been proposed already for your current problem. Sean
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Ok But R.app does not show justGCRMA package But via google I find it in gcrma So I do > Gibran81 <- justGCRMA() #81 .cel files And voila I get Computing affinities.Done. Adjusting for optical effect................................................................ ...... ............Done. Adjusting for non-specific binding............................................................... ...... ............Done. Normalizing Calculating Expression > objects() [1] "Gibran81" "affinity.spline.coefs" It did take 25" but then what is 25"? And justGCRMA(..., filenames=character(0), widget=getOption("BioC")$affy$use.widgets, compress=getOption("BioC")$affy$compress.cel, celfile.path=getwd(), sampleNames=NULL, phenoData=NULL, description=NULL, notes="", normalize=TRUE, bgversion=2, affinity.info=NULL, type=c("fullmodel","affinities","mm","constant"), k=6*fast+0.5*(1-fast), stretch=1.15*fast+1*(1-fast), correction=1, rho=0.7, optical.correct=TRUE, verbose=TRUE, fast=TRUE, minimum=1, optimize.by = c("speed","memory"), cdfname = NULL, read.verbose = FALSE) Is rather scary, especially k But assuming "default" is Ok, it is finished, I have gcrma of 81 .cel files, thank you very much Also please see new thread in R-Mac on R.app ?bug, thank you Loren Engrav Univ Washington Seattle From: Sean Davis <sdavis2@mail.nih.gov> Date: Sat, 8 Dec 2007 13:26:23 -0500 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 8, 2007 11:36 AM, Loren Engrav <engrav at="" u.washington.edu=""> wrote: > > And most of our previous stuff is gcrma and not sure mixing is a good idea > if this is mixing You might look at justGCRMA(), the GCRMA. Sean
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Well I guess not done So I have the justGCRMA object "Gibran81" And try > QCReport(Gibran81,file="AffyQCReportGibran81.pdf") And get back Error in box(...) : invalid 'which' specification In addition: Warning messages: 1: In plot.window(...) : "which" is not a graphical parameter 2: In plot.xy(xy, type, ...) : "which" is not a graphical parameter 3: In axis(side = side, at = at, labels = labels, ...) : "which" is not a graphical parameter 4: In axis(side = side, at = at, labels = labels, ...) : "which" is not a graphical parameter Maybe I am out of my league Funny, a few months ago I did 60 chips and mixed linear regression worked just fine Loren Engrav Univ Washington Seattl > From: Loren Engrav <engrav at="" u.washington.edu=""> > Date: Sat, 08 Dec 2007 15:19:01 -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 > But R.app does not show justGCRMA package > But via google I find it in gcrma > So I do >> Gibran81 <- justGCRMA() #81 .cel files > And voila I get > > Computing affinities.Done. > Adjusting for optical > effect.............................................................. ........ > ............Done. > Adjusting for non-specific > binding............................................................. ........ > ............Done. > Normalizing > Calculating Expression >> objects() > [1] "Gibran81" "affinity.spline.coefs" > > It did take 25" but then what is 25"? > And > justGCRMA(..., filenames=character(0), > widget=getOption("BioC")$affy$use.widgets, > compress=getOption("BioC")$affy$compress.cel, > celfile.path=getwd(), > sampleNames=NULL, > phenoData=NULL, > description=NULL, > notes="", > normalize=TRUE, > bgversion=2, affinity.info=NULL, > type=c("fullmodel","affinities","mm","constant"), > k=6*fast+0.5*(1-fast), stretch=1.15*fast+1*(1-fast), > correction=1, rho=0.7, optical.correct=TRUE, > verbose=TRUE, fast=TRUE, minimum=1, optimize.by = c("speed","memory"), > cdfname = NULL, read.verbose = FALSE) > Is rather scary, especially k > > But assuming "default" is Ok, it is finished, I have gcrma of 81 .cel files, > thank you very much > > Also please see new thread in R-Mac on R.app ?bug, thank you > > Loren Engrav > Univ Washington > Seattle > > > > > > From: Sean Davis <sdavis2 at="" mail.nih.gov=""> > Date: Sat, 8 Dec 2007 13:26:23 -0500 > 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 8, 2007 11:36 AM, Loren Engrav <engrav at="" u.washington.edu=""> wrote: >> >> And most of our previous stuff is gcrma and not sure mixing is a good idea >> if this is mixing > > You might look at justGCRMA(), the GCRMA. > > Sean > > _______________________________________________ > 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
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I think you are correct thank you justGCRMA "solved" the memory problem but now a "class" problem to solve or maybe just buy the RAM From: Sean Davis <sdavis2@mail.nih.gov> Date: Sun, 9 Dec 2007 08:09:41 -0500 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 8, 2007 11:52 PM, Loren Engrav <engrav at="" u.washington.edu=""> wrote: > Well I guess not done > > So I have the justGCRMA object "Gibran81" > > And try > >> QCReport(Gibran81,file="AffyQCReportGibran81.pdf") You might check the help for QCReport(). Does QCReport take for input an ExpressionSet? What is the class of Gibran81? Is it a class that would be expected to work with QCReport() given what the help file says? Sean
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So ReadAffy for 81 .cel files failed memory (I had 2.5gig) justGCRMA loaded 81 but created a class problem for other processes Was out shopping and The Mac Store had RAM sale, 25% off So put in 4gig, now totaling 6gig Video editing and other RAM hungry apps are now in heaven But I try ReadAffy() for 81 .cel files and.... Same thing, cannot allocate vector I guess hitting the 32bit limit at 4gig I guess 1) reduce chips 2) study piecemeal 3) try 64bit R MacOS 10.4.11 -- Loren Engrav Univ Washington Seattle > From: Loren Engrav <engrav at="" u.washington.edu=""> > Date: Sun, 09 Dec 2007 08:01:42 -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 > > I think you are correct thank you > justGCRMA "solved" the memory problem but now a "class" problem to solve > or maybe just buy the RAM > > > > > From: Sean Davis <sdavis2 at="" mail.nih.gov=""> > Date: Sun, 9 Dec 2007 08:09:41 -0500 > 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 8, 2007 11:52 PM, Loren Engrav <engrav at="" u.washington.edu=""> wrote: >> Well I guess not done >> >> So I have the justGCRMA object "Gibran81" >> >> And try >> >>> QCReport(Gibran81,file="AffyQCReportGibran81.pdf") > > You might check the help for QCReport(). Does QCReport take for input an > ExpressionSet? What is the class of Gibran81? Is it a class that would be > expected to work with QCReport() given what the help file says? > > Sean > > >
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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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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 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). > > _______________________________________________ > 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
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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). >> >> _______________________________________________ >> 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 > > _______________________________________________ > 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
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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 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? Thank you -- Loren Engrav Univ Washington Seattle > 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). >>> >>> _______________________________________________ >>> 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 >> >> _______________________________________________ >> 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 >
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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). >>>> >>>> _______________________________________________ >>>> 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 >>> >>> _______________________________________________ >>> 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 >> > > _______________________________________________ > 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
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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). >>>>> >>>>> _______________________________________________ >>>>> 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 >>>> >>>> _______________________________________________ >>>> 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 >>> >> >> _______________________________________________ >> 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 >
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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). >>>>>> >>>>>> _______________________________________________ >>>>>> 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 >>>>> >>>>> _______________________________________________ >>>>> 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 >>>> >>> >>> _______________________________________________ >>> 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 >> > > _______________________________________________ > 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
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Hi Loren, Loren Engrav wrote: [...] > 1) does the biocLite method of packages work with R64bit Like for the CRAN packages, Bioconductor universal binary packages work for the i386 and ppc archs only. So if you start R in 64-bit mode (with --arch=x86_64 or --arch=ppc64), you will be able to install the universal binary with biocLite() but you won't be able to load it: > library(Biostrings) Error: package 'Biostrings' is not installed for 'arch=x86_64' So what you need to do is install from source. Either with: options(pkgType="source") or with biocLite("Biostrings", type="source") Cheers, H.
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On Dec 11, 2007, at 11:40 AM, Herve Pages wrote: > Hi Loren, > > Loren Engrav wrote: > [...] >> 1) does the biocLite method of packages work with R64bit > > Like for the CRAN packages, Bioconductor universal binary packages > work for > the i386 and ppc archs only. So if you start R in 64-bit mode (with > --arch=x86_64 > or --arch=ppc64), you will be able to install the universal binary > with biocLite() > but you won't be able to load it: So this might be a bit confusing to Loren: when you install a a package on a mac there are two options: 1) Install a binary package. This is nice and quick. All that happens is that a zip file gets downloaded and unpackaged and mostly everything just works. This is probably how most people install packages for the mac. 2) install a source package. Here you just download the source code and then it needs to be compiled (this happens automatically). The drawback to this method is a) It takes longer to compiler than to unzip - this is not a bit issue on a fast machine and b) that you need a set of tools installed. >> library(Biostrings) > Error: package 'Biostrings' is not installed for 'arch=x86_64' > > So what you need to do is install from source. Either with: > > options(pkgType="source") > > or with > > biocLite("Biostrings", type="source") This is how you change your option. If you type getOption("pkgType") you see what your default option is - you probably have "mac.binary" Kasper > Cheers, > H. > > _______________________________________________ > 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
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Thank you I tried and failed, you are right, I am confused Am using R64 2.3.1 and the monster pack since it is available and I have not installed Leopard as yet But R64 2.3.1 monster does not include affyQCReport and I have failed at loading it into R64 2.3.1 inspite of your trying to help By the way, if I get Leopard up this weekend, where is an R64 for Leopard with affyQCReport and affy? Thank you -- Loren Engrav Univ Washington Seattle > From: Kasper Daniel Hansen <khansen at="" stat.berkeley.edu=""> > Date: Tue, 11 Dec 2007 12:19:35 -0800 > To: Herve Pages <hpages at="" fhcrc.org=""> > Cc: Loren Engrav <engrav at="" u.washington.edu="">, "bioconductor at stat.math.ethz.ch" > <bioconductor at="" stat.math.ethz.ch=""> > Subject: Re: [BioC] Wow, what have I done > > On Dec 11, 2007, at 11:40 AM, Herve Pages wrote: > >> Hi Loren, >> >> Loren Engrav wrote: >> [...] >>> 1) does the biocLite method of packages work with R64bit >> >> Like for the CRAN packages, Bioconductor universal binary packages >> work for >> the i386 and ppc archs only. So if you start R in 64-bit mode (with >> --arch=x86_64 >> or --arch=ppc64), you will be able to install the universal binary >> with biocLite() >> but you won't be able to load it: > > So this might be a bit confusing to Loren: when you install a a > package on a mac there are two options: > 1) Install a binary package. This is nice and quick. All that happens > is that a zip file gets downloaded and unpackaged and mostly > everything just works. This is probably how most people install > packages for the mac. > 2) install a source package. Here you just download the source code > and then it needs to be compiled (this happens automatically). The > drawback to this method is a) It takes longer to compiler than to > unzip - this is not a bit issue on a fast machine and b) that you > need a set of tools installed. > >>> library(Biostrings) >> Error: package 'Biostrings' is not installed for 'arch=x86_64' >> >> So what you need to do is install from source. Either with: >> >> options(pkgType="source") >> >> or with >> >> biocLite("Biostrings", type="source") > > This is how you change your option. If you type > getOption("pkgType") > you see what your default option is - you probably have "mac.binary" > > Kasper > > >> Cheers, >> H. >> >> _______________________________________________ >> 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 >
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I can't speak to specifics of the various mac builds and installing R/BioC. But keep in mind that there is a new release of R every six months or so and a corresponding release of BioConductor at about the same time. Given that the current release of R is the 2.6.X series (and corresponding BioC release is 2.1) that puts your 2.3.1 (BioC 1.8) back about 2 years ago. And in a fairly fast moving dynamic project like BioC 2 years is a long time. Additionally, unlike your garden variety package on CRAN, there is a huge level of interdependence between packages meaning you'd have to make sure that all those packages work with whatever version of affyQCreport you are trying to get working. All that makes a huge support headache and thus there is little interest for people to put the effort into helping you with trying to get things working on an out of date version of the software, ergo the refrain for you to attempt to get the most recent release version of R and BioC going. Best, Ben On Tue, 2007-12-11 at 16:02 -0800, Loren Engrav wrote: > Thank you > I tried and failed, you are right, I am confused > Am using R64 2.3.1 and the monster pack since it is available and I have not > installed Leopard as yet > But R64 2.3.1 monster does not include affyQCReport and I have failed at > loading it into R64 2.3.1 inspite of your trying to help > > By the way, if I get Leopard up this weekend, where is an R64 for Leopard > with affyQCReport and affy? > > Thank you >
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That is so very true and you are so correct And when I used to code stuff it irritated me when people used old versions Nevermind that Balmer wishes to preserve legacy to 1990 But I need (or want) a 64bit version or R and affyQCReport And on the 64 bit page (http://r.research.att.com/exp/) I find two 2.5.0 for Intel and 2.3.1 for PPC I do not have Intel so am trying to use 2.3.1 People have been trying to help and I am grateful Maybe the answer is 2.3.1 is dead and I need to buy a new Intel Mac computer But it is tempting to think I can load affyQCReport into 2.3.1 and solve the problem fast But maybe I just cannot get there from here -- Loren Engrav Univ Washington Seattle > From: Ben Bolstad <bmb at="" bmbolstad.com=""> > Date: Tue, 11 Dec 2007 17:48:17 -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 > > I can't speak to specifics of the various mac builds and installing > R/BioC. But keep in mind that there is a new release of R every six > months or so and a corresponding release of BioConductor at about the > same time. Given that the current release of R is the 2.6.X series (and > corresponding BioC release is 2.1) that puts your 2.3.1 (BioC 1.8) back > about 2 years ago. And in a fairly fast moving dynamic project like BioC > 2 years is a long time. Additionally, unlike your garden variety package > on CRAN, there is a huge level of interdependence between packages > meaning you'd have to make sure that all those packages work with > whatever version of affyQCreport you are trying to get working. > > All that makes a huge support headache and thus there is little interest > for people to put the effort into helping you with trying to get things > working on an out of date version of the software, ergo the refrain for > you to attempt to get the most recent release version of R and BioC > going. > > Best, > > Ben > > > > On Tue, 2007-12-11 at 16:02 -0800, Loren Engrav wrote: >> Thank you >> I tried and failed, you are right, I am confused >> Am using R64 2.3.1 and the monster pack since it is available and I have not >> installed Leopard as yet >> But R64 2.3.1 monster does not include affyQCReport and I have failed at >> loading it into R64 2.3.1 inspite of your trying to help >> >> By the way, if I get Leopard up this weekend, where is an R64 for Leopard >> with affyQCReport and affy? >> >> Thank you >> >
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If we had the revenue streams of Microsoft we could put the energy into support, but we don't. Here is one more alternative suggestion. Why don't you put the effort into figuring out the underlying functions being used by affyQCreport? Sure you won't get the nicely formatted report (and people can feel free to correct me if that is not what it does), but you should be able to get access to all the underlying QC statistics. For instance AffyRNAdeg(), hist() and boxplot() from affy qc() from simpleaffy : Best, Ben On Tue, 2007-12-11 at 18:09 -0800, Loren Engrav wrote: > That is so very true and you are so correct > And when I used to code stuff it irritated me when people used old > versions > Nevermind that Balmer wishes to preserve legacy to 1990 > > But I need (or want) a 64bit version or R and affyQCReport > > And on the 64 bit page (http://r.research.att.com/exp/) I find two > 2.5.0 for Intel and 2.3.1 for PPC > > I do not have Intel so am trying to use 2.3.1 > > People have been trying to help and I am grateful > > Maybe the answer is > 2.3.1 is dead and I need to buy a new Intel Mac computer > > But it is tempting to think I can load affyQCReport into 2.3.1 and > solve the > problem fast > > But maybe I just cannot get there from here > > -- > Loren Engrav > Univ Washington > Seattle > > > From: Ben Bolstad <bmb at="" bmbolstad.com=""> > > Date: Tue, 11 Dec 2007 17:48:17 -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 > > > > I can't speak to specifics of the various mac builds and installing > > R/BioC. But keep in mind that there is a new release of R every six > > months or so and a corresponding release of BioConductor at about > the > > same time. Given that the current release of R is the 2.6.X series > (and > > corresponding BioC release is 2.1) that puts your 2.3.1 (BioC 1.8) > back > > about 2 years ago. And in a fairly fast moving dynamic project like > BioC > > 2 years is a long time. Additionally, unlike your garden variety > package > > on CRAN, there is a huge level of interdependence between packages > > meaning you'd have to make sure that all those packages work with > > whatever version of affyQCreport you are trying to get working. > > > > All that makes a huge support headache and thus there is little > interest > > for people to put the effort into helping you with trying to get > things > > working on an out of date version of the software, ergo the refrain > for > > you to attempt to get the most recent release version of R and BioC > > going. > > > > Best, > > > > Ben > > > > > > > > On Tue, 2007-12-11 at 16:02 -0800, Loren Engrav wrote: > >> Thank you > >> I tried and failed, you are right, I am confused > >> Am using R64 2.3.1 and the monster pack since it is available and I > have not > >> installed Leopard as yet > >> But R64 2.3.1 monster does not include affyQCReport and I have > failed at > >> loading it into R64 2.3.1 inspite of your trying to help > >> > >> By the way, if I get Leopard up this weekend, where is an R64 for > Leopard > >> with affyQCReport and affy? > >> > >> Thank you > >> > > > > _______________________________________________ > 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 >
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Again, you are correct, true, on track, thank you My effort to use 2.3.1 is not working, I have no 2.3.1 64bit R and affyQCReport, and cannot find a more recent version for PPC 64bit R and Bio But me doing affyRNAdeg(), hist(), boxplot(), etc? That is rather like me playing for the Seahawks as a running back. Quite out of my league. In fact, that may be the answer. I may be out of my league. But as has been said "It ain't over till it's over" Maybe if I get up Leopard this weekend And a Leopard 64bit PPC disk image comes up with affyQCReport I am golden Again thank you for commenting, I am grateful -- Loren Engrav Univ Washington Seattle > From: Ben Bolstad <bmb at="" bmbolstad.com=""> > Date: Tue, 11 Dec 2007 18:42:13 -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 > > If we had the revenue streams of Microsoft we could put the energy into > support, but we don't. > > Here is one more alternative suggestion. Why don't you put the effort > into figuring out the underlying functions being used by affyQCreport? > Sure you won't get the nicely formatted report (and people can feel free > to correct me if that is not what it does), but you should be able to > get access to all the underlying QC statistics. > > For instance > > AffyRNAdeg(), hist() and boxplot() from affy > qc() from simpleaffy > : > > Best, > > Ben > > On Tue, 2007-12-11 at 18:09 -0800, Loren Engrav wrote: >> That is so very true and you are so correct >> And when I used to code stuff it irritated me when people used old >> versions >> Nevermind that Balmer wishes to preserve legacy to 1990 >> >> But I need (or want) a 64bit version or R and affyQCReport >> >> And on the 64 bit page (http://r.research.att.com/exp/) I find two >> 2.5.0 for Intel and 2.3.1 for PPC >> >> I do not have Intel so am trying to use 2.3.1 >> >> People have been trying to help and I am grateful >> >> Maybe the answer is >> 2.3.1 is dead and I need to buy a new Intel Mac computer >> >> But it is tempting to think I can load affyQCReport into 2.3.1 and >> solve the >> problem fast >> >> But maybe I just cannot get there from here >> >> -- >> Loren Engrav >> Univ Washington >> Seattle >> >>> From: Ben Bolstad <bmb at="" bmbolstad.com=""> >>> Date: Tue, 11 Dec 2007 17:48:17 -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 >>> >>> I can't speak to specifics of the various mac builds and installing >>> R/BioC. But keep in mind that there is a new release of R every six >>> months or so and a corresponding release of BioConductor at about >> the >>> same time. Given that the current release of R is the 2.6.X series >> (and >>> corresponding BioC release is 2.1) that puts your 2.3.1 (BioC 1.8) >> back >>> about 2 years ago. And in a fairly fast moving dynamic project like >> BioC >>> 2 years is a long time. Additionally, unlike your garden variety >> package >>> on CRAN, there is a huge level of interdependence between packages >>> meaning you'd have to make sure that all those packages work with >>> whatever version of affyQCreport you are trying to get working. >>> >>> All that makes a huge support headache and thus there is little >> interest >>> for people to put the effort into helping you with trying to get >> things >>> working on an out of date version of the software, ergo the refrain >> for >>> you to attempt to get the most recent release version of R and BioC >>> going. >>> >>> Best, >>> >>> Ben >>> >>> >>> >>> On Tue, 2007-12-11 at 16:02 -0800, Loren Engrav wrote: >>>> Thank you >>>> I tried and failed, you are right, I am confused >>>> Am using R64 2.3.1 and the monster pack since it is available and I >> have not >>>> installed Leopard as yet >>>> But R64 2.3.1 monster does not include affyQCReport and I have >> failed at >>>> loading it into R64 2.3.1 inspite of your trying to help >>>> >>>> By the way, if I get Leopard up this weekend, where is an R64 for >> Leopard >>>> with affyQCReport and affy? >>>> >>>> Thank you >>>> >>> >> >> _______________________________________________ >> 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 >> >
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On Dec 11, 2007, at 6:09 PM, Loren Engrav wrote: > And on the 64 bit page (http://r.research.att.com/exp/) I find two > 2.5.0 for Intel and 2.3.1 for PPC > > I do not have Intel so am trying to use 2.3.1 > > People have been trying to help and I am grateful > > Maybe the answer is > 2.3.1 is dead and I need to buy a new Intel Mac computer > > But it is tempting to think I can load affyQCReport into 2.3.1 and > solve the > problem fast > > But maybe I just cannot get there from here I think I have described quite carefully how you get the current R/ Bioconductor running as 64bit on your system. Why don't you follow that advice and accept that it actually might be true and that there are no easy shortcuts. It is possible to hack together a version of AffyQCReport to use with R-2.3 as Ben suggested, and you will have to decide whether it is worth it. My guess is that AffyQCReport did not exist back in the R-2.3 days and hence is not included in your monsterpack. Kasper
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Thank you for helping Ok, I will bag 2.3.1 monster and do Leopard this weekend and your method thereafter as I have your emails Again Thank you much Am still working for R64 and ReadAffy and affyQCReport and 81 .cel files -- Loren Engrav Univ Washington Seattle > From: Kasper Daniel Hansen <khansen at="" stat.berkeley.edu=""> > Date: Tue, 11 Dec 2007 19:06:01 -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 11, 2007, at 6:09 PM, Loren Engrav wrote: > >> And on the 64 bit page (http://r.research.att.com/exp/) I find two >> 2.5.0 for Intel and 2.3.1 for PPC >> >> I do not have Intel so am trying to use 2.3.1 >> >> People have been trying to help and I am grateful >> >> Maybe the answer is >> 2.3.1 is dead and I need to buy a new Intel Mac computer >> >> But it is tempting to think I can load affyQCReport into 2.3.1 and >> solve the >> problem fast >> >> But maybe I just cannot get there from here > > I think I have described quite carefully how you get the current R/ > Bioconductor running as 64bit on your system. Why don't you follow > that advice and accept that it actually might be true and that there > are no easy shortcuts. > > It is possible to hack together a version of AffyQCReport to use with > R-2.3 as Ben suggested, and you will have to decide whether it is > worth it. My guess is that AffyQCReport did not exist back in the > R-2.3 days and hence is not included in your monsterpack. > > Kasper
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Dear Loren As an alternative you could try package "xps", which I have developed on my Titanium PowerBook and which works with R-2.6.1. It is able to handle your 70 HGU133p2 CEL-files with even 1GB RAM only. However, it supplies RMA and MAS5 only but not GCRMA. Regards Christian _._._._._._._._._._._._._._._._ C.h.i.s.t.i.a.n S.t.r.a.t.o.w.a V.i.e.n.n.a A.u.s.t.r.i.a e.m.a.i.l: cstrato at aon.at _._._._._._._._._._._._._._._._ Loren Engrav wrote: > Thank you all and sorry for the unclear subject > > I did get down to this in the documentation.......... > > Depending on the size of your dataset and on the memory available to your > system, you might experience errors like ?Cannot allocate vector . . . ?. An > obvious option is to increase the memory available to your R process (by > adding memory and/or closing external applications2 . An another option is > to use the function justRMA. (or explore ulimit) > R> eset <- justRMA() > This reads the data and performs the ?RMA? way to preprocess them at the C > level. One does not need to call ReadAffy, probe level data is never stored > in an AffyBatch. rma continues to be the recommended function for computing > RMA. > > So... > I tried killing other processes and it went a little further but then failed > with same message > > I then tried > >> library(affy) >> library(hgu133plus2cdf) >> GibranGlue81 <- justRMA() #load 81 .cel files >> > > And it returned > Background correcting > Error in density.default(x, kernel = "epanechnikov", n = 2^14) : > need at least 2 points to select a bandwidth automatically > > And most of our previous stuff is gcrma and not sure mixing is a good idea > if this is mixing > > And finally as per the documentation I examined "ulimit", but that might be > a little aggressive for me at this point given my knowledge of unix > > Again > >> sessionInfo() >> > R version 2.6.1 (2007-11-26) > powerpc-apple-darwin8.10.1 > > 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] tools stats graphics grDevices utils datasets methods > base > > other attached packages: > [1] hgu133plus2cdf_2.0.0 affy_1.16.0 preprocessCore_1.0.0 > affyio_1.6.1 Biobase_1.16.1 > > > Thank you again for the help > > Loren Engrav > Univ Washington > Seattle > > > > > > > From: Sean Davis <sdavis2 at="" mail.nih.gov=""> > Date: Sat, 8 Dec 2007 07:49:36 -0500 > 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 8, 2007 1:00 AM, Loren Engrav <engrav at="" u.washington.edu=""> wrote: > >> Ok >> SessionInfo now returns >> >> >>> sessionInfo() >>> >> R version 2.6.1 (2007-11-26) >> powerpc-apple-darwin8.10.1 >> >> 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] tools stats graphics grDevices utils datasets methods >> base >> >> other attached packages: >> [1] affy_1.16.0 preprocessCore_1.0.0 affyio_1.6.1 >> Biobase_1.16.1 >> >> But I still get >> >>> Gibran70 <- ReadAffy() >>> >> Error: cannot allocate vector of size 723.6 Mb >> Although not big red messages which is not quite so hostile >> >> I guess time to go to bed and in the AM buy some RAM >> >> Thank you so much for the help >> >> Engrav >> >> >> >>> From: Benilton Carvalho <bcarvalh at="" jhsph.edu=""> >>> Date: Sat, 8 Dec 2007 00:23:10 -0500 >>> To: Loren Engrav <engrav at="" u.washington.edu=""> >>> Cc: "bioconductor at stat.math.ethz.ch <mailto:bioconductor at="" stat.math.ethz.ch=""> >>> " <bioconductor at="" stat.math.ethz.ch=""> >>> Subject: Re: [BioC] Wow, what have I done >>> >>> In that case, assuming that R-2.6.1 behaves just like R-2.6.0-patched >>> in terms of memory management, you might want to define beforehand >>> what you're going to be doing and, probably, use functions like >>> justRMA(). >>> > > > Hi, Loren. I would really consider following the advice that Benilton gave > you and use justRMA(). The reason justRMA() was created in the first place > was to solve the memory problem that you are describing. I didn't see that > you had tried this yet (but I might be mistaken), so I just wanted to remind > you to try it. If justRMA() will not work for your particular application > for some reason, it is probably worth outlining for us what you want to do, > as it may not be necessary to load all the arrays at once to accomplish the > task. > > In the end, you may want to buy RAM for other reasons, but I think a > solution might have been proposed already for your current problem. > > Sean > > _______________________________________________ > 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 > > >
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