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.
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
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
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
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
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
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
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
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
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
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
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
>
>
>
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).
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
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
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
>
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
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
>
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
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.
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
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
>
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
>
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
>>
>
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
>
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
>>
>
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
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
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
>
>
>
