[BioC] error message with GCRMA

[James MacDonald]

Rich,

That most certainly is at least a major part of the problem. R is now
at version 2.1.1, so the version you are running is dirt-old and not
compatible with anything (don't you love how time flies?). Try upgrading
to R-2.1.1 and running getBioC().

You may also need the developer tools installed (not sure about that
one, but I believe you need this in order to compile anything that has C
or Fortran code).

Best,

Jim



>>> Richard Friedman <friedman at cancercenter.columbia.edu> 6/27/2005
2:11:02 PM >>>
Jim,

	Is tried downloading the affy bundle and it said that I needed
R greater than 2.0 (I am running 1.9.0) Can that be part of my
problem?

Thanks and best wishes,
Rich

On Jun 27, 2005, at 2:03 PM, Richard Friedman wrote:

> Jim,
>
> 	Thanks as always for your prompt reply.
> I tried it, but it didn't work.
>
> Here is a record of the session.
>
> Best wishes,
> Rich
> 	
>
> library(reposTools)
>> install.packages2("mgu74av2probe")
> Warning message:
> cannot open: HTTP status was `403 Forbidden'
> Note: http://www.bioconductor.org/repository/devel/package/Win32
does
> not seem to have a valid repository, skipping
> Note: You did not specify a download type.  Using a default value
of:
> Source
> This will be fine for almost all users
>
> Error in if ((is.null(deps)) || (length(deps) == 0) || (deps == ""))
> return(NULL) :
> 	missing value where TRUE/FALSE needed
>> ls()
> [1] "Data"                  "affinity.spline.coefs" "last.warning"
>      "mgu74av2cdf"
>> ls(packages:mgu74av2probe)
> Error in try(name) : Object "mgu74av2probe" not found
> Error in as.environment(pos) : no item called
"packages:mgu74av2probe"
> in the search list
>
> On Jun 27, 2005, at 1:17 PM, James MacDonald wrote:
>
>> Hi Rich,
>>
>> The package is supposed to get downloaded and installed for you,
but
>> evidently there is some more work to be done there. What you need
is
>> the
>> mgu74av2probe package, which is different from the mgu74av2
package.
>> For
>> now you can install by hand and go from there. I would recommend
using
>> reposTools:
>>
>> library(reposTools)
>> install.packages2("mgu74av2probe")
>>
>> Should get you going.
>>
>> Best,
>>
>> Jim
>>
>>
>>
>>>>> Richard Friedman <friedman at cancercenter.columbia.edu> 6/27/2005
>> 12:53:16 PM >>>
>> Dear Bioconductor list,
>>
>> 	I am returning to using bioconductor after
>> a long break and wish to use gcrma. I
>> get the error message
>>   eset<-gcrma(Data)
>> Computing affinitiesError in library(probepackagename,
character.only 
>> =
>>
>> TRUE) :
>> 	There is no package called 'mgu74av2probe'
>>
>> I have previously tried library(mgu74av2)
>>
>> How can I load this library?
>> I have it installed.
>>
>> I am running under Mac OS X.
>>
>> Thanks and best wishes,
>> Rich
>> ------------------------------------------------------------
>> Richard A. Friedman, PhD
>> Associate Research Scientist
>> Herbert Irving Comprehensive Cancer Center
>> Oncoinformatics Core
>> Lecturer
>> Department of Biomedical Informatics
>> Box 95, Room 130BB or P&S 1-420C
>> Columbia University Medical Center
>> 630 W. 168th St.
>> New York, NY 10032
>> (212)305-6901 (5-6901) (voice)
>> friedman at cancercenter.columbia.edu 
>> http://cancercenter.columbia.edu/~friedman/ 
>>
>> " I know what is going to happen next in 'Middlemarch'.
>> Mr. Featherstone left Fred his money,
>> and the lady who wants his money is going to tell everybody
>> that Fred gambles and it is going to be in all the papers in
>> Middlemarch."
>> Rose Friedman, age 8
>>
>> 	[[alternative text/enriched version deleted]]
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor at stat.math.ethz.ch 
>> https://stat.ethz.ch/mailman/listinfo/bioconductor 
>>
>>
>> **********************************************************
>> Electronic Mail is not secure, may not be read every day, and
should
>> not be used for urgent or sensitive issues.
>>
> ------------------------------------------------------------
> Richard A. Friedman, PhD
> Associate Research Scientist
> Herbert Irving Comprehensive Cancer Center
> Oncoinformatics Core
> Lecturer
> Department of Biomedical Informatics
> Box 95, Room 130BB or P&S 1-420C
> Columbia University Medical Center
> 630 W. 168th St.
> New York, NY 10032
> (212)305-6901 (5-6901) (voice)
> friedman at cancercenter.columbia.edu 
> http://cancercenter.columbia.edu/~friedman/ 
>
> " I know what is going to happen next in 'Middlemarch'.
> Mr. Featherstone left Fred his money,
> and the lady who wants his money is going to tell everybody
> that Fred gambles and it is going to be in all the papers in
> Middlemarch."
> Rose Friedman, age 8
>
>
> 	[[alternative text/enriched version deleted]]
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch 
> https://stat.ethz.ch/mailman/listinfo/bioconductor 
>
------------------------------------------------------------
Richard A. Friedman, PhD
Associate Research Scientist
Herbert Irving Comprehensive Cancer Center
Oncoinformatics Core
Lecturer
Department of Biomedical Informatics
Box 95, Room 130BB or P&S 1-420C
Columbia University Medical Center
630 W. 168th St.
New York, NY 10032
(212)305-6901 (5-6901) (voice)
friedman at cancercenter.columbia.edu 
http://cancercenter.columbia.edu/~friedman/ 

" I know what is going to happen next in 'Middlemarch'.
Mr. Featherstone left Fred his money,
and the lady who wants his money is going to tell everybody
that Fred gambles and it is going to be in all the papers in 
Middlemarch."
Rose Friedman, age 8

_______________________________________________
Bioconductor mailing list
Bioconductor at stat.math.ethz.ch 
https://stat.ethz.ch/mailman/listinfo/bioconductor


**********************************************************
Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.