[BioC] Problem with Installing affylmGUI on MAC OS X

[Richard Friedman]

Jim,

	Thanks. I am working on something else now and will see
if they reply by Monday. There were some special problems
with compiling R packages on Mac OS X last time I tried,
but these difficulties might have been worked out by now.
Also, the command line Limma manual is now more throughly
annotated than the last time I looked at it, and I now know
a little about linear models and statistics in R (last time around I 
used
R for normalization and SAS for statistics) so I may try the command
line version first.

	I have printed out your methods comparison paper and look
forward to reading it.

Best wishes,
Rich

On Jul 8, 2005, at 3:40 PM, James MacDonald wrote:

> Hi Rich,
>
> I think there is a binary version available, but it looks like the link
> is broken. Since it is now Saturday in Oz I think you may be out of 
> luck
> unless Gordon Smyth or James Wettenhall happen to be working this
> weekend.
>
> I don't use MacOS, but from reading the lists, it appears all you have
> to do is install the Developer tools and then you can install using R
> CMD INSTALL just like on other *nix boxes. Might be worth it to try 
> that
> route.
>
> Best,
>
> Jim
>
>
>
>>>> Richard Friedman <friedman at cancercenter.columbia.edu> 7/8/2005
> 2:21:20 PM >>>
> Dear Jim and Everybody,
>
> 	As best I can see the version of affylmGU that I just downloaded
> is in
> source rather
> than binary form.
> 	 Am I correct in this?
> 	If  so, is a binary version for Mac OS X available?
>
> Thanks and best wishes,
> Rich
>
> On Jul 8, 2005, at 12:29 PM, James W. MacDonald wrote:
>
>> Richard Friedman wrote:
>>> Dear Bioconductoir List,
>>> 	I am having a problem installing affylmGUI in R 1.11 for Mac OSX
> (R
>>> Framework 2.1)
>>> under mac OS X Version 10.3.9.
>>>> .libPaths()
>>> [1] "/Library/Frameworks/R.framework/Resources/library"
>>>>
>>> install.packages("affylmGUI",contriburl="http://bioinf.wehi.edu.au/
>
>>> affylmGUI",
> lib="/Library/Frameworks/R.framework/Resources/library")
>>> trying URL
> 'http://bioinf.wehi.edu.au/affylmGUI/affylmGUI_1.3.1.tgz'
>>> Error in download.file(url, destfile, method, mode = "wb") :
>>> 	cannot open URL
>>> 'http://bioinf.wehi.edu.au/affylmGUI/affylmGUI_1.3.1.tgz'
>>> In addition: Warning message:
>>> cannot open: HTTP status was '404 Not Found'
>>
>> This error is probably due to the fact that the correct url is
>>
>> http://bioinf.wehi.edu.au/affylmGUI/affylmGUI_1.3.1.tar.gz
>>
>> Note that it is a .tar.gz, not .tgz file. I have no idea how to fix
>> this from within R, but you could always download by hand and
> install.
>>
>> HTH,
>>
>> Jim
>>
>>
>>>>
>>> Does this error message mean that the problem is with the
> remote-site
>>>  or with my configuration?
>>> here is what happens when I try the install.packages pulldown:
>>> trying URL 'http://www.bioconductor.org/bin/macosx/2.1/PACKAGES'
>>> Content type 'text/plain; charset=ISO-8859-1' length 11959 bytes
>>> opened URL
>>> ==================================================
>>> downloaded 11Kb
>>> I would appreciate any suggestions.
>>> Thanksand 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
>>> _______________________________________________
>>> Bioconductor mailing list
>>> Bioconductor at stat.math.ethz.ch
>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>
>>
>> -- 
>> James W. MacDonald
>> Affymetrix and cDNA Microarray Core
>> University of Michigan Cancer Center
>> 1500 E. Medical Center Drive
>> 7410 CCGC
>> Ann Arbor MI 48109
>> 734-647-5623
>>
> ------------------------------------------------------------
> 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
>
>
>
> **********************************************************
> 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