[BioC] Problem with Installing affylmGUI on MAC OS X

Fri Jul 8 23:24:27 CEST 2005

Hi
affylmGUI is available in binary form and can be installed from  
inside R.app using the internal package installer.
.tgz is the file extension used on R for OS X of binary packages.

Form R.app menus, Packages & Data -> Package Installer, don't use  
"bioconductor" (there is a bug in R.app 1.11 fixed in the forthcoming  
version 1.12, it is the bug you are experimenting with the pull down  
menu: instead of the package it retrieves the list of packages twice)  
but choose "other repository" and specify "binary format" and the  
bioc url, http://www.bioconductor.org, "get the list", click on  
affylmGUI and install it.

In the next coming days the R.app (1.12) + R 2.1.1 will be available  
on CRAN (under bin/macosx)

Hope it helps.

stefano
p.s. if you want to install package from source you need 1) read the  
R for Mac OS X Faq and 2) specify options(pkgType="source") before  
using install.packages()

p.s. the complete list of BioC packages for OS X at: http:// 
www.bioconductor.org/bin/macosx/2.1/PACKAGES
On 08/lug/05, at 21:47, Richard Friedman wrote:

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