[BioC] recipe for installing and using Bioconductor with Mac OS X 10.3 and R GUI 1.9

[Marc Salit]

Dear Colleagues --

Thanks for the hints, though I'm still stuck. Here's what happens when 
I run the R 1.9.0 Beta GUI and go to the Packages menu, and try to 
download the affy bundle from the Bioconductor sub-menu:

 > local({source(paste(getOption('BIOC'), 'getBioC.R',sep='/'), 
local=TRUE); getBioC('affy', destdir=.libPaths()[1])})
Running getBioC version 1.2.54....
If you encounter problems, first make sure that
you are running the latest version of getBioC()
which can be found at: www.bioconductor.org/getBioC.R

Please direct any concerns or questions to 
bioconductor at stat.math.ethz.ch.

Loading required package: reposTools
[1] "Attempting to download genefilter from 
http://www.bioconductor.org/repository/release1.3/package/Source"
[1] "Download complete."
[1] "Installing genefilter"
[1] "Attempting to download multtest from 
http://www.bioconductor.org/repository/release1.3/package/Source"
[1] "Download complete."
[1] "Installing multtest"
Note: You did not specify a download type.  Using a default value of: 
Source
This will be fine for almost all users

[1] "Attempting to download XML from 
http://www.bioconductor.org//CRANrepository"
[1] "Download complete."
[1] "Installing XML"
Note: You did not specify a download type.  Using a default value of: 
Source
This will be fine for almost all users

[1] "Attempting to download XML from 
http://www.bioconductor.org//CRANrepository"
[1] "Download complete."
[1] "Installing XML"
[1] "Attempting to download MAGEML from 
http://www.bioconductor.org/repository/release1.3/package/Source"
[1] "Download complete."
[1] "Installing MAGEML"
[1] "Attempting to download affyPLM from 
http://www.bioconductor.org/repository/release1.3/package/Source"
[1] "Download complete."
[1] "Installing affyPLM"
[1] "Attempting to download matchprobes from 
http://www.bioconductor.org/repository/release1.3/package/Source"
[1] "Download complete."
[1] "Installing matchprobes"
[1] "Attempting to download makecdfenv from 
http://www.bioconductor.org/repository/release1.3/package/Source"
[1] "Download complete."
[1] "Installing makecdfenv"
 From URL:  
http://www.bioconductor.org/repository/release1.3/package/Source
	genefilter version 1.3.1
	multtest version 1.3.7
	MAGEML version 1.0.6
	affyPLM version 1.0.0
	matchprobes version 1.0.0
	makecdfenv version 1.4.1

 From URL:  http://www.bioconductor.org//CRANrepository
	XML version 0.95-6
	XML version 0.95-6

Warning messages:
1: 'package.description' is deprecated.
Use 'packageDescription' instead.
See help("Deprecated")
2: 'package.description' is deprecated.
Use 'packageDescription' instead.
See help("Deprecated")
3: Installation of package genefilter had non-zero exit status in: 
installPkg(fileName, pkg, pkgVer, type, lib, repEntry, versForce)
4: Installation of package multtest had non-zero exit status in: 
installPkg(fileName, pkg, pkgVer, type, lib, repEntry, versForce)
5: Installation of package XML had non-zero exit status in: 
installPkg(fileName, pkg, pkgVer, type, lib, repEntry, versForce)
6: Installation of package XML had non-zero exit status in: 
installPkg(fileName, pkg, pkgVer, type, lib, repEntry, versForce)
7: Installation of package MAGEML had non-zero exit status in: 
installPkg(fileName, pkg, pkgVer, type, lib, repEntry, versForce)
8: Installation of package affyPLM had non-zero exit status in: 
installPkg(fileName, pkg, pkgVer, type, lib, repEntry, versForce)
9: Installation of package matchprobes had non-zero exit status in: 
installPkg(fileName, pkg, pkgVer, type, lib, repEntry, versForce)
10: Installation of package makecdfenv had non-zero exit status in: 
installPkg(fileName, pkg, pkgVer, type, lib, repEntry, versForce)
 > library(affy)
Error: package affy was built for  powerpc-apple-darwin7.2.0
 >

Any ideas???

Thanks in advance,
Marc Salit


On Apr 13, 2004, at 5:15 PM, Marc Salit wrote:

> Dear Colleagues --
>
> I've been trying unsuccessfully to use Bioconductor (mostly the affy 
> package) on a Mac with OS X 10.3.3, running R with a GUI, either 1.8.1 
> or 1.9.0 beta. I've tried to install Bioconductor with getBioC.R, 
> which doesn't work all the way, and also tried to use a shell command 
> to install downloaded packages, a la R CMD INSTALL 
> /path/to/pkg_version.tar.gz , which also doesn't work all the way 
> (stops when it can't find a 'make' command in SHLIB.
>
> Suggestions? Caveats? Will this work? Shall I give up and 'switch' 
> back to a PC???
>
> Cheers & TIA,
> Marc Salit
>
-- 
Dr. Marc Salit
Research Chemist
NIST
Chemical Science and Technology Laboratory
100 Bureau Drive, Stop 8391
Gaithersburg, MD 20899-8391
email: Salit at NIST.gov
voice: +1 301 975-3646
fax:   +1 301 869-0413_______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
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