[BioC] R 2.15.2 trouble

[Paul Leo]

I think  the problem is related to:
-------------------------
2: installed directory not writable, cannot update packages 'foreign', 'lattice', 'MASS',
  'Matrix', 'nlme', 'rpart', 'survival' 
--------------

perhaps you have installed R as sudo or superuser so the core
'foreign', 'lattice', 'MASS',
  'Matrix', 'nlme', 'rpart', 'survival' 
packages are in a directory where "/Users/Julie Tseng-Crank"
can't write to.  BioC wants to update these but not have permission to do so.

If you start R as sudo OR give user "/Users/Julie Tseng-Crank" permission to write to the directory
where 'foreign', 'lattice', 'MASS',
  'Matrix', 'nlme', 'rpart', 'survival'  
is located (and can modify files there too) you shoudl be ok.

Cheers
Paul



Dr Paul Leo
Senior Bioinformatician
The University of Queensland Diamantina Institute
---------------------------------------------------------------------
TRI, level  ,  37 Kent Street,  Woolloongabba QLD 4102
Tel: +61 7 3443 7072  Mob: 041 303 8691  Fax: +61 7 3443 6966 

-----Original Message-----
From: Julie Tseng-Crank [guest] <guest at bioconductor.org>
To: bioconductor at r-project.org, jtsengcr at yahoo.com
Cc: affy Maintainer <rafa at jhu.edu>
Subject: [BioC] R 2.15.2 trouble
Date: Tue, 22 Jan 2013 23:03:04 -0800

I uninstalled R 2.14 and then installed R 2.15.2 instead updated R, because I wanted to remove the start up setting.  When I tried to install affy, limma, and gcrma, I got warming messages "packages â?~affyâ?T, â?~gcrmaâ?T, â?~limmaâ?T are not available (for R version 2.15.2)".  Tried "biocLite("BiocUpgrade")" and then installed again, still the same warming message.  Thank you for help.

 -- output of sessionInfo(): 

> source("http://bioconductor.org/biocLite.R")
Installing package(s) into â?~C:/Users/Julie Tseng-Crank/Documents/R/win-library/2.15â?T
(as â?~libâ?T is unspecified)
trying URL 'http://www.bioconductor.org/packages/2.11/bioc/bin/windows/contrib/2.15/BiocInstaller_1.8.3.zip'
Content type 'application/zip' length 43242 bytes (42 Kb)
opened URL
downloaded 42 Kb

package â?~BiocInstallerâ?T successfully unpacked and MD5 sums checked

The downloaded binary packages are in
        C:\Users\Julie Tseng-Crank\AppData\Local\Temp\RtmpGEYYeQ\downloaded_packages
Bioconductor version 2.11 (BiocInstaller 1.8.3), ?biocLite for help
> biocLite()
BioC_mirror: http://bioconductor.org
Using Bioconductor version 2.11 (BiocInstaller 1.8.3), R version 2.15.
Installing package(s) 'Biobase' 'IRanges' 'AnnotationDbi'
also installing the dependencies â?~BiocGenericsâ?T, â?~DBIâ?T, â?~RSQLiteâ?T

trying URL 'http://bioconductor.org/packages/2.11/bioc/bin/windows/contrib/2.15/BiocGenerics_0.4.0.zip'
Content type 'application/zip' length 246934 bytes (241 Kb)
opened URL
downloaded 241 Kb

trying URL 'http://cran.stat.sfu.ca/bin/windows/contrib/2.15/DBI_0.2-5.zip'
Content type 'application/zip' length 394390 bytes (385 Kb)
opened URL
downloaded 385 Kb

trying URL 'http://cran.stat.sfu.ca/bin/windows/contrib/2.15/RSQLite_0.11.2.zip'
Content type 'application/zip' length 1129539 bytes (1.1 Mb)
opened URL
downloaded 1.1 Mb

trying URL 'http://bioconductor.org/packages/2.11/bioc/bin/windows/contrib/2.15/Biobase_2.18.0.zip'
Content type 'application/zip' length 2346708 bytes (2.2 Mb)
opened URL
downloaded 2.2 Mb

trying URL 'http://bioconductor.org/packages/2.11/bioc/bin/windows/contrib/2.15/IRanges_1.16.4.zip'
Content type 'application/zip' length 2048202 bytes (2.0 Mb)
opened URL
downloaded 2.0 Mb

trying URL 'http://bioconductor.org/packages/2.11/bioc/bin/windows/contrib/2.15/AnnotationDbi_1.20.3.zip'
Content type 'application/zip' length 4199125 bytes (4.0 Mb)
opened URL
downloaded 4.0 Mb

package â?~BiocGenericsâ?T successfully unpacked and MD5 sums checked
package â?~DBIâ?T successfully unpacked and MD5 sums checked
package â?~RSQLiteâ?T successfully unpacked and MD5 sums checked
package â?~Biobaseâ?T successfully unpacked and MD5 sums checked
package â?~IRangesâ?T successfully unpacked and MD5 sums checked
package â?~AnnotationDbiâ?T successfully unpacked and MD5 sums checked

The downloaded binary packages are in
        C:\Users\Julie Tseng-Crank\AppData\Local\Temp\RtmpGEYYeQ\downloaded_packages
Warning message:
installed directory not writable, cannot update packages 'foreign', 'lattice', 'MASS',
  'Matrix', 'nlme', 'rpart', 'survival' 
> biocLite("affy", "gcrma", "limma")
Error in !suppressAutoUpdate : invalid argument type
> install.packages(c("affy", "gcrma", "limma"))
Installing package(s) into â?~C:/Users/Julie Tseng-Crank/Documents/R/win-library/2.15â?T
(as â?~libâ?T is unspecified)
Warning message:
packages â?~affyâ?T, â?~gcrmaâ?T, â?~limmaâ?T are not available (for R version 2.15.2) 
> library()
> biocLite("BiocUpgrade")
BioC_mirror: http://bioconductor.org
Using Bioconductor version 2.11 (BiocInstaller 1.8.3), R version 2.15.
Warning messages:
1: Bioconductor version 2.11 is the latest available for R version 2.15 
2: installed directory not writable, cannot update packages 'foreign', 'lattice', 'MASS',
  'Matrix', 'nlme', 'rpart', 'survival' 
> install.packages(c("affy", "gcrma", "limma"))
Installing package(s) into â?~C:/Users/Julie Tseng-Crank/Documents/R/win-library/2.15â?T
(as â?~libâ?T is unspecified)
Warning message:
packages â?~affyâ?T, â?~gcrmaâ?T, â?~limmaâ?T are not available (for R version 2.15.2) 
> 


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