[BioC] R 2.15.2 trouble

[Martin Morgan]

On 01/22/2013 11:03 PM, Julie Tseng-Crank [guest] wrote:
>
> 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 ‘affy’, ‘gcrma’, ‘limma’ 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 ‘C:/Users/Julie Tseng-Crank/Documents/R/win-library/2.15’
> (as ‘lib’ 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 ‘BiocInstaller’ 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 ‘BiocGenerics’, ‘DBI’, ‘RSQLite’
>
> 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 ‘BiocGenerics’ successfully unpacked and MD5 sums checked
> package ‘DBI’ successfully unpacked and MD5 sums checked
> package ‘RSQLite’ successfully unpacked and MD5 sums checked
> package ‘Biobase’ successfully unpacked and MD5 sums checked
> package ‘IRanges’ successfully unpacked and MD5 sums checked
> package ‘AnnotationDbi’ 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

oops, that should have been biocLite(c("affy", "gcrma", "limma"))

>> install.packages(c("affy", "gcrma", "limma"))
> Installing package(s) into ‘C:/Users/Julie Tseng-Crank/Documents/R/win-library/2.15’
> (as ‘lib’ is unspecified)
> Warning message:
> packages ‘affy’, ‘gcrma’, ‘limma’ 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 ‘C:/Users/Julie Tseng-Crank/Documents/R/win-library/2.15’
> (as ‘lib’ is unspecified)
> Warning message:
> packages ‘affy’, ‘gcrma’, ‘limma’ are not available (for R version 2.15.2)

using install.packages by default means that you are looking on CRAN for 
Bioconductor packages, so the Bioconductor packages are not found.

Just biocLite(c("affy", "gcrma", "limma"))

Martin

>>
>
>
> --
> Sent via the guest posting facility at bioconductor.org.
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
>


-- 
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

Location: Arnold Building M1 B861
Phone: (206) 667-2793