[BioC] Bioc 2.4 biocLite() install error

[Elliot Kleiman]

Hi BioC,

I am unable to install the new BioC 2.4
as I am receiving the following error,

Error in normalizePath(path) :
path[1]="C:\Program Files\R\R-2.9.0\library/GO.db": The system cannot 
find the file specified

Please below for full description:

 > source("http://bioconductor.org/biocLite.R")
 > biocLite()
Running biocinstall version 2.4.10 with R version 2.9.0
Your version of R requires version 2.4 of Bioconductor.
Will install the following packages:
[1] "affy" "affydata" "affyPLM" "annaffy" "annotate" "Biobase" "biomaRt" 
"Biostrings" "DynDoc" "gcrma"
[11] "genefilter" "geneplotter" "hgu95av2.db" "limma" "marray" 
"multtest" "vsn" "xtable" "affyQCReport"
Please wait...

Warning: unable to access index for repository 
http://brainarray.mbni.med.umich.edu/bioc/bin/windows/contrib/2.9
also installing the dependencies ‘DBI’, ‘RSQLite’, ‘affyio’, 
‘preprocessCore’, ‘GO.db’, ‘KEGG.db’, ‘AnnotationDbi’, ‘XML’, ‘RCurl’, 
‘IRanges’, ‘RColorBrewer’, ‘simpleaffy’

trying URL 'http://cran.fhcrc.org/bin/windows/contrib/2.9/DBI_0.2-4.zip'
Content type 'application/zip' length 442028 bytes (431 Kb)
opened URL
downloaded 431 Kb

trying URL 'http://cran.fhcrc.org/bin/windows/contrib/2.9/RSQLite_0.7-1.zip'
Content type 'application/zip' length 61197 0 bytes (597 Kb)
opened URL
downloaded 597 Kb

trying URL 
'http://bioconductor.org/packages/2.4/bioc/bin/windows/contrib/2.9/affyio_1.12.0.zip'
Content type 'application/zip' length 100024 bytes (97 Kb)
opened URL
downloaded 97 Kb

trying URL 
'http://bioconductor.org/packages/2.4/bioc/bin/windows/contrib/2.9/preprocessCore_1.6.0.zip'
Content type 'application/zip' length 159025 bytes (155 Kb)
opened URL
downloaded 155 Kb

trying URL 
'http://bioconductor.org/packages/2.4/data/annotation/bin/windows/contrib/2.9/GO.db_2.2.11.zip'
Content type 'application/zip' length 13966597 bytes (13.3 Mb)
opened URL
downloaded 13.3 Mb

trying URL 
'http://bioconductor.org/packages/2.4/data/annotation/bin/windows/contrib/2.9/KEGG.db_2.2.11.zip'
Content type 'application/zip' length 980640 bytes (957 Kb)
opened URL
downloaded 957 Kb

trying URL 
'http://bioconductor.org/packages/2.4/bioc/bin/windows/contrib/2.9/AnnotationDbi_1.6.0.zip'
Content type 'application/zip' length 4743216 bytes (4.5 Mb)
opened URL
downloaded 4.5 Mb

trying URL 
'http://bioconductor.org/packages/2.4/extra/bin/windows/contrib/2.9/XML_1.99-0.zip'
Content type 'application/zip' length 1799534 bytes (1.7 Mb)
opened URL
downloaded 1.7 Mb

trying URL 
'http://bioconductor.org/packages/2.4/extra/bin/windows/contrib/2.9/RCurl_0.94-1.zip'
Content type 'application/zip' length 1363382 bytes (1.3 Mb)
opened URL
downloaded 1.3 Mb

trying URL 
'http://bioconductor.org/packages/2.4/bioc/bin/windows/contrib/2.9/IRanges_1.2.0.zip'
Content type 'application/zip' length 1273292 bytes (1.2 Mb)
opened URL
downloaded 1.2 Mb

trying URL 
'http://cran.fhcrc.org/bin/windows/contrib/2.9/RColorBrewer_1.0-2.zip'
Content type 'application/zip' length 40534 bytes (39 Kb)
opened URL
downloaded 39 Kb

trying URL 
'http://bioconductor.org/packages/2.4/bioc/bin/windows/contrib/2.9/simpleaffy_2.20.0.zip'
Content type 'application/zip' length 844981 bytes (825 Kb)
opened URL
downloaded 825 Kb

trying URL 
'http://bioconductor.org/packages/2.4/bioc/bin/windows/contrib/2.9/affy_1.22.0.zip'
Content type 'application/zip' length 1959456 bytes (1.9 Mb)
opened URL
downloaded 1.9 Mb

trying URL 
'http://bioconductor.org/packages/2.4/data/experiment/bin/windows/contrib/2.9/affydata_1.11.5.zip'
Content type 'application/zip' length 12731547 bytes (12.1 Mb)
opened URL
downloaded 12.1 Mb

trying URL 
'http://bioconductor.org/packages/2.4/bioc/bin/windows/contrib/2.9/affyPLM_1.20.0.zip'
Content type 'application/zip' length 5274268 bytes (5.0 Mb)
opened URL
downloaded 5.0 Mb

trying URL 
'http://bioconductor.org/packages/2.4/bioc/bin/windows/contrib/2.9/annaffy_1.16.0.zip'
Content type 'application/zip' length 395978 bytes (386 Kb)
opened URL
downloaded 386 Kb

trying URL 
'http://bioconductor.org/packages/2.4/bioc/bin/windows/contrib/2.9/annotate_1.22.0.zip'
Content type 'application/zip' length 2021900 bytes (1.9 Mb)
opened URL
downloaded 1.9 Mb

trying URL 
'http://bioconductor.org/packages/2.4/bioc/bin/windows/contrib/2.9/Biobase_2.4.0.zip'
Content type 'application/zip' length 2579193 bytes (2.5 Mb)
opened URL
downloaded 2.5 Mb

trying URL 
'http://bioconductor.org/packages/2.4/bioc/bin/windows/contrib/2.9/biomaRt_2.0.0.zip'
Content type 'application/zip' length 307857 bytes (300 Kb)
opened URL
downloaded 300 Kb

trying URL 
'http://bioconductor.org/packages/2.4/bioc/bin/windows/contrib/2.9/Biostrings_2.12.0.zip'
Content type 'application/zip' length 2007785 bytes (1.9 Mb)
opened URL
downloaded 1.9 Mb

trying URL 
'http://bioconductor.org/packages/2.4/bioc/bin/windows/contrib/2.9/DynDoc_1.22.0.zip'
Content type 'application/zip' length 129397 bytes (126 Kb)
opened URL
downloaded 126 Kb

trying URL 
'http://bioconductor.org/packages/2.4/bioc/bin/windows/contrib/2.9/gcrma_2.16.0.zip'
Content type 'application/zip' length 200354 bytes (195 Kb)
opened URL
downloaded 195 Kb

trying URL 
'http://bioconductor.org/packages/2.4/bioc/bin/windows/contrib/2.9/genefilter_1.24.0.zip'
Content type 'application/zip' length 485721 bytes (474 Kb)
opened URL
downloaded 474 Kb

trying URL 
'http://bioconductor.org/packages/2.4/bioc/bin/windows/contrib/2.9/geneplotter_1.22.0.zip'
Content type 'application/zip' length 1815803 bytes (1.7 Mb)
opened URL
downloaded 1.7 Mb

trying URL 
'http://bioconductor.org/packages/2.4/data/annotation/bin/windows/contrib/2.9/hgu95av2.db_2.2.11.zip'
Content type 'application/zip' length 15266089 bytes (14.6 Mb)
opened URL
downloaded 14.6 Mb

trying URL 
'http://bioconductor.org/packages/2.4/bioc/bin/windows/contrib/2.9/limma_2.18.0.zip'
Content type 'application/zip' length 1553301 bytes (1.5 Mb)
opened URL
downloaded 1.5 Mb

trying URL 
'http://bioconductor.org/packages/2.4/bioc/bin/windows/contrib/2.9/marray_1.22.0.zip'
Content type 'application/zip' length 5086618 bytes (4.9 Mb)
open ed URL
downloaded 4.9 Mb

trying URL 
'http://bioconductor.org/packages/2.4/bioc/bin/windows/contrib/2.9/multtest_2.0.0.zip'
Content type 'application/zip' length 1823205 bytes (1.7 Mb)
opened URL
downloaded 1.7 Mb

trying URL 
'http://bioconductor.org/packages/2.4/bioc/bin/windows/contrib/2.9/vsn_3.12.0.zip'
Content type 'application/zip' length 1342723 bytes (1.3 Mb)
opened URL
downloaded 1.3 Mb

trying URL 'http://cran.fhcrc.org/bin/windows/contrib/2.9/xtable_1.5-5.zip'
Content type 'application/zip' length 216385 bytes (211 Kb)
opened URL
downloaded 211 Kb

trying URL 
'http://bioconductor.org/packages/2.4/bioc/bin/windows/contrib/2.9/affyQCReport_1.22.0.zip'
Content type 'application/zip' length 193188 bytes (188 Kb)
opened URL
downloaded 188 Kb

package 'DBI' successfully unpacked and MD5 sums checked
package 'RSQLite' successfully unpacked and MD5 sums checked
package 'affyio' successfully unpacked and MD5 sums checked
package 'preprocessCore' successfully unpacked and MD5 sums checked
package 'GO.db' successfully unpacked and MD5 sums checked
Error in normalizePath(path) :
path[1]="C:\Program Files\R\R-2.9.0\library/GO.db": The system cannot 
find the file specified

# print session info
 > sessionInfo()
R version 2.9.0 (2009-04-17)
i386-pc-mingw32

locale:
LC_COLLATE=English_United States.1252;LC_CTYPE=English_United 
States.1252;LC_MONETARY=English_United 
States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252

attached base packages:
[1] stats graphics grDevices utils datasets methods base

loaded via a namespace (and not attached):
[1] tools_2.9.0

* What am I missing here?

Thank you,

... Elliot

-- 
MS graduate student 
Computational Science Program 
San Diego State University
http://www.csrc.sdsu.edu/ 
http://www.sdsu.edu/