[BioC] Bioc 2.4 biocLite() install error

Martin Morgan mtmorgan at fhcrc.org
Fri Apr 24 04:57:56 CEST 2009


Elliot Kleiman <kleiman at rohan.sdsu.edu> writes:

> 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

Hi Elliot -- 

The R-help and R-devel lists suggest this might be related to
anti-virus software, especially if the failure changes over time. One
useful possibility is to say

trace(normalizePath, quote(cat("path=", path, "\n")))

before biocLite(). You'll see the arguments called each time
normalizePath() is invoked, and it'll likely rule out a number of
possibilities, e.g., spaces in the path name or use of \ and / 

HTH, Martin

>
> 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

-- 
Martin Morgan
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



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