[BioC] Bioc 2.4 biocLite() install error

Elliot Kleiman kleiman at rohan.sdsu.edu
Sat Apr 25 07:04:41 CEST 2009


Hi Martin,

After disabling my windows XP Norton Internet Security firewall
and anti-virus software protection, biocLite() for BioC 2.4 is now
working again. Disabling the anti-virus software for me was the
key!

I noticed that my windows R versions 2.8.1 and later don't like
the anti-virus protection for some reason.

Thank you for your help!

... Elliot

Martin Morgan wrote:
> 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
>>     
>
>   


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



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