[BioC] Bioc 2.4 biocLite() install error
Elliot Kleiman
kleiman at rohan.sdsu.edu
Fri Apr 24 04:30:38 CEST 2009
Hi Keith,
Thank you for your suggestions.
I installed the latest Rtools,
[ http://www.murdoch-sutherland.com/Rtools/Rtools29.exe ]
and re-installed R version 2.9.0 for windows to "C:\R\R-2.9.0"
and tried installing BioC 2.4 via biocLite() and got the same error,
> 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"
[6] "Biobase" "biomaRt" "Biostrings" "DynDoc"
"gcrma"
[11] "genefilter" "geneplotter" "hgu95av2.db" "limma"
"marray"
[16] "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’
...
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
Error in normalizePath(path) :
path[1]="C:\R\R-2.9.0\library/preprocessCore": The system cannot find
the file specified
Hmm. Any other suggestions?
Btw, I am trying to install R 2.9.0 on an old windows Dell laptop
running Windows XP Home
Edition Version 2002 SP 3
Thanks,
Elliot
# 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
Keith Satterley wrote:
> Hi Elliot,
>
> If it is any consolation, mine worked ok on 2009-04-20, using
> > sessionInfo()
> R version 2.9.0 (2009-04-17)
> i386-pc-mingw32
>
> locale:
> LC_COLLATE=English_Australia.1252;LC_CTYPE=English_Australia.1252;LC_MONETARY=English_Australia.1252;LC_NUMERIC=C;LC_TIME=English_Australia.1252
>
>
> attached base packages:
> [1] stats graphics grDevices datasets utils methods base
>
> The relevant section of my log file is:
> ...
> package 'preprocessCore' successfully unpacked and MD5 sums checked
> package 'tkWidgets' successfully unpacked and MD5 sums checked
> package 'hgu95av2cdf' successfully unpacked and MD5 sums checked
> package 'hgu133acdf' successfully unpacked and MD5 sums checked
> package 'GO.db' successfully unpacked and MD5 sums checked
> package 'KEGG.db' successfully unpacked and MD5 sums checked
> package 'AnnotationDbi' successfully unpacked and MD5 sums checked
> package 'rae230a.db' successfully unpacked and MD5 sums checked
> package 'rae230aprobe' successfully unpacked and MD5 sums checked
> ...
>
> One difference is that I use C:\R\R-2.9.0 to install R in. There were
> issues with some tools not liking spaces in file pathnames, though I
> thought this had been fixed. You may wish to install R into a path
> without spaces or perhaps your Rtools maybe old. Get the latest
> (Rtools29.exe) from:
>
> http://www.murdoch-sutherland.com/Rtools/index.html
>
>
> cheers,
>
> Keith
>
> ========================
> Keith Satterley
> Bioinformatics Division
> The Walter and Eliza Hall Institute of Medical Research
> Parkville, Melbourne,
> Victoria, Australia
> =======================
>
> Elliot Kleiman wrote:
>> 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/
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