[BioC] problem installing package GOstats

[James W. MacDonald]

Hi Artur,

I've seen weirdness like this before. Try restarting R and see if that 
helps.

Best,

Jim



Artur Veloso wrote:
> Hi all,
> 
> I'm having some issues trying to install the GOstats package.  Does anyone
> have any idea what I could be doing wrong?
> 
> Thanks a lot!
> Artur Veloso
> 
>> source("http://bioconductor.org/biocLite.R")
>>     biocLite("GOstats")
> Running biocinstall version 2.2.9 with R version 2.7.0
> Your version of R requires version 2.2 of BioConductor.
> also installing the dependencies 'RBGL', 'Category'
> 
> trying URL '
> http://bioconductor.org/packages/2.2/bioc/bin/windows/contrib/2.7/RBGL_1.16.0.zip
> '
> Content type 'application/zip' length 1105523 bytes (1.1 Mb)
> opened URL
> downloaded 13 Kb
> 
> trying URL '
> http://bioconductor.org/packages/2.2/bioc/bin/windows/contrib/2.7/Category_2.6.0.zip
> '
> Content type 'application/zip' length 678484 bytes (662 Kb)
> opened URL
> downloaded 662 Kb
> 
> trying URL '
> http://bioconductor.org/packages/2.2/bioc/bin/windows/contrib/2.7/GOstats_2.6.0.zip
> '
> Content type 'application/zip' length 2824122 bytes (2.7 Mb)
> opened URL
> downloaded 899 Kb
> 
> Error in gzfile(file, "r") : cannot open the connection
> In addition: Warning messages:
> 1: In download.file(url, destfile, method, mode = "wb", ...) :
>   downloaded length 13480 != reported length 1105523
> 2: In download.file(url, destfile, method, mode = "wb", ...) :
>   downloaded length 921295 != reported length 2824122
> 3: In zip.unpack(pkg, tmpDir) : error 1 in extracting from zip file
> 4: In gzfile(file, "r") :
>   cannot open compressed file 'RBGL/DESCRIPTION', probable reason 'No such
> file or directory'
>> sessionInfo()
> R version 2.7.0 (2008-04-22)
> 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_2.7.0
> 
> 	[[alternative HTML version deleted]]
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623