[BioC] GEOquerry and virtualArray

Tue Apr 8 16:42:09 CEST 2014

Sorry.
I downloaded bitops (there wasn't one before); the command    > library("bitops")   is OK, no error messages, but GEOquerry download still does not work.
I included the whole session with error messages here:

R version 3.0.3 (2014-03-06) -- "Warm Puppy"
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Platform: x86_64-w64-mingw32/x64 (64-bit)

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  Natural language support but running in an English locale

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> source("http://bioconductor.org/biocLite.R")
Bioconductor version 2.13 (BiocInstaller 1.12.0), ?biocLite for help
>     biocLite("GEOquery")
BioC_mirror: http://bioconductor.org
Using Bioconductor version 2.13 (BiocInstaller 1.12.0), R version
  3.0.3.
Installing package(s) 'GEOquery'
also installing the dependency 'RCurl'

trying URL 'http://cran.fhcrc.org/bin/windows/contrib/3.0/RCurl_1.95-4.1.zip'
Content type 'application/zip' length 2836490 bytes (2.7 Mb)
opened URL
downloaded 528 Kb

trying URL 'http://bioconductor.org/packages/2.13/bioc/bin/windows/contrib/3.0/GEOquery_2.28.0.zip'
Content type 'application/zip' length 13721218 bytes (13.1 Mb)
opened URL
downloaded 13.1 Mb

Error in read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package", "Type")) : 
  cannot open the connection
In addition: Warning messages:
1: In download.file(url, destfile, method, mode = "wb", ...) :
  downloaded length 541387 != reported length 2836490
2: In unzip(zipname, exdir = dest) : error 1 in extracting from zip file
3: In read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package", "Type")) :
  cannot open compressed file 'RCurl/DESCRIPTION', probable reason 'No such file or directory'
>
---------------------------

Here's the sessionInfo():
> sessionInfo()
R version 3.0.3 (2014-03-06)
Platform: x86_64-w64-mingw32/x64 (64-bit)

locale:
[1] LC_COLLATE=English_United States.1252 
[2] LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

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

other attached packages:
[1] bitops_1.0-6         BiocInstaller_1.12.0

loaded via a namespace (and not attached):
[1] tools_3.0.3

Thanks for the help!
Miki.

_______________________________________________________________

Original Message-----
From: James W. MacDonald [mailto:jmacdon at uw.edu] 
Sent: Tuesday, April 08, 2014 9:59 AM
To: Blumenberg, Miroslav
Cc: 'bioconductor at r-project.org'
Subject: Re: [BioC] GEOquerry and virtualArray

Hi Miroslav,

On 4/8/2014 9:53 AM, Blumenberg, Miroslav wrote:
> I tried to load GEOquerry and virtualArray but am getting the following error messages (even after re-loading latest versions of R and Bioconductor):
>
> Error in read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package", "Type")) :
>    cannot open the connection
> In addition: Warning messages:
> 1: In download.file(url, destfile, method, mode = "wb", ...) :
>    downloaded length 7031 != reported length 35878
> 2: In unzip(zipname, exdir = dest) : error 1 in extracting from zip 
> file
> 3: In read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package", "Type")) :
>    cannot open compressed file 'bitops/DESCRIPTION', probable reason 'No such file or directory'
>
> In addition: Warning messages:
> 1: In download.file(url, destfile, method, mode = "wb", ...) :
>    downloaded length 7031 != reported length 35878
> 2: In download.file(url, destfile, method, mode = "wb", ...) :
>    downloaded length 188067 != reported length 1145037
> 3: In download.file(url, destfile, method, mode = "wb", ...) :
>    downloaded length 539927 != reported length 2836490
> 4: In download.file(url, destfile, method, mode = "wb", ...) :
>    downloaded length 7031 != reported length 51601
> 5: In download.file(url, destfile, method, mode = "wb", ...) :
>    downloaded length 193909 != reported length 320154
> 6: In unzip(zipname, exdir = dest) : error 1 in extracting from zip 
> file
> 7: In read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package", "Type")) :
>    cannot open compressed file 'bitops/DESCRIPTION', probable reason 'No such file or directory'

It looks at the very least like your bitops package is broken, so I would re-install that. You also neglect to show what code you were running before you got these errors, so any further troubleshooting is difficult to do.

You also neglected to include your sessionInfo().

Best,

Jim

>
> What am I doing wrong? My RankProd is working fine.
> Please help,
> Miki Blumenberg, NYU Med School.
>
>
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--
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099

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