[BioC] problem installing XML

[James W. MacDonald]

Hi Anthony,

Looks like you got a corrupted download. I just tried this and it worked 
without problems. Have you tried again?

 > biocLite("XML")
BioC_mirror: http://bioconductor.org
Using Bioconductor version 2.13 (BiocInstaller 1.12.0), R version 3.0.2.
Installing package(s) 'XML'
trying URL 'http://cran.fhcrc.org/bin/windows/contrib/3.0/XML_3.98-1.1.zip'
Content type 'application/zip' length 4288136 bytes (4.1 Mb)
opened URL
downloaded 4.1 Mb

package ‘XML’ successfully unpacked and MD5 sums checked

 > sessionInfo()
R version 3.0.2 (2013-09-25)
Platform: i386-w64-mingw32/i386 (32-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 base

other attached packages:
[1] BiocInstaller_1.12.0

loaded via a namespace (and not attached):
[1] tools_3.0.2

Best,

Jim



On 3/26/2014 12:44 AM, Anthony Bosco [guest] wrote:
> Dear BioC,
>
> I am having some difficulty installing XML.
>
> Please see below for error message and session info..
>
> Best regards,
>
> Anthony
>
>> setInternet2(TRUE)
>> source("http://bioconductor.org/biocLite.R")
> Bioconductor version 2.13 (BiocInstaller 1.12.0), ?biocLite for help
>> biocLite("XML")
> BioC_mirror: http://bioconductor.org
> Using Bioconductor version 2.13 (BiocInstaller 1.12.0), R version 3.0.2.
> Installing package(s) 'XML'
> trying URL 'http://cran.fhcrc.org/bin/windows/contrib/3.0/XML_3.98-1.1.zip'
> Content type 'application/zip' length 4288136 bytes (4.1 Mb)
> opened URL
> downloaded 4.1 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 4259840 != reported length 4288136
> 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 'XML/DESCRIPTION', probable reason 'No such file or directory'
>
>
>   -- output of sessionInfo():
>
> R version 3.0.2 (2013-09-25)
> Platform: x86_64-w64-mingw32/x64 (64-bit)
>
> locale:
> [1] 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 utils     datasets  methods   base
>
> other attached packages:
> [1] BiocInstaller_1.12.0
>
> loaded via a namespace (and not attached):
> [1] tools_3.0.2
>
> --
> Sent via the guest posting facility at bioconductor.org.
>
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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