[BioC] can't downlaod package "beadarrayExampleData"

[Dan Tenenbaum]

2011/12/26 易士 路 <math_servant at hotmail.com>:
> I got this messenge as below
>
>> sessionInfo()
> R version 2.14.0 (2011-10-31)
> Platform: i386-pc-mingw32/i386 (32-bit)
> locale:
> [1] LC_COLLATE=Chinese (Traditional)_Taiwan.950
> [2] LC_CTYPE=Chinese (Traditional)_Taiwan.950
> [3] LC_MONETARY=Chinese (Traditional)_Taiwan.950
> [4] LC_NUMERIC=C
> [5] LC_TIME=Chinese (Traditional)_Taiwan.950
> attached base packages:
> [1] grid      stats     graphics  grDevices utils     datasets  methods
> [8] base
> other attached packages:
>  [1] sv a_3.0.2           mgcv_1.7-9          corpcor_1.6.0
>  [4] beadarray_2.4.1     ggplot2_0.8.9       proto_0.3-9.2
>  [7] reshape_0.8.4       plyr_1.6            lumi_2.6.0
> [10] nleqslv_1.9.1       methylumi_2.0.1     Biobase_2.14.0
> [13] BiocInstaller_1.2.1
> loaded via a namespace (and not attached):
> 錯誤在x[["Version"]] : 下標超出邊界
> 此外: Warning message:
> In FUN(c("affy", "affyio", "annotate", "AnnotationDbi", "DBI", "hdrcde",  :
>   DESCRIPTION file of package 'IRanges' is missing or broken
>
> I think that maybe the point is package 'IRanges'.
> But when I download package 'IRanges', it is also interrupted.


I suggest reinstalling IRanges;
source("http://bioconductor.org/biocLite.R")
biocLite("IRanges")

If that doesn't work, try uninstalling and reinstaling R.

Dan



>
> Thanks.
>
> Louis
>
>
>
>> Date: Mon, 26 Dec 2011 00:19:40 -0800
>> Subject: Re: [BioC] can't downlaod package "beadarrayExampleData"
>> From: dtenenba at fhcrc.org
>> To: math_servant at hotmail.com
>> CC: bioconductor at r-project.org
>
>>
>> On Sun, Dec 25, 2011 at 9:39 PM, 易士 路 <math_servant at hotmail.com> wrote:
>> >
>> >
>> >
>> >
>> > hi, I try to download package "beadarrayExampleData" using windows R.
>> > But something is wrong. > biocLite(c("beadarrayExampleData",
>> > "beadarrayExampleData"))
>> > BioC_mirror: 'http://www.bioconductor.org'
>> > Using R version 2.14, BiocInstall er version 1.2.1.
>
>> > Installing package(s) 'beadarrayExampleData' 'beadarrayExampleData'
>> > Installing package(s) into
>> > 'C:/Users/A00460/Documents/R/win-library/2.14'
>> > (as 'lib' is unspecified)
>> > 試開URL
>> > 'http://www.bioconductor.org/packages/2.9/data/experiment/bin/windows/contrib/2.14/beadarrayExampleData_1.0.3.zip'
>> > Content type 'application/zip' length 31355200 bytes (29.9 Mb)
>> > 開啟了 URL
>> > downloaded 10.7 Mb錯誤在read.dcf(file.path(pkgname, "DESCRIPTION"),
>> > c("Package", "Type")) :
>> > 無法開啟連結
>> > 此外: Warning messages:
>> > 1: In download.file(url, destfile, method, mode = "wb", ...) :
>> > 下載的長度 11185933 != 報告的長度 31355200
>> > 2: In unzip(zipname, exdir = dest) : 從 zip 檔案中解開 1 時發生錯誤
>> > 3: In read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package", "Type"))
>> > :
>> > cannot open compressed file 'beadarrayExampl eData/DESCRIPTION',
>> > probable reason 'No such file or directory' Is the file unavailable now?
>
>> > Thanks in advance. Louis
>>
>> I was able to install this package using the same command, on R 2.14
>> on Windows, It sounds like maybe your download was interrupted? If you
>> try again in a fresh R session, do you get the same result?
>> If you are still having a problem, please post the output of
>> sessionInfo().
>> Dan
>>
>>
>> > [[alternative HTML version deleted]]
>> >
>> >
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