[BioC] [Bioc-devel] XML package downloading problem with bioconductor.org

[Steve Lianoglou]

Hmm,

On Mon, Sep 19, 2011 at 11:19 AM, Liu,Bin <BLiu1 at mdanderson.org> wrote:
> Thanks for quick response. Actually I can download other packages. Please see below and only the XML package was downloaded as 751 kb that is not matching the original file (885kb). I even used the  URL 'http://cran.fhcrc.org/src/contrib/XML_3.4-3.tar.gz' with two different computers. It also gave me the error. Is there way to get around this? or anyone can attach this file over the email? Thanks a lot.

If you just download the file directly from that URL (ie, not through
biocLite or install.packages or whatever), what is the size of the
file you get? I'm getting 885.1kb when I d/l the link you sent.

If you just download like that, maybe you can just install that
package from the command line (which is another way to say that I
don't know why you are having problems installing through R).

-steve

>
> Bin
>
>
>> biocLite("GenomicFeatures")
> BioC_mirror = 'http://www.bioconductor.org', change using
> chooseBioCmirror().
> Using R version 2.14, BiocInstaller version 1.1.27.
> Installing package(s) 'GenomicFeatures'
> Installing package(s) into ‘/home/bliu1/R/i686-pc-linux-gnu-library/2.14’
> (as ‘lib’ is unspecified)
> also installing the dependencies ‘XML’, ‘GenomicRanges’, ‘rtracklayer’, ‘biomaRt’
>
> trying URL 'http://cran.fhcrc.org/src/contrib/XML_3.4-3.tar.gz'
> Content type 'application/x-gzip' length 906364 bytes (885 Kb)
> opened URL
> ==========================================
> downloaded 751 Kb
>
> trying URL 'http://www.bioconductor.org/packages/2.9/bioc/src/contrib/GenomicRanges_1.5.42.tar.gz'
> Content type 'application/x-gzip' length 1217669 bytes (1.2 Mb)
> opened URL
> ==================================================
> downloaded 1.2 Mb
>
> trying URL 'http://www.bioconductor.org/packages/2.9/bioc/src/contrib/rtracklayer_1.13.14.tar.gz'
> Content type 'application/x-gzip' length 1571972 bytes (1.5 Mb)
> opened URL
> ==================================================
> downloaded 1.5 Mb
>
> trying URL 'http://www.bioconductor.org/packages/2.9/bioc/src/contrib/biomaRt_2.9.2.tar.gz'
> Content type 'application/x-gzip' length 277036 bytes (270 Kb)
> opened URL
> ==================================================
> downloaded 270 Kb
>
> trying URL 'http://www.bioconductor.org/packages/2.9/bioc/src/contrib/GenomicFeatures_1.5.21.tar.gz'
> Content type 'application/x-gzip' length 316288 bytes (308 Kb)
> opened URL
> ==================================================
> downloaded 308 Kb
>
>
>
> ________________________________________
> From: Vincent Carey [stvjc at channing.harvard.edu]
> Sent: Monday, September 19, 2011 10:11 AM
> To: Liu,Bin
> Cc: bioconductor at r-project.org; bioc-devel at r-project.org
> Subject: Re: [Bioc-devel] XML package downloading problem with bioconductor.org
>
> I cannot reproduce this.  It is a problem with your system, perhaps your disk is full or you have some network
> restriction imposed.
>
> On Mon, Sep 19, 2011 at 11:03 AM, Liu,Bin <BLiu1 at mdanderson.org<mailto:BLiu1 at mdanderson.org>> wrote:
> Hi, I am trying to download the XML package that is required for "GenomicFeatures" package. However, I got following error message.
> It seems that the gz file couldn't be downloaded. Whenever the downloading reached 751kb, an error was displayed.I am using R2.14.0 devel version.
> It works for other packages. Thanks
>
> Bin
>
> Bin Liu, Ph.D.
> Assistant Professor
> Department of Genetics
> The University of Texas M. D. Anderson Cancer Center
> 1515 Holcombe Blvd
> Houston, TX 77030
>
> -------------------------------------------------------------------------------
>> biocLite("XML")
> BioC_mirror = 'http://www.bioconductor.org', change using
> chooseBioCmirror().
> Using R version 2.14, BiocInstaller version 1.1.27.
> Installing package(s) 'XML'
> Installing package(s) into ‘/home/abc001/R/i686-pc-linux-gnu-library/2.14’
> (as ‘lib’ is unspecified)
> trying URL 'http://cran.fhcrc.org/src/contrib/XML_3.4-3.tar.gz'
> Content type 'application/x-gzip' length 906364 bytes (885 Kb)
> opened URL
> ==========================================
> downloaded 751 Kb
>
> Error in untar2(tarfile, files, list, exdir) : incomplete block on file
>
> The downloaded packages are in
>       ‘/tmp/Rtmpn6rDdk/downloaded_packages’
> Warning messages:
> 1: In download.file(url, destfile, method, mode = "wb", ...) :
>  downloaded length 769652 != reported length 906364
> 2: In install.packages(pkgs = pkgs, repos = repos, ...) :
>  installation of package ‘XML’ had non-zero exit status
>
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>
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>



-- 
Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact