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

[Liu,Bin]

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.

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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