[BioC] XML Windows binary package added to 2.2/extra repos (was Re: biocLite() failed to get CRAN package...)
Patrick Aboyoun
paboyoun at fhcrc.org
Thu May 1 21:56:15 CEST 2008
I just added the Windows binary package for XML to
http://bioconductor.org/packages/2.2/extra
You can now download and install this version of the Windows binary
package using biocLite("XML") on Windows with R 2.7.0. Since CRAN
maintains versions of the XML package in source and Mac OS X binary
form, only the Windows binary package version will be stored in the
bioconductor extra repository.
Patrick
Patrick Aboyoun wrote:
> Jenny,
> By default, the biocLite function on Windows grabs the Windows binary
> packages from the biocinstallRepos():
>
> [1] "http://bioconductor.org/packages/2.2/bioc" [2]
> "http://bioconductor.org/packages/2.2/data/annotation"
> [3] "http://bioconductor.org/packages/2.2/data/experiment"
> [4] "http://bioconductor.org/packages/2.2/extra" [5]
> "http://cran.fhcrc.org"
> The reason why it didn't grab the XML package from CRAN is because the
> XML binary package is not maintained there (but is provided by
> Professor Brian Ripley at
> http://www.stats.ox.ac.uk/pub/RWin/bin/windows/contrib/2.7/). You can,
> however, use biocLite to get the XML source package from CRAN and
> build the binary package on your machine, provided you Windows box is
> configured to do so, if you specify type = "source" in your biocLite
> function call.
>
> We are planning on adding a version of the XML Windows binary package
> in our BioC "extras" repository at
>
> "http://bioconductor.org/packages/2.2/extra"
>
> in the near future. I will send an announcement to this message board
> when it is in place.
>
>
> Cheers,
> Patrick
>
>
> Jenny Drnevich wrote:
>> Hi everyone,
>>
>> I just upgraded to R 2.7.0 and used biocLite() to install many
>> Bioconductor packages. The base install of biocLite() worked fine,
>> but when I used it to install some other packages, at the end I got a
>> warning message that "dependency 'XML' is not available" (screen
>> output and sessionInfo below). However, I then used the install menu
>> on PC and was able to download and install XML from CRAN. So I'm not
>> sure what happened that biocLite() wasn't able to get it...
>>
>> Cheers,
>> Jenny
>>
>> > x <-
>> c("affycoretools","convert","made4","plier","simpleaffy","tkWidgets","widgetTools","RWinEdt")
>>
>> > biocLite(x)
>> Running biocinstall version 2.2.7 with R version 2.7.0
>> Your version of R requires version 2.2 of BioConductor.
>> also installing the dependencies 'graph', 'RBGL', 'Category',
>> 'RCurl', 'GOstats', 'biomaRt', 'ade4'
>>
>> trying URL
>> 'http://bioconductor.org/packages/2.2/bioc/bin/windows/contrib/2.7/graph_1.18.0.zip'
>>
>> Content type 'application/zip' length 856239 bytes (836 Kb)
>> opened URL
>> downloaded 836 Kb
>>
>> trying URL
>> 'http://bioconductor.org/packages/2.2/bioc/bin/windows/contrib/2.7/RBGL_1.16.0.zip'
>>
>> Content type 'application/zip' length 1074190 bytes (1.0 Mb)
>> opened URL
>> downloaded 1.0 Mb
>>
>> trying URL
>> 'http://bioconductor.org/packages/2.2/bioc/bin/windows/contrib/2.7/Category_2.6.0.zip'
>>
>> Content type 'application/zip' length 643858 bytes (628 Kb)
>> opened URL
>> downloaded 628 Kb
>>
>> trying URL
>> 'http://bioconductor.org/packages/2.2/extra/bin/windows/contrib/2.7/RCurl_0.8-1.zip'
>>
>> Content type 'application/zip' length 944881 bytes (922 Kb)
>> opened URL
>> downloaded 922 Kb
>>
>> trying URL
>> 'http://bioconductor.org/packages/2.2/bioc/bin/windows/contrib/2.7/GOstats_2.6.0.zip'
>>
>> Content type 'application/zip' length 2802070 bytes (2.7 Mb)
>> opened URL
>> downloaded 2.7 Mb
>>
>> trying URL
>> 'http://bioconductor.org/packages/2.2/bioc/bin/windows/contrib/2.7/biomaRt_1.14.0.zip'
>>
>> Content type 'application/zip' length 420193 bytes (410 Kb)
>> opened URL
>> downloaded 410 Kb
>>
>> trying URL
>> 'http://cran.fhcrc.org/bin/windows/contrib/2.7/ade4_1.4-7.zip'
>> Content type 'application/zip' length 3023234 bytes (2.9 Mb)
>> opened URL
>> downloaded 2.9 Mb
>>
>> trying URL
>> 'http://bioconductor.org/packages/2.2/bioc/bin/windows/contrib/2.7/affycoretools_1.12.0.zip'
>>
>> Content type 'application/zip' length 6992261 bytes (6.7 Mb)
>> opened URL
>> downloaded 6.7 Mb
>>
>> trying URL
>> 'http://bioconductor.org/packages/2.2/bioc/bin/windows/contrib/2.7/convert_1.16.0.zip'
>>
>> Content type 'application/zip' length 46834 bytes (45 Kb)
>> opened URL
>> downloaded 45 Kb
>>
>> trying URL
>> 'http://bioconductor.org/packages/2.2/bioc/bin/windows/contrib/2.7/made4_1.14.0.zip'
>>
>> Content type 'application/zip' length 937469 bytes (915 Kb)
>> opened URL
>> downloaded 915 Kb
>>
>> trying URL
>> 'http://bioconductor.org/packages/2.2/bioc/bin/windows/contrib/2.7/plier_1.10.0.zip'
>>
>> Content type 'application/zip' length 47646 bytes (46 Kb)
>> opened URL
>> downloaded 46 Kb
>>
>> trying URL
>> 'http://bioconductor.org/packages/2.2/bioc/bin/windows/contrib/2.7/simpleaffy_2.16.0.zip'
>>
>> Content type 'application/zip' length 802232 bytes (783 Kb)
>> opened URL
>> downloaded 783 Kb
>>
>> trying URL
>> 'http://bioconductor.org/packages/2.2/bioc/bin/windows/contrib/2.7/tkWidgets_1.18.0.zip'
>>
>> Content type 'application/zip' length 503016 bytes (491 Kb)
>> opened URL
>> downloaded 491 Kb
>>
>> trying URL
>> 'http://bioconductor.org/packages/2.2/bioc/bin/windows/contrib/2.7/widgetTools_1.16.0.zip'
>>
>> Content type 'application/zip' length 271188 bytes (264 Kb)
>> opened URL
>> downloaded 264 Kb
>>
>> trying URL
>> 'http://cran.fhcrc.org/bin/windows/contrib/2.7/RWinEdt_1.7-9.zip'
>> Content type 'application/zip' length 397216 bytes (387 Kb)
>> opened URL
>> downloaded 387 Kb
>>
>> package 'graph' successfully unpacked and MD5 sums checked
>> package 'RBGL' successfully unpacked and MD5 sums checked
>> package 'Category' successfully unpacked and MD5 sums checked
>> package 'RCurl' successfully unpacked and MD5 sums checked
>> package 'GOstats' successfully unpacked and MD5 sums checked
>> package 'biomaRt' successfully unpacked and MD5 sums checked
>> package 'ade4' successfully unpacked and MD5 sums checked
>> package 'affycoretools' successfully unpacked and MD5 sums checked
>> package 'convert' successfully unpacked and MD5 sums checked
>> package 'made4' successfully unpacked and MD5 sums checked
>> package 'plier' successfully unpacked and MD5 sums checked
>> package 'simpleaffy' successfully unpacked and MD5 sums checked
>> package 'tkWidgets' successfully unpacked and MD5 sums checked
>> package 'widgetTools' successfully unpacked and MD5 sums checked
>> package 'RWinEdt' successfully unpacked and MD5 sums checked
>>
>> The downloaded packages are in
>> C:\Documents and Settings\drnevich\Local
>> Settings\Temp\RtmpPZtAmS\downloaded_packages
>> updating HTML package descriptions
>> Warning message:
>> dependency 'XML' is not available
>>
>> > utils:::menuInstallPkgs()
>> --- Please select a CRAN mirror for use in this session ---
>> trying URL
>> 'http://www.stats.ox.ac.uk/pub/RWin/bin/windows/contrib/2.7/XML_1.94-0.1.zip'
>>
>> Content type 'application/zip' length 1659232 bytes (1.6 Mb)
>> opened URL
>> downloaded 1.6 Mb
>>
>> package 'XML' successfully unpacked and MD5 sums checked
>>
>> The downloaded packages are in
>> C:\Documents and Settings\drnevich\Local
>> Settings\Temp\RtmpPZtAmS\downloaded_packages
>> updating HTML package descriptions
>>
>> >sessionInfo()
>> R version 2.7.0 (2008-04-22)
>> i386-pc-mingw32
>>
>> locale:
>> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
>> States.1252;LC_MONETARY=English_United
>> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
>>
>> attached base packages:
>> [1] stats graphics grDevices utils datasets methods base
>>
>> loaded via a namespace (and not attached):
>> [1] tools_2.7.0
>>
>>
>>
>> Jenny Drnevich, Ph.D.
>>
>> Functional Genomics Bioinformatics Specialist
>> W.M. Keck Center for Comparative and Functional Genomics
>> Roy J. Carver Biotechnology Center
>> University of Illinois, Urbana-Champaign
>>
>> 330 ERML
>> 1201 W. Gregory Dr.
>> Urbana, IL 61801
>> USA
>>
>> ph: 217-244-7355
>> fax: 217-265-5066
>> e-mail: drnevich at uiuc.edu
>>
>> _______________________________________________
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>
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