[BioC] biocLite() failed to get CRAN package...
Patrick Aboyoun
paboyoun at fhcrc.org
Thu May 1 17:41:22 CEST 2008
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
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
More information about the Bioconductor
mailing list