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_1.9 4-0.1.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 > > _______________________________________________ > 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