Hi all, I have just installed R version 2.13.0 on a windows 7 machine but don't seem to be able to install some packages from bioconductor. The culprit may be package XML namespace. Below are details while trying to install package ArrayExpress. Important to note that a similar error occurs when I try to install GEOquery. Please, any ideas shall be much appreciated > biocLite('ArrayExpress') Using R version 2.13.0, biocinstall version 2.8.4. Installing Bioconductor version 2.8 packages: [1] "ArrayExpress" Please wait... Installing package(s) into ‘C:/Users/Teku/Documents/R/win- library/2.13’ (as ‘lib’ is unspecified) trying URL ' http://bioconductor.org/packages/2.8/bioc/bin/windows/contrib/2.13/Arr ayExpress_1.12.0.zip ' Content type 'application/zip' length 217981 bytes (212 Kb) opened URL downloaded 212 Kb package 'ArrayExpress' successfully unpacked and MD5 sums checked The downloaded packages are in C:\Users\Teku\AppData\Local\Temp\RtmpKMihJ3\downloaded_packages > library(ArrayExpress) Error : package 'XML' does not have a name space Error: package/namespace load failed for 'ArrayExpress' > sessionInfo() R version 2.13.0 (2011-04-13) Platform: i386-pc-mingw32/i386 (32-bit) locale: [1] LC_COLLATE=Finnish_Finland.1252 LC_CTYPE=Finnish_Finland.1252 [3] LC_MONETARY=Finnish_Finland.1252 LC_NUMERIC=C [5] LC_TIME=Finnish_Finland.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] Biobase_2.12.1 loaded via a namespace (and not attached): [1] tools_2.13.0 [[alternative HTML version deleted]]

Hi Gabriel, On Sun, May 1, 2011 at 12:08 PM, gabriel teku <gabbyteku at="" gmail.com=""> wrote: > Hi all, > I have just installed R version 2.13.0 on a windows 7 machine but don't seem > to be able to install some packages from bioconductor. The culprit may be > package XML namespace. Below are details while trying to install package > ArrayExpress. Important to note that a similar error occurs when I try to > install GEOquery. > Please, any ideas shall be much appreciated > >> biocLite('ArrayExpress') > Using R version 2.13.0, biocinstall version 2.8.4. > Installing Bioconductor version 2.8 packages: > [1] "ArrayExpress" > Please wait... > > Installing package(s) into ?C:/Users/Teku/Documents/R/win- library/2.13? > (as ?lib? is unspecified) > trying URL ' > http://bioconductor.org/packages/2.8/bioc/bin/windows/contrib/2.13/A rrayExpress_1.12.0.zip > ' > Content type 'application/zip' length 217981 bytes (212 Kb) > opened URL > downloaded 212 Kb > > package 'ArrayExpress' successfully unpacked and MD5 sums checked > > The downloaded packages are in > ? ? ? ?C:\Users\Teku\AppData\Local\Temp\RtmpKMihJ3\downloaded_packages >> library(ArrayExpress) > Error : package 'XML' does not have a name space > Error: package/namespace load failed for 'ArrayExpress' >> sessionInfo() > R version 2.13.0 (2011-04-13) > Platform: i386-pc-mingw32/i386 (32-bit) > > locale: > [1] LC_COLLATE=Finnish_Finland.1252 ?LC_CTYPE=Finnish_Finland.1252 > [3] LC_MONETARY=Finnish_Finland.1252 LC_NUMERIC=C > [5] LC_TIME=Finnish_Finland.1252 > > attached base packages: > [1] stats ? ? graphics ?grDevices utils ? ? datasets ?methods ? base > > other attached packages: > [1] Biobase_2.12.1 > > loaded via a namespace (and not attached): > [1] tools_2.13.0 > I can't reproduce this. What happens when you type: source("http://bioconductor.org/biocLite.R") biocinstallRepos() ? I get the following: "http://bioconductor.org/packages/2.8/bioc" "http://bioconductor.org/packages/2.8/data/annotation" "http://bioconductor.org/packages/2.8/data/experiment" "http://bioconductor.org/packages/2.8/extra" "http://brainarray.mbni.med.umich.edu/bioc" CRAN "http://cran.fhcrc.org" CRANextra "http://www.stats.ox.ac.uk/pub/RWin" > So I am downloading XML from "CRANextra". You could force this as follows: install.packages("XML", repos="http://www.stats.ox.ac.uk/pub/RWin") Then try: biocLite("ArrayExpress") again. Dan > ? ? ? ?[[alternative HTML version deleted]] > > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >