Hi Dan, Thanks a lot. After following your advice, it is now running nicely. Regards, Omar On Wed, May 4, 2011 at 11:34 PM, Dan Tenenbaum <dtenenba@fhcrc.org> wrote: > On Wed, May 4, 2011 at 2:28 PM, Omar Gutierrez Arenas > <tardebut@gmail.com> wrote: > > Dear Colleagues, > > > > I'm trying to install the bioconductor package "arrayQualityMetrics". > > However, after downloading it succesfully, it fails to be load by > > library(arrayQualityMetrics) despite it is listed among the available > > packages. > > > > *> source("**http://bioconductor.org/biocLite.R*< > http://bioconductor.org/biocLite.R> > > *") > > BioC_mirror = **http://bioconductor.org* <http: bioconductor.org=""/> > > *Change using chooseBioCmirror(). > > Warning messages: > > 1: In safeSource() : Redefining ‘biocinstall’ > > 2: In safeSource() : Redefining ‘biocinstallPkgGroups’ > > 3: In safeSource() : Redefining ‘biocinstallRepos’* > > > > *> biocLite("arrayQualityMetrics") > > Using R version 2.13.0, biocinstall version 2.8.4. > > Installing Bioconductor version 2.8 packages: > > [1] "arrayQualityMetrics" > > Please wait...* > > *Installing package(s) into ‘C:/Users/Omar/Documents/R/win- library/2.13’ > > (as ‘lib’ is unspecified) > > also installing the dependencies ‘beadarray’, ‘Cairo’, ‘hwriter’, > ‘setRNG’, > > ‘SVGAnnotation’* > > *trying URL ' > > > http://bioconductor.org/packages/2.8/bioc/bin/windows/contrib/2.13/b eadarray_2.2.0.zip > > ' > > Content type 'application/zip' length 13099122 bytes (12.5 Mb) > > opened URL > > downloaded 12.5 Mb* > > *trying URL ' > http://cran.fhcrc.org/bin/windows/contrib/2.13/Cairo_1.4-9.zip' > > Content type 'application/zip' length 1015277 bytes (991 Kb) > > opened URL > > downloaded 991 Kb* > > *trying URL ' > http://cran.fhcrc.org/bin/windows/contrib/2.13/hwriter_1.3.zip' > > Content type 'application/zip' length 137651 bytes (134 Kb) > > opened URL > > downloaded 134 Kb* > > *trying URL ' > > http://cran.fhcrc.org/bin/windows/contrib/2.13/setRNG_2009.11-1.zip' > > Content type 'application/zip' length 56609 bytes (55 Kb) > > opened URL > > downloaded 55 Kb* > > *trying URL ' > > > http://bioconductor.org/packages/2.8/extra/bin/windows/contrib/2.13/ SVGAnnotation_0.9-0.zip > > ' > > Content type 'application/zip' length 3060112 bytes (2.9 Mb) > > opened URL > > downloaded 2.9 Mb* > > *trying URL ' > > > http://bioconductor.org/packages/2.8/bioc/bin/windows/contrib/2.13/a rrayQualityMetrics_3.8.0.zip > > ' > > Content type 'application/zip' length 699040 bytes (682 Kb) > > opened URL > > downloaded 682 Kb* > > *package 'beadarray' successfully unpacked and MD5 sums checked > > package 'Cairo' successfully unpacked and MD5 sums checked > > package 'hwriter' successfully unpacked and MD5 sums checked > > package 'setRNG' successfully unpacked and MD5 sums checked > > package 'SVGAnnotation' successfully unpacked and MD5 sums checked > > package 'arrayQualityMetrics' successfully unpacked and MD5 sums checked* > > *The downloaded packages are in > > C:\Users\Omar\AppData\Local\Temp\RtmpaOw228\downloaded_packages > >> library(arrayQualityMetrics) > > Error : package 'XML' does not have a name space > > Error: package/namespace load failed for 'arrayQualityMetrics'* > > > > > Hi Omar, > > There was a bad version of the XML package floating around a few days ago. > You can replace it as follows, in a fresh R session: > > source("http://bioconductor.org/biocLite.R") > biocLite("XML") > > -- or -- > > install.packages("XML", repos="http://www.stats.ox.ac.uk/pub/RWin") > > Then try > > biocLite("arrayQualityMetrics") > > again. > > Dan > > > > > > I look forward to hear from you. > > > > Omar > > > > [[alternative HTML version deleted]] > > > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@r-project.org > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > [[alternative HTML version deleted]]