Galina, I just updated the XML Windows binary package for R 2.9 in the bioconductor extra repository. You can now obtain it using source("http://bioconductor.org/biocLite.R") biocLite("XML") Patrick Martin Morgan wrote: > Hi Galina -- > > Looks like your XML package is out-of-date. You'll need to update it or > all of your packages, following the instructions at > > http://bioconductor.org/docs/install/ > > Martin > > Glazko, Galina wrote: > >> Dear all, >> >> >> >> Last week I updated R to the version 2.9.0 and Bioconductor to the >> version 2.4 >> >> I am trying to install KEGGSOAP now but something strange happens: >> >> >> >> >>> biocLite('KEGGSOAP') >>> >> Running biocinstall version 2.4.10 with R version 2.9.0 >> Your version of R requires version 2.4 of Bioconductor. >> Warning: unable to access index for repository >> http://brainarray.mbni.med.umich.edu/bioc/bin/windows/contrib/2.9 >> trying URL >> 'http://bioconductor.org/packages/2.4/bioc/bin/windows/contrib/2.9/ KEGGS >> OAP_1.18.0.zip' >> Content type 'application/zip' length 104952 bytes (102 Kb) >> opened URL >> downloaded 102 Kb >> >> package 'KEGGSOAP' successfully unpacked and MD5 sums checked >> >> The downloaded packages are in >> C:\Documents and Settings\Galina\Local >> Settings\Temp\RtmpIMZxc6\downloaded_packages >> updating HTML package descriptions >> >> >> >> - so the installation seems to be OK? >> >> >> >> >>> library('KEGGSOAP') >>> >> Error in inDL(x, as.logical(local), as.logical(now), ...) : >> unable to load shared library >> 'C:/PROGRA~1/R/R-29~1.0/library/XML/libs/XML.dll': >> LoadLibrary failure: The specified module could not be found. >> >> >> Error : .onLoad failed in 'loadNamespace' for 'XML' >> Error: package/namespace load failed for 'KEGGSOAP' >> >> >> >> Could someone point what is wrong? >> >> Thank you! >> >> >> >> Best regards >> >> Galina >> >> >> >> >>> sessionInfo() >>> >> R version 2.9.0 (2009-04-17) >> i386-pc-mingw32 >> >> >> >> >> >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> 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 >

Dear Martin and Vincent, Thank you very much! The "XML" update solved my problem. Best regards Galina ________________________________ From: Vincent Carey [mailto:stvjc@channing.harvard.edu] Sent: Tuesday, April 28, 2009 12:05 PM To: Glazko, Galina Cc: bioconductor@stat.math.ethz.ch Subject: Re: [BioC] KEGGSOAP problem your XML package installation is flawed. According to omegahat.org There is also a Windows version available from the Omegahat repository. Use install.packages("XML", repos = "http://www.omegahat.org/R") If that does not solve your problem let us know. On Tue, Apr 28, 2009 at 11:31 AM, Glazko, Galina <galina_glazko@urmc.rochester.edu> wrote: Dear all, Last week I updated R to the version 2.9.0 and Bioconductor to the version 2.4 I am trying to install KEGGSOAP now but something strange happens: > biocLite('KEGGSOAP') Running biocinstall version 2.4.10 with R version 2.9.0 Your version of R requires version 2.4 of Bioconductor. Warning: unable to access index for repository http://brainarray.mbni.med.umich.edu/bioc/bin/windows/contrib/2.9 trying URL 'http://bioconductor.org/packages/2.4/bioc/bin/windows/contrib/2.9/KEG GS OAP_1.18.0.zip' Content type 'application/zip' length 104952 bytes (102 Kb) opened URL downloaded 102 Kb package 'KEGGSOAP' successfully unpacked and MD5 sums checked The downloaded packages are in C:\Documents and Settings\Galina\Local Settings\Temp\RtmpIMZxc6\downloaded_packages updating HTML package descriptions - so the installation seems to be OK? > library('KEGGSOAP') Error in inDL(x, as.logical(local), as.logical(now), ...) : unable to load shared library 'C:/PROGRA~1/R/R-29~1.0/library/XML/libs/XML.dll': LoadLibrary failure: The specified module could not be found. Error : .onLoad failed in 'loadNamespace' for 'XML' Error: package/namespace load failed for 'KEGGSOAP' Could someone point what is wrong? Thank you! Best regards Galina > sessionInfo() R version 2.9.0 (2009-04-17) i386-pc-mingw32 [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Vincent Carey, PhD Biostatistics, Channing Lab 617 525 2265 [[alternative HTML version deleted]]