Hi Naveed, I was aware of this installation problem of XML package with outdated R/Biocondutor. Please always try to upgrade to the latest verison of R (3.0)/Bioconductor (2.12) for simpler installation and better use of Pathview. If you have to stick to your old version of R/Bioconductor. You may install XML package manually. You may download it from CRAN (http://cran.r-project.org/web/packages/XML/index.html) and then do something like: install.packages("/your/local/directory/XML_3.95-0.2.zip", repos = NULL) For more problems check with the Installation section of pathview vignette or webpage at http://pathview.r-forge.r-project.org/. HTH. Weijun -------------------------------------------- On Thu, 7/4/13, Naveed Shaikh <naveed.shaikh at="" gmail.com=""> wrote: Subject: Problem running pathview due to broken XML package Date: Thursday, July 4, 2013, 8:54 AM Hello Weijun, I came across your bioconductor package ?pathview? and wanted to take it for a run but realized that one of the packages down the dependency chain (XML package) is broken. This is apparently due to corrupt archiving. http://cran.fhcrc.org/web/packages/XML/index.html I noticed the same for the older archives of XML package. I am wondering if you encountered similar issue and if so, how did you go about resolving it? If it is of any help, I have attached the log file from R when I installed pathview. Let me know if you are aware of this issue and if there is a fix for it.Thanks.Regards,Naveed?