Hi BioC, When trying to update my R-2.7.2/BioC-2.2 release, the update script errs out, # source the update file > source("http://bioconductor.org/biocLite.R") Warning messages: 1: In safeSource() : Redefining 'biocinstall' 2: In safeSource() : Redefining 'biocinstallPkgGroups' 3: In safeSource() : Redefining 'biocinstallRepos' # update packages > update.packages(repos=biocinstallRepos(), ask=FALSE) trying URL 'http://cran.fhcrc.org/src/contrib/XML_2.1-0.tar.gz' Error in download.file(url, destfile, method, mode = "wb", ...) : cannot open URL 'http://cran.fhcrc.org/src/contrib/XML_2.1-0.tar.gz' In addition: Warning message: In download.file(url, destfile, method, mode = "wb", ...) : cannot open: HTTP status was '404 Not Found' Warning in download.packages(p0, destdir = tmpd, available = available, : download of package 'XML' failed [:Question:] * What am I doing wrong here? i.e., it used to work fine ... # print sessionInfo() > sessionInfo() R version 2.7.2 (2008-08-25) i686-pc-linux-gnu locale: LC_CTYPE=en_US;LC_NUMERIC=C;LC_TIME=en_US; LC_COLLATE=C;LC_MONETARY=C;LC_MESSAGES=en_US; LC_PAPER=en_US;LC_NAME=C;LC_ADDRESS=C; LC_TELEPHONE=C;LC_MEASUREMENT=en_US; LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] tools_2.7.2 Thank you, ... Elliot -- MS graduate student Computational Science Program San Diego State University http://www.csrc.sdsu.edu/ http://www.sdsu.edu/

Elliot, My best guess at this time is that the bioconductor.org mirroring didn't properly capture the newly updated XML package. Interestingly, the XML packaged page at http://cran.fhcrc.org has a link to version 2.1-0 of XML and the PACKAGES file mentions version 2.1-0, but the CRAN repository at fhcrc.org still had version 1.99-0 of the XML source package. I just hand downloaded version 2.1-0 of the source package for XML to the CRAN mirror at fhcrc.org and tested downloading XML via biocLite and all looks well now. Give it a try. Patrick Quoting Elliot Kleiman <kleiman at="" rohan.sdsu.edu="">: > Hi BioC, > > When trying to update my R-2.7.2/BioC-2.2 > release, the update script errs out, > > # source the update file >> source("http://bioconductor.org/biocLite.R") > Warning messages: > 1: In safeSource() : Redefining 'biocinstall' > 2: In safeSource() : Redefining 'biocinstallPkgGroups' > 3: In safeSource() : Redefining 'biocinstallRepos' > > # update packages >> update.packages(repos=biocinstallRepos(), ask=FALSE) > trying URL 'http://cran.fhcrc.org/src/contrib/XML_2.1-0.tar.gz' > Error in download.file(url, destfile, method, mode = "wb", ...) : > cannot open URL 'http://cran.fhcrc.org/src/contrib/XML_2.1-0.tar.gz' > In addition: Warning message: > In download.file(url, destfile, method, mode = "wb", ...) : > cannot open: HTTP status was '404 Not Found' > Warning in download.packages(p0, destdir = tmpd, > available = available, : download of package 'XML' failed > > [:Question:] > * What am I doing wrong here? > i.e., it used to work fine ... > > # print sessionInfo() >> sessionInfo() > R version 2.7.2 (2008-08-25) > i686-pc-linux-gnu > > locale: > LC_CTYPE=en_US;LC_NUMERIC=C;LC_TIME=en_US; > LC_COLLATE=C;LC_MONETARY=C;LC_MESSAGES=en_US; > LC_PAPER=en_US;LC_NAME=C;LC_ADDRESS=C; > LC_TELEPHONE=C;LC_MEASUREMENT=en_US; > LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > loaded via a namespace (and not attached): > [1] tools_2.7.2 > > Thank you, > > ... Elliot > > -- > MS graduate student Computational Science Program San Diego State University > http://www.csrc.sdsu.edu/ http://www.sdsu.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