BioC 2.2 release update.packages error
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@elliot-kleiman-2565
Last seen 10.3 years ago
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/
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Patrick Aboyoun ★ 1.6k
@patrick-aboyoun-6734
Last seen 10.3 years ago
United States
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
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