Dear List I'm having difficulties download Bioconductor onto an OpenSUSE 11.1 system. Many of the Biobase component packages install fine, but the full set won't download, nor will other Bioconductor packages eg GEOquery. Below is the final bit of the ouptput including error messages - the RCurl package seems to be a problem. Any ideas how to get round this? Thanks Jonathan Sive Warning in library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc = lib.loc) : there is no package called 'affy' Error : package 'affy' could not be loaded ERROR: lazy loading failed for package ‘affyQCReport’ * removing ‘/home/POGBDOM/regmjs9/R/x86_64-unknown-linux-gnu- library/2.10/affyQCReport’ The downloaded packages are in ‘/tmp/Rtmpp2hkWJ/downloaded_packages’ There were 13 warnings (use warnings() to see them) > warnings() Warning messages: 1: In install.packages(pkgs = pkgs, repos = repos, ...) : installation of package 'affyio' had non-zero exit status 2: In install.packages(pkgs = pkgs, repos = repos, ...) : installation of package 'XML' had non-zero exit status 3: In install.packages(pkgs = pkgs, repos = repos, ...) : installation of package 'RCurl' had non-zero exit status 4: In install.packages(pkgs = pkgs, repos = repos, ...) : installation of package 'affy' had non-zero exit status 5: In install.packages(pkgs = pkgs, repos = repos, ...) : installation of package 'biomaRt' had non-zero exit status 6: In install.packages(pkgs = pkgs, repos = repos, ...) : installation of package 'affydata' had non-zero exit status 7: In install.packages(pkgs = pkgs, repos = repos, ...) : installation of package 'annaffy' had non-zero exit status 8: In install.packages(pkgs = pkgs, repos = repos, ...) : installation of package 'gcrma' had non-zero exit status 9: In install.packages(pkgs = pkgs, repos = repos, ...) : installation of package 'vsn' had non-zero exit status 10: In install.packages(pkgs = pkgs, repos = repos, ...) : installation of package 'affyPLM' had non-zero exit status 11: In install.packages(pkgs = pkgs, repos = repos, ...) : installation of package 'genefilter' had non-zero exit status 12: In install.packages(pkgs = pkgs, repos = repos, ...) : installation of package 'simpleaffy' had non-zero exit status 13: In install.packages(pkgs = pkgs, repos = repos, ...) : installation of package 'affyQCReport' had non-zero exit status ********************************************************************** This email and any files transmitted with it are confide...{{dropped:10}}

On Thu, Nov 26, 2009 at 8:56 AM, Jonathan Sive <jonathan.sive at="" cancer.ucl.ac.uk=""> wrote: > Dear List > > I'm having difficulties download Bioconductor onto an OpenSUSE 11.1 system. > Many of the Biobase component packages install fine, but the full set won't download, nor will other Bioconductor packages eg GEOquery. > > Below is the final bit of the ouptput including error messages - the RCurl package seems to be a problem. Did you install libcurl and the devel libraries for it? Sean > Any ideas how to get round this? > > Thanks > Jonathan Sive > > > Warning in library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc = lib.loc) : > ?there is no package called 'affy' > Error : package 'affy' could not be loaded > ERROR: lazy loading failed for package ?affyQCReport? > * removing ?/home/POGBDOM/regmjs9/R/x86_64-unknown-linux-gnu- library/2.10/affyQCReport? > > The downloaded packages are in > ? ? ? ??/tmp/Rtmpp2hkWJ/downloaded_packages? > There were 13 warnings (use warnings() to see them) >> warnings() > Warning messages: > 1: In install.packages(pkgs = pkgs, repos = repos, ...) : > ?installation of package 'affyio' had non-zero exit status > 2: In install.packages(pkgs = pkgs, repos = repos, ...) : > ?installation of package 'XML' had non-zero exit status > 3: In install.packages(pkgs = pkgs, repos = repos, ...) : > ?installation of package 'RCurl' had non-zero exit status > 4: In install.packages(pkgs = pkgs, repos = repos, ...) : > ?installation of package 'affy' had non-zero exit status > 5: In install.packages(pkgs = pkgs, repos = repos, ...) : > ?installation of package 'biomaRt' had non-zero exit status > 6: In install.packages(pkgs = pkgs, repos = repos, ...) : > ?installation of package 'affydata' had non-zero exit status > 7: In install.packages(pkgs = pkgs, repos = repos, ...) : > ?installation of package 'annaffy' had non-zero exit status > 8: In install.packages(pkgs = pkgs, repos = repos, ...) : > ?installation of package 'gcrma' had non-zero exit status > 9: In install.packages(pkgs = pkgs, repos = repos, ...) : > ?installation of package 'vsn' had non-zero exit status > 10: In install.packages(pkgs = pkgs, repos = repos, ...) : > ?installation of package 'affyPLM' had non-zero exit status > 11: In install.packages(pkgs = pkgs, repos = repos, ...) : > ?installation of package 'genefilter' had non-zero exit status > 12: In install.packages(pkgs = pkgs, repos = repos, ...) : > ?installation of package 'simpleaffy' had non-zero exit status > 13: In install.packages(pkgs = pkgs, repos = repos, ...) : > ?installation of package 'affyQCReport' had non-zero exit status > > > > > > > ********************************************************************** > This email and any files transmitted with it are confide...{{dropped:10}} > > > _______________________________________________ > 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 >