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gravatar for Jonathan Sive
8.9 years ago by
Jonathan Sive30 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. 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}}
ADD COMMENTlink modified 8.9 years ago by Seth Falcon150 • written 8.9 years ago by Jonathan Sive30
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gravatar for Seth Falcon
8.9 years ago by
Seth Falcon150
Seth Falcon150 wrote:
Hi Jonathan, On Thu, Nov 26, 2009 at 5:55 AM, Jonathan Sive <jonathan.sive at="" cancer.ucl.ac.uk=""> wrote: > 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? Can you provide some additional details on how you are trying to install these packages? It is hard to tell exactly what steps you took to receive the messages you are seeing. If you are not using the biocLite helper function, please try it. + seth -- Seth Falcon | @sfalcon | http://userprimary.net/user
ADD COMMENTlink written 8.9 years ago by Seth Falcon150
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