Install of 1.5 Packages fails
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Thomas Girke ★ 1.7k
@thomas-girke-993
Last seen 9 weeks ago
United States
I am experiencing some problems installing the new Bioconductor Package Release 1.5 under R-2.0.0 on a Linux Debian machine. Below are my commands and the error summary. As a result, none of the packages that I need are working under R-2.0.0. Any help with this would be highly appreciated. > source("http://www.bioconductor.org/getBioC.R") > getBioC() Running getBioC version 1.2.68.... .............stuff................ You have downloaded a default set of packages. If you wish to see other download options, please go to the URL: http://www.bioconductor.org/faq.html#getBioC Warning messages: 1: Installation of package affyPLM had non-zero exit status in: installPkg(fileName, pkg, pkgVer, type, lib, repEntry, versForce) 2: Installation of package annaffy had non-zero exit status in: installPkg(fileName, pkg, pkgVer, type, lib, repEntry, versForce) 3: Installation of package genefilter had non-zero exit status in: installPkg(fileName, pkg, pkgVer, type, lib, repEntry, versForce) 4: Installation of package edd had non-zero exit status in: installPkg(fileName, pkg, pkgVer, type, lib, repEntry, versForce) 5: Installation of package marray had non-zero exit status in: installPkg(fileName, pkg, pkgVer, type, lib, repEntry, versForce) -- Thomas Girke 108 Noel T. Keen Hall University of California Riverside, CA 92521 E-mail: thomas.girke@ucr.edu Website: http://faculty.ucr.edu/~tgirke Ph: 951-787-2469 Fax: 951-787-4437
GO edd genefilter annaffy affyPLM marray GO edd genefilter annaffy affyPLM marray • 1.2k views
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Jeff Gentry ★ 3.9k
@jeff-gentry-12
Last seen 9.7 years ago
> I am experiencing some problems installing the new Bioconductor > Package Release 1.5 under R-2.0.0 on a Linux Debian machine. Below are > my commands and the error summary. As a result, none of the packages > that I need are working under R-2.0.0. Any help with this would be > highly appreciated. You're going to need to provide more specific information as to why those packages failed to install for you - either by going back through the log for the specific code or trying it by hand. W/ the amount of info you've provided here it is basically impossible to tell you much of anything. -J
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rgentleman ★ 5.5k
@rgentleman-7725
Last seen 9.1 years ago
United States
On Tue, Nov 02, 2004 at 01:21:22PM -0800, Thomas Girke wrote: > I am experiencing some problems installing the new Bioconductor Package Release 1.5 > under R-2.0.0 on a Linux Debian machine. Below are my commands and the error summary. > As a result, none of the packages that I need are working under R-2.0.0. > Any help with this would be highly appreciated. > > > source("http://www.bioconductor.org/getBioC.R") > > getBioC() > Running getBioC version 1.2.68.... > .............stuff................ > You have downloaded a default set of packages. > If you wish to see other download options, please go to the URL: > http://www.bioconductor.org/faq.html#getBioC > Warning messages: > 1: Installation of package affyPLM had non-zero exit status in: > installPkg(fileName, pkg, pkgVer, type, lib, repEntry, versForce) try just install one of these individually, something like: library(reposTools) install.packages2("affyPLM") and see what the output of that is. In particular it should give you some hints about the problem - fix these, and repeat for the other packages. Robert > 2: Installation of package annaffy had non-zero exit status in: > installPkg(fileName, pkg, pkgVer, type, lib, repEntry, > versForce) > 3: Installation of package genefilter had non-zero exit status > in: installPkg(fileName, pkg, pkgVer, type, lib, repEntry, > versForce) > 4: Installation of package edd had non-zero exit status in: > installPkg(fileName, pkg, pkgVer, type, lib, repEntry, > versForce) > 5: Installation of package marray had non-zero exit status in: > installPkg(fileName, pkg, pkgVer, type, lib, repEntry, > versForce) > > > > -- > Thomas Girke > 108 Noel T. Keen Hall > University of California > Riverside, CA 92521 > > E-mail: thomas.girke@ucr.edu > Website: http://faculty.ucr.edu/~tgirke > Ph: 951-787-2469 > Fax: 951-787-4437 > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor -- +--------------------------------------------------------------------- ------+ | Robert Gentleman phone : (617) 632-5250 | | Associate Professor fax: (617) 632-2444 | | Department of Biostatistics office: M1B20 | | Harvard School of Public Health email: rgentlem@jimmy.harvard.edu | +--------------------------------------------------------------------- ------+
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Robert, Thanks, this solved my problem. Thomas On Tue 11/02/04 16:43, Robert Gentleman wrote: > On Tue, Nov 02, 2004 at 01:21:22PM -0800, Thomas Girke wrote: > > I am experiencing some problems installing the new Bioconductor Package Release 1.5 > > under R-2.0.0 on a Linux Debian machine. Below are my commands and the error summary. > > As a result, none of the packages that I need are working under R-2.0.0. > > Any help with this would be highly appreciated. > > > > > source("http://www.bioconductor.org/getBioC.R") > > > getBioC() > > Running getBioC version 1.2.68.... > > .............stuff................ > > You have downloaded a default set of packages. > > If you wish to see other download options, please go to the URL: > > http://www.bioconductor.org/faq.html#getBioC > > Warning messages: > > 1: Installation of package affyPLM had non-zero exit status in: > > installPkg(fileName, pkg, pkgVer, type, lib, repEntry, versForce) > > try just install one of these individually, > something like: > > library(reposTools) > install.packages2("affyPLM") > > and see what the output of that is. In particular it should give you > some hints about the problem - fix these, and repeat for the other > packages. > > Robert > > > > 2: Installation of package annaffy had non-zero exit status in: > > installPkg(fileName, pkg, pkgVer, type, lib, repEntry, > > versForce) > > 3: Installation of package genefilter had non-zero exit status > > in: installPkg(fileName, pkg, pkgVer, type, lib, repEntry, > > versForce) > > 4: Installation of package edd had non-zero exit status in: > > installPkg(fileName, pkg, pkgVer, type, lib, repEntry, > > versForce) > > 5: Installation of package marray had non-zero exit status in: > > installPkg(fileName, pkg, pkgVer, type, lib, repEntry, > > versForce) > > > > > > > > -- > > Thomas Girke > > 108 Noel T. Keen Hall > > University of California > > Riverside, CA 92521 > > > > E-mail: thomas.girke@ucr.edu > > Website: http://faculty.ucr.edu/~tgirke > > Ph: 951-787-2469 > > Fax: 951-787-4437 > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@stat.math.ethz.ch > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > -- > +------------------------------------------------------------------- --------+ > | Robert Gentleman phone : (617) 632-5250 | > | Associate Professor fax: (617) 632-2444 | > | Department of Biostatistics office: M1B20 | > | Harvard School of Public Health email: rgentlem@jimmy.harvard.edu | > +------------------------------------------------------------------- --------+ > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > -- Thomas Girke 108 Noel T. Keen Hall University of California Riverside, CA 92521 E-mail: thomas.girke@ucr.edu Website: http://faculty.ucr.edu/~tgirke Ph: 951-787-2469 Fax: 951-787-4437
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