On Wed, Feb 29, 2012 at 8:58 AM, Henriquez, Nick <n.henriquez at="" ucl.ac.uk=""> wrote: > Not posted/worked on R in ages. I am encountering a reproducible problem using BeadarrayUseCases from BioC downloadsite with R2.14.1. For clarity the session info, actual pasted command and full error are all pasted below. > > When I paste the command from the vignette into R (x64 or x32) I get "(all packages listed) ... are not available (for R version 2.14.1)". > > The problem was resolved by installing/using 2.14.0 instead (as the vignette was compiled in 2.14.0) meaning I can get on with my work. > > I just thought I should report it since it seems excessive that a minor version change would stop such a recent package from working. Especially since the advice given when installing BioC is to get the latest version. > > Whatever the cause may affect multiple packages meaning people would be forced to "downgrade" for some applications. > > Keep up the good work! Nick > > > CMD: > biocLite (c(" beadarray ", " limma ", " GEOquery ", " illuminaHumanv1 .db", > 3 + " illuminaHumanv2 .db", " illuminaHumanv3 .db", " BeadArrayUseCases ")) > There should not be spaces around the package names within quotes, and the "3 +" is going to cause problems. Dan > > Warning message: > In getDependencies(pkgs, dependencies, available, lib) : > ?packages ' beadarray ', ' limma ', ' GEOquery ', ' illuminaHumanv1 .db', ' illuminaHumanv2 .db', ' illuminaHumanv3 .db', ' BeadArrayUseCases ' are not available (for R version 2.14.1) > > > > R version 2.14.1 (2011-12-22) > Platform: i386-pc-mingw32/i386 (32-bit) > > locale: > [1] LC_COLLATE=English_United Kingdom.1252 > [2] LC_CTYPE=English_United Kingdom.1252 > [3] LC_MONETARY=English_United Kingdom.1252 > [4] LC_NUMERIC=C > [5] LC_TIME=English_United Kingdom.1252 > > attached base packages: > [1] stats ? ? graphics ?grDevices utils ? ? datasets ?methods ? base > > other attached packages: > [1] BiocInstaller_1.2.1 > > loaded via a namespace (and not attached): > [1] tools_2.14.1 > > ? ? ? ?[[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

I mistakenly replied to Dan only: --Thanks Dan, but that's not the issue. R tries to load the packages, finds them correctly, and decides they're not for 2.14.1. That's the problem. With special apologies to Dan; If I carefully copy line-by-line from the Rscript (as opposed to the PDF) and take care broken lines get pasted onto a single one in R, the commands provided on the download page for beadarrayUseCases do work correctly under 2.14.1. So, as Dan surmised, my problem stems from spaces/characters introduced by my copying commands from vignettes. In my defence, this was something I used to do successfully when I started using R/BioC in 2007. Perhaps a word of warning could be added in the various Vignettes/BioC instructions that (at least for windows users) copy-pasting commands from vignettes can/will lead to problems. Thanks for the help. Nick -----Original Message----- From: Dan Tenenbaum [mailto:dtenenba@fhcrc.org] Sent: 03 March 2012 08:48 To: Henriquez, Nick Cc: bioconductor at r-project.org Subject: Re: [BioC] beadarray vignette has broken code in R2.14.1? On Wed, Feb 29, 2012 at 8:58 AM, Henriquez, Nick <n.henriquez at="" ucl.ac.uk=""> wrote: > Not posted/worked on R in ages. I am encountering a reproducible problem using BeadarrayUseCases from BioC downloadsite with R2.14.1. For clarity the session info, actual pasted command and full error are all pasted below. > > When I paste the command from the vignette into R (x64 or x32) I get "(all packages listed) ... are not available (for R version 2.14.1)". > > The problem was resolved by installing/using 2.14.0 instead (as the vignette was compiled in 2.14.0) meaning I can get on with my work. > > I just thought I should report it since it seems excessive that a minor version change would stop such a recent package from working. Especially since the advice given when installing BioC is to get the latest version. > > Whatever the cause may affect multiple packages meaning people would be forced to "downgrade" for some applications. > > Keep up the good work! Nick > > > CMD: > biocLite (c(" beadarray ", " limma ", " GEOquery ", " illuminaHumanv1 > .db", > 3 + " illuminaHumanv2 .db", " illuminaHumanv3 .db", " > BeadArrayUseCases ")) > There should not be spaces around the package names within quotes, and the "3 +" is going to cause problems. Dan > > Warning message: > In getDependencies(pkgs, dependencies, available, lib) : > ?packages ' beadarray ', ' limma ', ' GEOquery ', ' illuminaHumanv1 > .db', ' illuminaHumanv2 .db', ' illuminaHumanv3 .db', ' > BeadArrayUseCases ' are not available (for R version 2.14.1) > > > > R version 2.14.1 (2011-12-22) > Platform: i386-pc-mingw32/i386 (32-bit) > > locale: > [1] LC_COLLATE=English_United Kingdom.1252 [2] LC_CTYPE=English_United > Kingdom.1252 [3] LC_MONETARY=English_United Kingdom.1252 [4] > LC_NUMERIC=C [5] LC_TIME=English_United Kingdom.1252 > > attached base packages: > [1] stats ? ? graphics ?grDevices utils ? ? datasets ?methods ? base > > other attached packages: > [1] BiocInstaller_1.2.1 > > loaded via a namespace (and not attached): > [1] tools_2.14.1 > > ? ? ? ?[[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor