[BioC] beadarray vignette has broken code in R2.14.1?
dtenenba at fhcrc.org
Sat Mar 3 09:48:27 CET 2012
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
> 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.
> 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)
>  LC_COLLATE=English_United Kingdom.1252
>  LC_CTYPE=English_United Kingdom.1252
>  LC_MONETARY=English_United Kingdom.1252
>  LC_NUMERIC=C
>  LC_TIME=English_United Kingdom.1252
> attached base packages:
>  stats graphics grDevices utils datasets methods base
> other attached packages:
>  BiocInstaller_1.2.1
> loaded via a namespace (and not attached):
>  tools_2.14.1
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