[BioC] beadarray vignette has broken code in R2.14.1?

Henriquez, Nick n.henriquez at ucl.ac.uk
Mon Mar 5 10:09:07 CET 2012

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.


-----Original Message-----
From: Dan Tenenbaum [mailto:dtenenba at 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.


> 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]]
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