[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.
Nick
-----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.
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
More information about the Bioconductor
mailing list