geneplotter installation error

Question

I've during the geneplotter (Bioconductor package) installation. I'm using R 2.14 on Linux Mint 9. I think the namespace is responsible for this but I don't know how to fix it ...

Here's the error :

> source("http://bioconductor.org/biocLite.R")
> biocLite("geneplotter")
BioC_mirror: 'http://www.bioconductor.org'
Using R version 2.14, BiocInstaller version 1.2.0.
Installing package(s) 'geneplotter'
Installing package(s) into ‘/home/nicolas/R/x86_64-pc-linux-gnu-library/2.14’
(as ‘lib’ is unspecified)
essai de l'URL 'http://www.bioconductor.org/packages/2.9/bioc/src/contrib/geneplotter_1.31.4.tar.gz'
Content type 'application/x-gzip' length 1387616 bytes (1.3 Mb)
URL ouverte
==================================================
downloaded 1.3 Mb

* installing *source* package ‘geneplotter’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   ‘byChroms.Rnw’ 
   ‘visualize.Rnw’ 
** testing if installed package can be loaded
Error in namespaceExport(ns, exports) : 
  undefined exports: .__C__file, .__C__connection
Erreur : le chargement a échoué
Exécution arrêtée
ERREUR : le chargement a échoué
* removing ‘/home/nicolas/R/x86_64-pc-linux-gnu-library/2.14/geneplotter’

The downloaded packages are in
    ‘/tmp/RtmpO1aY1T/downloaded_packages’
Message d'avis :
In install.packages(pkgs = pkgs, repos = repos, ...) :
  installation of package ‘geneplotter’ had non-zero exit status

Thanks in advance,

N.

Answer 1

Looking into this more closely, geneplotter failed to build for the initial release. So the version you are picking up is the penultimate version. The issue you identify was corrected yesterday, in time for the next build cycle. geneplotter should install correctly when it builds correctly, probably at noon PDT; look for version 1.32.1. In retrospect not a SO question; the Bioconductor mailing list has a post facility that does not require subscription.