[BioC] Error installing geneplotter

Ignacio Lopez de Ullibarri [guest] guest at bioconductor.org
Wed Nov 2 16:57:13 CET 2011

Dear list,

I get the following error when trying to update geneplotter to the version packaged with the new Bioconductor 2.9:

> update.packages(repos=biocinstallRepos(), ask=F,checkBuilt=T)
trying 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)
opened URL
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 ...
** testing if installed package can be loaded
Error in namespaceExport(ns, exports) : 
  undefined exports: .__C__file, .__C__connection
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/usr/local/lib/R/site-library/geneplotter’
* restoring previous ‘/usr/local/lib/R/site-library/geneplotter’

The downloaded packages are in
Warning message:
In install.packages(update[instlib == l, "Package"], l, contriburl = contriburl,  :
  installation of package ‘geneplotter’ had non-zero exit status

 -- output of sessionInfo(): 

R version 2.14.0 (2011-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)

 [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8    
 [7] LC_PAPER=C                 LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] BiocInstaller_1.2.0

loaded via a namespace (and not attached):
 [1] annotate_1.32.0      AnnotationDbi_1.16.0 Biobase_2.14.0      
 [4] DBI_0.2-5            genefilter_1.36.0    IRanges_1.12.0      
 [7] mnormt_1.4-3         RSQLite_0.10.0       sn_0.4-17           
[10] splines_2.14.0       survival_2.36-10     tcltk_2.14.0        
[13] tools_2.14.0         xtable_1.6-0    

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