[BioC] Error installing geneplotter

[Dan Tenenbaum]

Hello,

On Wed, Nov 2, 2011 at 8:57 AM, Ignacio Lopez de Ullibarri [guest]
<guest at bioconductor.org> wrote:
>
> 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 ...
>   ‘byChroms.Rnw’
>   ‘visualize.Rnw’
> ** 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
>        ‘/tmp/RtmpUnjUVh/downloaded_packages’
> 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)
>
> locale:
>  [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C
>  [3] LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8
>  [5] LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=en_GB.UTF-8
>  [7] LC_PAPER=C                 LC_NAME=C
>  [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=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
>
> --
> Sent via the guest posting facility at bioconductor.org.

We will have an updated version of geneplotter (1.32.1) available in a
couple of hours.

Thanks,
Dan


>
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