[BioC] Error in installing Gviz

[Martin Morgan]

On 10/05/2013 08:39 AM, 马磊 wrote:
> Hi everyone,
>        When I install Gviz_1.4.5.tar.gz, I enconter the following error messeage. Would you help me to resovle these errors?
>
>   * installing *source* package 'Gviz' ...
> ** R
> ** data
> ** inst
> ** preparing package for lazy loading
> Error : object 'subseq' is not exported by 'namespace:IRanges'
> ERROR: lazy loading failed for package 'Gviz'

Hi --

I think that you have incompatible versions of packages, specifically the 
'devel' (odd-numbered second field in version number) version of IRanges. Try

   source('http://bioconductor.org/biocLite.R')
   biocValid()

and follow instructions to update packages. If this does not work please provide 
the output of

   sessionInfo()

after (trying to) installing Gviz. If instead you'd like to use 'devel', 
including the devel version of Gviz, then follow the instructions at

   http://bioconductor.org/developers/how-to/useDevel/

Here is my sessionInfo()

 > sessionInfo()
R version 3.0.2 Patched (2013-10-02 r64018)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
  [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

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

other attached packages:
[1] Gviz_1.4.5

loaded via a namespace (and not attached):
  [1] AnnotationDbi_1.22.6   Biobase_2.20.1         BiocGenerics_0.6.0
  [4] biomaRt_2.16.0         Biostrings_2.28.0      biovizBase_1.8.1
  [7] bitops_1.0-6           BSgenome_1.28.0        cluster_1.14.4
[10] colorspace_1.2-4       DBI_0.2-7              dichromat_2.0-0
[13] GenomicFeatures_1.12.4 GenomicRanges_1.12.5   Hmisc_3.12-2
[16] IRanges_1.18.4         labeling_0.2           lattice_0.20-23
[19] munsell_0.4.2          parallel_3.0.2         plyr_1.8
[22] RColorBrewer_1.0-5     RCurl_1.95-4.1         rpart_4.1-3
[25] Rsamtools_1.12.4       RSQLite_0.11.4         rtracklayer_1.20.4
[28] scales_0.2.3           stats4_3.0.2           stringr_0.6.2
[31] tools_3.0.2            XML_3.98-1.1           zlibbioc_1.6.0

>
>   Best wishes,
>
>   Mark
> 	[[alternative HTML version deleted]]
>
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