[Bioc-devel] failed to build BSgenome data package in R-2.13 alpha (2011-03027 r55091)

[Hervé Pagès]

Hi Jian-Feng,

Seems like you have some version mismatch issues. Make sure that the R
you use when doing R CMD INSTALL is the one that was used for installing
all the stuff you have under /ebio/abt6/jmao/bin/R-2.13/Rpacks. In
particular, it should be R 2.13.

You can check this with 'which R', or just start 'R' and check the
version. If that's not the R you want, then use something like:

   /full/path/to/my/R CMD INSTALL BSgenome/ 
--library=/ebio/abt6/jmao/bin/R-2.13/Rpacks

Let me know if that's still not working.

H.


On 03/30/2011 02:17 AM, Mao Jianfeng wrote:
> Dear Pages,
>
> Thanks for your helps and directions.
>
> I did what you have showed me. But, it did not work for me.
>
> I show you the INFO of my failing. I am feeling sorry for my troubles
> to you. If the compatibility of BSgenome with R-2.13.0 can be worked
> out soon by you. I just want to wait for that.
>
> Thanks a lot.
>
> Jian-Feng,
>
> #########################################
> (1) command and the return
>
> $ R CMD INSTALL BSgenome/ --library=/ebio/abt6/jmao/bin/R-2.13/Rpacks
> * installing *source* package ‘BSgenome’ ...
> ** R
> ** inst
> ** preparing package for lazy loading
> Warning: package 'IRanges' was built under R version 2.13.0
> Warning in .recacheSubclasses(def at className, def, doSubclasses, env) :
>    Undefined subclass, "activeBindingFunction", of class
> "expressionORfunction"; definition not updated
> Warning in .recacheSubclasses(def at className, def, doSubclasses, env) :
>    Undefined subclass, "refMethodDef", of class "expressionORfunction";
> definition not updated
> Warning in .recacheSubclasses(def at className, def, doSubclasses, env) :
>    Undefined subclass, "defaultBindingFunction", of class
> "expressionORfunction"; definition not updated
> Warning in .recacheSubclasses(def at className, def, doSubclasses, env) :
>    Undefined subclass, "activeBindingFunction", of class
> "functionORNULL"; definition not updated
> Warning in .recacheSubclasses(def at className, def, doSubclasses, env) :
>    Undefined subclass, "refMethodDef", of class "functionORNULL";
> definition not updated
> Warning in .recacheSubclasses(def at className, def, doSubclasses, env) :
>    Undefined subclass, "defaultBindingFunction", of class
> "functionORNULL"; definition not updated
> Warning in .recacheSubclasses(def at className, def, doSubclasses, env) :
>    Undefined subclass, "namedList", of class "vectorORfactor";
> definition not updated
> Warning in .recacheSubclasses(def at className, def, doSubclasses, env) :
>    Undefined subclass, "listOfMethods", of class "vectorORfactor";
> definition not updated
>
> Attaching package: 'IRanges'
>
>
> 	The following object(s) are masked from package:base :
>
> 	 Map,
> 	 cbind,
> 	 eval,
> 	 intersect,
> 	 mapply,
> 	 order,
> 	 paste,
> 	 pmax,
> 	 pmax.int,
> 	 pmin,
> 	 pmin.int,
> 	 rbind,
> 	 rep.int,
> 	 setdiff,
> 	 table,
> 	 union
>
> Warning: package 'GenomicRanges' was built under R version 2.13.0
> Error in sub("([^-]+)_.*", "\\1", info$pkgname) :
>    7 arguments passed to .Internal(sub) which requires 8
> Error : unable to load R code in package 'GenomicRanges'
> Error : package 'GenomicRanges' could not be loaded
> ERROR: lazy loading failed for package ‘BSgenome’
> * removing ‘/ebio/abt6/jmao/bin/R-2.13/Rpacks/BSgenome’
> * restoring previous ‘/ebio/abt6/jmao/bin/R-2.13/Rpacks/BSgenome’
>
> #########################################
> (2) my R version and GenomicRanges library
>> version
>                 _
> platform       x86_64-unknown-linux-gnu
> arch           x86_64
> os             linux-gnu
> system         x86_64, linux-gnu
> status         alpha
> major          2
> minor          13.0
> year           2011
> month          03
> day            27
> svn rev        55091
> language       R
> version.string R version 2.13.0 alpha (2011-03-27 r55091)
>> sessionInfo()
> R version 2.13.0 alpha (2011-03-27 r55091)
> 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=C              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] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] GenomicRanges_1.3.29 IRanges_1.9.28
>
> loaded via a namespace (and not attached):
> [1] tools_2.13.0


-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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