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

[Mao Jianfeng]

2011/3/30 Hervé Pagès <hpages at fhcrc.org>:
> 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

It works for me, Thanks a lot.


>
> 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
> 1100 Fairview Ave. N, M2-B876
> P.O. Box 19024
> Seattle, WA 98109-1024
>
> E-mail: hpages at fhcrc.org
> Phone:  (206) 667-5791
> Fax:    (206) 667-1319
>



-- 
Jian-Feng, Mao

the Institute of Botany,
Chinese Academy of Botany,