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

[Mao Jianfeng]

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