[Bioc-devel] Biobase 1.15.33 depends on ALL problem

[Keith Satterley]

In addition to what I wrote previously, my immediate problem is this error:

 > library("affy")
Error: package 'Biobase' 1.15.33 was found, but >= c(1, 13, 41) is required by 
'affy'

affy has a Depends...Biobase (>= 1.13.41) in its DESCRIPTION file

I'm assuming this is a problem not unique to my installation of R

cheers,
Keith


Keith Satterley wrote:
> When I used biocLite("Biobase") I couldn't get version 1.15.33, so I downloaded 
> the source and I was doing and "R CMD check Biobase" on the source code. I 
> installed the latest Rtools.
> 
> Initially I got the warnings:
> 
> Found the following sources/headers with CR or CRLF line endings:
>    src/envir.c
>    src/Rinit.c
> 
> which I fixed to avoid these warnings.
> 
> There were also 6 warnings under:
>   Package vignettes without corresponding PDF:
> relating to .Rnw files in Biobase/inst/doc.
> 
> However, what are these errors reported in 00check.log:
> 
> *** Weave Errors ***
> File 
> W:/aaa-R/dev/R-2.6.0dev/Biobase/compile_version/ver-1.15.31/Biobase.Rcheck/inst/doc/Qviews.Rnw 
> :
> Error :  chunk 1 (label=doa)
> Error : package 'Biobase' 1.15.33 is loaded, but >= c(1, 12, 0) is required by 'ALL'
> *** Source Errors ***
> File 
> W:/aaa-R/dev/R-2.6.0dev/Biobase/compile_version/ver-1.15.31/Biobase.Rcheck/inst/doc/Qviews.R 
> :
> Error : package 'Biobase' 1.15.33 is loaded, but >= c(1, 12, 0) is required by 'ALL'
> 
> 
> I'm not very familiar with this sort of code, but on looking at the ALL package 
> which has "Depends: Biobase (>= 1.12.0)" in its DESCRIPTION file and on looking 
> at the svn log of Biobase I'm wondering if it is related to a change on Revision 
> 26853, which says:
> 
> Accomodate changes in base::package_version
> 
> - use numeric_version rather than package_version
> 
> - internal .as.numeric_version
> 
> - stronger checks on valid version comparisons
> 
> Need I worry about this? It installs OK and loads OK when I run R.
>  > sessionInfo()
> R version 2.6.0 Under development (unstable) (2007-09-02 r42744)
> i386-pc-mingw32
> 
> locale:
> LC_COLLATE=English_Australia.1252;LC_CTYPE=English_Australia.1252;LC_MONETARY=English_Australia.1252;LC_NUMERIC=C;LC_TIME=English_Australia.1252
> 
> attached base packages:
> [1] tools     stats     graphics  grDevices datasets  utils     methods   base
> 
> other attached packages:
> [1] Biobase_1.15.33
> 
> cheers,
> 
> Keith
> 
> ========================
> Keith Satterley
> Bioinformatics Division
> The Walter and Eliza Hall Institute of Medical Research
> Parkville, Melbourne,
> Victoria, Australia
> 
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