[Bioc-devel] Biobase 1.15.33 depends on ALL problem

Keith Satterley keith at wehi.EDU.AU
Thu Sep 6 09:01:02 CEST 2007

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:

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 ***
Error :  chunk 1 (label=doa)
Error : package 'Biobase' 1.15.33 is loaded, but >= c(1, 12, 0) is required by 'ALL'
*** Source Errors ***
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)


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

other attached packages:
[1] Biobase_1.15.33



Keith Satterley
Bioinformatics Division
The Walter and Eliza Hall Institute of Medical Research
Parkville, Melbourne,
Victoria, Australia

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