[Bioc-devel] Biobase 1.15.33 depends on ALL problem

[Keith Satterley]

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