[Bioc-devel] Biobase 1.15.33 depends on ALL problem
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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